Intelligent Design, the best explanation of Origins

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Cyanobacteria, amazing evidence of design

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1 Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 4:56 pm

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Cyanobacterias, amazing evidence of design

http://reasonandscience.heavenforum.org/t1551-cyanobacteria-amazing-evidence-of-design

They’re the most numerous organisms on the planet. There are more of them on Earth than there are observable stars in the Universe and these little creatures are what enabled you – and every other complex living thing that has ever lived on the planet, from dinosaurs to daffodils – to exist.

The main source for food and oxygen are cyanobacteria and chloroplasts that do photosynthesis. Cyanobacteria are essential for the nitrogen cycle, and so to transform nitrogen in the atmosphere into useful form for organisms to make the basic building blocks for life. The end product of photosynthesis is glucose, - needed as food source for almost all life forms. For a proponent that life took millions of years to emerge gradually and biodiversity as well, and so cyanobacteria and chloroplasts, that came hundreds of millions of years after life started, that is a huge problem. No oxygen in the atmosphere and UV radiation would kill the organisms. Nor could they emerge without an adequate food source. Looking everything in that perspective, it makes a lot of sense to believe God created everything in six days. And created the atmosphere with oxygen, and the nitrogen cycle fully setup, and plants and animals like cyanobacteria, essential in the food chain and nitrogen cycle. That would solve the - problem of nutrition, - the problem of UV radiation - and the problem of the nitrogen source required for life.

The existence in the same organism of cyanobacteria of two conflicting metabolic systems, oxygen-evolving photosynthesis and oxygen-sensitive nitrogen fixation, is a puzzling paradox. Explanations are pure guesswork.

Researchers have long been puzzled as to how the cyanobacteria could make all that oxygen without poisoning themselves. To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet? The explanations are fantasious at best.

Nick Lane describes the dilemma in the book Oxygen, the molecule that made the world:
Before cells could commit to oxygenic photosynthesis, they must have learned to deal with its toxic waste, or they would surely have been killed, as modern anaerobes are today. But how could they adapt to oxygen if they were not yet producing it? An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favor such a catastrophic history. In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

If there was a reduced atmosphere without oxygen some time back in the past ( which is btw quite controversial ) then there would be no ozone layer, and if there was no ozone layer the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacterias however would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this ?

Cyanobacteria are the prerequisite for complex life forms. They are said to exist already 3,5 bio years, and did not change morphologically. They do oxygenic photosynthesis, where the energy of light is used to split water molecules into oxygen, protons, and electrons. It occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide.

They have ATP synthase nano-motors. How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox!

ATP Synthase is a molecular machine found in every living organisms. It serves as a miniature power-generator, producing an energy-carrying molecule, adenosine triphosphate, or ATP. The ATP synthase machine has many parts we recognize from human-designed technology, including a rotor, a stator, a camshaft or driveshaft, and other basic components of a rotary engine. This machine is just the final step in a long and complex metabolic pathway involving numerous enzymes and other molecules—all so the cell can produce ATP to power biochemical reactions, and provide energy for other molecular machines in the cell. Each of the human body’s 14 trillion cells performs this reaction about a million times per minute. Over half a body weight of ATP is made and consumed every day!

A rotary molecular motor that can work at near 100% efficiency.
http://www.pnas.org/content/early/2011/10/12/1106787108.full.pdf

We found that the maximum work performed by F1-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase.

http://reasonandscience.heavenforum.org/t1439-atp-synthase#2204

How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox! Also, consider that ATP synthase is made by processes that all need ATP—such as the unwinding of the DNA helix with helicase to allow transcription and then translation of the coded information into the proteins that make up ATP synthase. And manufacture of the 100 enzymes/machines needed to achieve this needs ATP! And making the membranes in which ATP synthase sits needs ATP, but without the membranes it would not work. This is a really vicious circle for evolutionists to explain.



They have aerobic respiration and anaerobic fermentation which uniquely occurs together in these prokaryotic cells. They do photosynthesis through complex Photosystem I and II and other electron transport complexes. They have a carbon concentration mechanism, which increases the concentration of carbon dioxide available to the initial carboxylase of the Calvin cycle, the enzyme RuBisCO, and transcriptional regulation, which is the change in gene expression levels by altering transcription rates. They are capable of performing the process of water-oxidizing photosynthesis by coupling the activity of photosystem  II and I, in a chain of events known as the Z-scheme. They metabolize Carbohydrates through the pentose phosphate pathway. They reduce Carbon dioxide to form carbohydrates through the Calvin cycle. Furthermore, they are able to reduce elemental sulfur by anaerobic respiration in the dark.

No nitrogen: no proteins, no enzymes, no life. We need nitrogen in our bodies, to form amino acids and nucleic acids. Cyanobacteria have the greatest contribution to nitrogen fixation. So in the beginning, not only was lack of oxygen a gigantic problem, but the lack of nitrogen was no less so. In order for the anaerobic organisms, whatever they might have been, to generate oxygen in quantity, they simply HAD to have nitrogen in their tissues (as enzymes etc). With nitrogen as unreactive as it is, then how did they fix it? N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms, and it requires a large amount of energy to break this bond. This is one of the hardest chemical bonds of all to break.The whole process requires eight electrons and at least sixteen ATP molecules. The process, nitrogenase,  works in a more exact and efficient way than the clumsy chemical processes of  human invention. Several atoms of iron and molybdenum are held in an organic lattice to form the active chemical site. With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue.

They are able to capture the energy of light with 95% efficiency. Recently it has been discovered, that they accomplish that through sophisticated quantum mechanics – an esoteric aspect of nature that even most scientists don’t understand. The use light harvesting antennas for that !!

They possess an autoregulatory transcriptional feedback mechanism called circadian clock and coordinate their activities such as sleep/wake behavior, body temperature, hormone secretion, and metabolism into daily cycles . This is an  intrinsic time-keeping mechanism that controls the daily rhythms of numerous physiological processes. They control the expression of numerous genes, including those that code for the oscillator proteins of the clock itself.Cyanobacteria have 1,054 protein families !!!

In a BBC report, they said: Oxygenic photosynthesis is a very complicated metabolism and it makes sense that the evolution of such a metabolism would take perhaps two billion years.

Cyanobacteria (Rai et al., 1998) are known to orient their movement with respect to the Earth’s magnetic field.

Feel free to explain how Cyanobacteria got these amazing capabilities, amongst others, in a relatively short evolutionary timescale?


Adventures with cyanobacteria: a personal perspective
Contradictory Phylogenies for Cyanobacteria
The Biogeochemical Cycles of Trace Metals in the Oceans
Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids
Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers
Biologie Uni Hamburg - Cyanobacteria
Cronodon Cyanobacteria, great !
Cyanobacteria microbiology

Some Cyanobacteria adjust their buoyancy by means of gas vacuoles, enabling them to adjust their position in the water column, floating near the surface during the day for photosynthesis and sinking deeper at night to harvest nutrients. Nitrogen fixation requires anaerobic conditions, but Cyanobacteria are aerobes. They solve this problem by having specialized cells called heterocysts which have thick walls impermeable to oxygen and in which nitrogen fixation can occur. Smart, huh?





http://phototroph.blogspot.com.br/2008_12_01_archive.html





By producing oxygen as a gas as a by-product of photosynthesis, cyanobacteria are thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the composition of life forms on Earth by stimulating biodiversity and leading to the near-extinction of oxygen-intolerant organisms. According to endosymbiotic theory, the chloroplasts found in plants and eukaryotic algae evolved from cyanobacterial ancestors via endosymbiosis.

The Cyanobacteria: Molecular Biology, Genomics, and Evolution

http://bioenergy.asu.edu/photosyn/books/cyanobk.html

Cyanobacteria are a fascinating and versatile group of bacteria of immense biological importance. Thought to be amongst the first organisms to colonize the earth, these bacteria are the photosynthetic ancestors of chloroplasts in eukaryotes, such as plants and algae. In addition, they can fix nitrogen, survive in very hostile environments (e.g. down to -60-degreesC), are symbiotic, have circadian rhythms, exhibit gliding mobility, and can differentiate into specialized cell types called heterocysts. This makes them ideal model systems for studying fundamental processes, such as nitrogen fixation and photosynthesis. In addition, cyanobacteria produce an array of bioactive compounds, some of which could become novel anti-microbial agents, anti-cancer drugs, UV protectants, etc. The amazing versatility of cyanobacteria has attracted huge scientific interest in recent years. Given that 24 genomes sequences have been completed and many more projects are currently underway, the point has been reached where there is an urgent need to summarize and review the current molecular biology, genomics, and evolution of these important organisms. This volume brings together the expertise and enthusiasm of an international panel of leading cyanobacterial researchers to provide a state-of-the art overview of the field. Topics covered include: evolution, comparative genomics, gene transfer, molecular ecology and environmental genomics, stress responses, bioactive compounds, circadian clock, structure of the photosynthetic apparatus, membrane systems, carbon acquisition, nitrogen assimilation, C/N balance sensing, and much more. This book will be essential for anyone with an interest in cyanobacteria, bacterial photosynthesis, bacterial nitrogen fixation, and symbiosis.

The Molecular Biology of Cyanobacteria summarizes more than a decade of progress in analyzing the taxonomy, biochemistry, physiology, cellular differentiation and developmental biology of cyanobacteria by modern molecular methods, especially molecular genetics. During this period cyanobacterial molecular biologists have been "studying those things that cyanobacteria do well," and they have made cyanobacteria the organisms of choice for detailed molecular analyses of oxygenic photosynthesis. Part 1 contains chapters describing the molecular evolution and taxonomy of the cyanobacteria as well as chapters describing cyanelles and the origins of algal and higher plant chloroplasts. Also included are chapters describing the picoplanktonic, oceanic cyanobacteria and prochlorophytes, "the other cyanobacteria." Part 2 is devoted to a detailed description of structural and functional aspects of the cyanobacterial photosynthetic apparatus. Included are chapters on thylakoid membrane organization, phycobiliproteins, and phycobilisomes, Photosystem I, Photosystem II, the cytochrome b6f complex, ATP synthase, and soluble electron carriers associated with photosynthetic electron transport. Structure as it relates to biological function, is heavily emphasized in this portion of the book. Part 3 describes other important biochemical processes, including respiration, carbon metabolism, inorganic carbon uptake and concentration, nitrogen metabolism, tetrapyrrole biosynthesis, and carotenoid biosynthesis. Part 4 describes the cyanobacterial genetic systems and gene regulatory phenomena in these organisms. Emphasis is placed on responses to environmental stimuli, such as light intensity, light wavelength, temperature, and nutrient availability. Cellular differentiation and development phenomena, including the formation of heterocysts for nitrogen fixation and hormogonia for dispersal of organisms in the environment, are described




Cyanobacteria are moss-like species that live in oxygen-poor environments bathed in light, such as in shallow bodies of water. They are the only bacteria that produce oxygen as a waste product07 -- which is an important task of this early life. They are exceedingly complex, far from what one would think to call primitive. They grow in long chains because when the cells reproduce they divide in half and tend to remain attached (Figure 2b). They secrete a kind of mucilage or slime which solidifies to form characteristic multi-layered dome-like structures called stromatolytes that grow in highly saline tidal basins -- shallow water between high and low tide. Living stromatolytes exist today in only a few locations worldwide, one being Hamelin Pool in Western Australia



If these fossils are cyanobacteria (or closely related ancestors), then it immediately poses a problem because -- as we will see -- cyanobacteia are advanced bacteria, not what one would assume to be representative of the earliest living species
Why bacteria and not archaea?


Some paleo-biologists insist that the earliest life was from the kingdom Archaea (indeed the name implies that they are the most ancient bacteria), based on the ability of archaea to manage in very hostile environments (which the early earth certainly was), and the claimed advantages of survival near deep water thermal vents.

It is not the purpose here to confirm or deny this possibility, but there are some good reasons to doubt that archaea could "be fruitful and multiply and fill the earth" [Gen. 1] to the degree required at this point in the earth's history: Archaea are too limited and specialized to fill that role. In addition, the genetic make-up of the archaea appears to be more advanced than that of bacteria, more akin to eukaryotes, and therefore (one would assume) a later development.

In the final analysis, though, it does not really matter whether the first living species were archaea; the first practical living species had to be bacteria -- oxygen-producing cyanobacteria (or close ancestors) -- and as a matter of fact, these were the first fossils preserved in the fossil record.

From the point of view that the main task of early life was to form a fit place for later life, it is significant that no known archaea species conduct photosynthesis or have oxygen as a waste product, and so they would be unable to convert the initial reducing environment to an oxidizing environment, required for advanced life.

Regarding the appearance of the first life, Alexandre Meinesz, How Life Began: Evolution's Three Geneses refers to "the strange fact that the ancestral bacteria were already highly diversified" when the first fossil evidence was found. He then continues, "The currently popular idea that life probably arose in warm subsurface waters along a mid-ocean ridge, the kind of environment where a great variety of heat-resisting bacteria thrive today, is a hypothesis without any scientific basis."




Could the oxygen and nitrogen cicle be explained by naturalistic means ? The reason for the abundance of oxygen in the atmosphere is the presence of a very large number of organisms which produce oxygen as a byproduct of their metabolism. Cyanobacteria or blue-green algae became the first microbes to produce oxygen by photosynthesis. They are one of the oldest bacteria that live on earth, said to exist perhaps as long  as 3.5 billion years. And their capabilities are nothing more than astounding.

 No cianobacteria, not enough oxygen, no higher life forms. These cianobacterias have incredibly sophisticated enzyme proteins and metabolic pathways, like the Z-scheme and electron transport chains, ATP synthase motors, circadian clock, the photosynthetic light reactions, carbon concentration mechanism, and transcriptional regulation , they produce binded nitrogen through nitrogenase, a highly sophisticated mechanism to bind nitrogen, used as a nutrient for plant and animal growth. The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen we would lose one of the most important elements on this planet, along with oxygen, hydrogen and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.There is no real starting point for the nitrogen cycle. It is an endless cycle. Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone.

It must have a degree of specificity that in all probability could not have been produced by chance. A given function or step in the system may be found in several different unrelated organisms. The removal of any one of the individual biological steps will resort in the loss of function of the system. The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system.The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. Its needed by all living things to build proteins and nucleic acids. This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things?

To be metabolically useful, atmospheric nitrogen must be reduced. It must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them. This process, known as nitrogen fixation, occurs through lightening, but most  in certain types of bacteria, namely cianobacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N?N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation). Nitrogenase is a very complex enzyme system. Nitrogenase genes are distributed throughout the prokaryotic kingdom, including representatives of the Archaea as well as the Eubacteria and Cyanobacteria.With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision.

In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism, but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’

If one merely substitutes the name of God for the word 'nature', the real picture emerges.These proteins use a collection of metal ions as the electron carriers that are responsible for the reduction of N2 to NH3. All organisms can then use this reduced nitrogen (NH3) to make amino acids. In humans, reduced nitrogen enters the physiological system in dietary sources containing amino acids. One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.Without cyanobacteria - no fixed nitrogen is available.Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised. Without DNA, no amino-acids,protein, or cyanobacteria are possible. So thats a interdependent system.


http://www.indiana.edu/~geol105b/1425chap10.htm

This time span was once considered too short for the emergence of something as complex as a living cell. Therefore, a number of people suggested that germs of life may have come to earth from outer space with cometary dust or even via a space probe sent out by some distant civilization.

http://openi.nlm.nih.gov/detailedresult.php?img=2078611_ijbsv03p0434g01&req=4

A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Where is the demonstration ??

http://www.chm.bris.ac.uk/motm/oec/motm.htm
http://www.pnas.org/content/103/35/13126.full
http://www.pnas.org/content/early/2013/01/09/1209927110.full.pdf+html
http://shodhganga.inflibnet.ac.in/bitstream/10603/9639/8/08_chapter%202.pdf
http://www.biomedcentral.com/1471-2148/11/45
http://www.ijbs.com/v03p0434.htm

The origin of multicellularity in cyanobacteria

This publication is unique among a number of books on cyanobacteria because it focuses on the bioenergetics of these widespread organisms which are the evolutionary prerequisite for the development of all higher forms of life on our "blue" planet. The book primarily addresses questions of energy conversion by the fundamental bioenergetic processes: (oxygenic) photosynthesis, (aerobic) respiration, and (anaerobic) fermentation which uniquely occur together in these prokaryotic cells. Thermophilic cyanobacteria offer the most suitable material for high resolution structure analyses of Photosystem I and II and other electron transport complexes by X-ray crystallography (for example, at present the structure of Photosystem II at atomic resolution is only known for these organisms). These achievements during the last decade represent a milestone in our understanding of the complexes which are crucial for solar energy exploitation through photosynthetic water splitting. The present work represents an ambitious attempt to achieve the goal of a synoptic state-of-the-art picture by casting together the mosaics of detailed knowledge described by leading experts in the field.

http://www.palaeocast.com/episode-16-multicellularity-in-cyanobacteria/#.Uqn8LbQucvk

Cyanobacteria represent one of the most morphologically diverse groups of prokaryotic organisms (Bacteria and Archaea).
Without the cyanobacteria life on this planet would not have started, and would certainly not be continuing to exist.


know that there has been a long-standing consensus on how the oxygen was actually produced: photosynthetic organisms called cyanobacteria

http://www.ucmp.berkeley.edu/bacteria/cyanofr.html

The cyanobacteria have an extensive fossil record. The oldest known fossils, in fact, are cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old. This may be somewhat surprising, since the oldest rocks are only a little older: 3.8 billion years old!

Cyanobacteria are among the easiest microfossils to recognize. Morphologies in the group have remained much the same for billions of years, and they may leave chemical fossils behind as well, in the form of breakdown products from pigments. Small fossilized cyanobacteria have been extracted from Precambrian rock, and studied through the use of SEM and TEM (scanning and transmission electron microscopy).


cianobacteria are fully developed eukaryotic cells *supposed* to live since the most early ages, said to be 3,5bio years.

reasonandscience.heavenforum.org/t1301-photosynthesis#1818

Cyanobacteria are one of the oldest and morphologically most diverse prokaryotic phyla on our planet. The early development of an oxygen-containing atmosphere approximately 2.45 - 2.22 billion years ago is attributed to the photosynthetic activity of cyanobacteria.

During Earth history, cyanobacteria have raised atmospheric oxygen levels starting approximately 2.45 - 2.22 billion years ago and provided the basis for the evolution of aerobic respiration

what a nice *accident*, isnt it ? why is it supposed to be rational, to evoke good luck or unsupported natural selection to explain such a event , that was necessary for complex life to arise ?

The latter have the ability to produce heterocysts for nitrogen fixation and akinetes (climate-resistant resting cells).

my question made previously, *of course* , remains unanswered:

How could those regulatory machines evolve at precisely the right rate so as to drop into the right place at precisely the right time to effect proper assembly of the nitrogenase machinery?

http://www.grisda.org/origins/60006.pdf

Unquestionably, biological nitrogen fixation is no simple process and design argument could be made based on this single step in the nitrogen cycle. It is unlikely to have been produced via a step-by-step Darwinian process because nitrogenase itself is immensely complex, requires auxiliary complex mechanisms to maintain low oxygen tension, and also needs reduced carbon backbones as substrates for amination to store ammonia as glutamine. In addition, regulatory mechanisms are needed to coordinate the entire energetically expensive activity and it's chemically reactive product, ammonia.

http://en.wikipedia.org/wiki/Prochlorococcus

Prochlorococcus is a genus of very small (0.6 µm) marine cyanobacteria with an unusual pigmentation (chlorophyll b). These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynthetic organism on Earth. Microbes of the genus Prochlorococcus are among the major primary producers in the ocean, responsible for at least 50% of atmospheric oxygen.[1] Analysis of the genome sequences of 12 Prochlorococcus strains shows that 1100 genes are common to all strains, and the average genome size is about 2000 genes.[1] In contrast, eukaryotic algae have over 10,000 genes

http://www.ps-19.org/Crea06EcoSys/index.html

Preparation for advanced life. The rapid multiplication of the early species of life was needed to prepare the earth for more advanced species. Almost three billion years separate the first fossils and the first eukaryotic fossils -- the first step towards complex, multicellular life.

Looking ahead, the main tasks for the early bacteria were:

• Distribute abundant amounts of organic food worldwide.
- This task is needed because advanced life cannot take the time or energy to be self-sufficient (autotrophic).
- In particular, this food provides fixed nitrogen, which is essential for all of life. Its manufacture from atmospheric nitrogen is a difficult, energy-consuming slow process (see below). No eukaryotic species is able to manufacture nitrogen. In fact, very few bacteria species are able to manufacture all of its own requirements for nitrogen. The nitrogen may be either organic or inorganic (in the form of nitrates or ammonia gas).

• Convert the earth's atmosphere and the oceans from reducing to oxidizing. The atmosphere must have around 20-25% oxygen content. Complex life requires at least the lower limit of abundance, and the upper bound is needed to avoid spontaneous combustion.

It appears that the limiting requirement was the oxygen supply, which took the full three billion years to achieve, with the aid of oxygen-producing bacteria. The global distribution of the food supply, fixed nitrogen, and the formation of vast mineral deposits that are so essential to the modern technological age were by-products of this push to develop the oxygen supply.

The cyanobacterial genome core and the origin of photosynthesis

http://www.pnas.org/content/103/35/13126.full

Cyanobacteria are one of the earliest branching groups of organisms on this planet (1, 2). They are the only known prokaryotes to carry out oxygenic photosynthesis, and there is little doubt that they played a key role in the formation of atmospheric oxygen ≈2.3 Gyr ago (2). Despite its evolutionary, environmental, and geochemical importance, many aspects of cyanobacterial cell life remain obscure (3–5). Genome sequencing opened a new chapter in cyanobacterial research. In the last few years, complete genome sequences of several freshwaters and marine cyanobacteria became available, providing ample data for systematic analysis. A comparison of the complete genomes from three different strains of Prochlorococcus spp. demonstrated a wide variety of gene complements within this genus due to massive genome reduction in some lineages (6, 7). Studies of the genes shared by cyanobacteria and other photosynthetic organisms allowed delineation of the “photosynthetic gene set” and demonstrated a significant extent of lateral gene transfer (LGT) among phototrophic bacteria (8–11). A somewhat surprising result of the latter work has been that genes for most proteins involved in photosynthesis (hereafter “photosynthetic genes”) were not in the photosynthetic gene set.

We compared proteins encoded in 15 complete cyanobacterial genomes, including five genomes of Prochlorococcus spp., to define the minimal set of genes common to all cyanobacteria and to trace the conservation of these genes among other taxa. We analyzed the phylogenetic affinities of genes in this set and identified previously unrecognized candidate photosynthetic genes. We further used this gene set to address the identity of the first phototrophs, a subject of intense discussion in recent years (8, 9, 12–33). We show that cyanobacteria and plants share numerous photosynthesis-related genes that are missing in genomes of other phototrophs. This observation suggests, in agreement with geological evidence, that (now extinct) anoxygenic ancestors of cyanobacteria are the most plausible candidates for the ancestral photoautotrophs, which apparently disseminated parts of their photosynthetic apparatus to other bacteria by way of LGT.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066060

Unicellular, diazotrophic cyanobacteria temporally separate dinitrogen (N2) fixation and photosynthesis to prevent inactivation of the nitrogenase by oxygen. This temporal segregation is regulated by a circadian clock with oscillating activities of N2 fixation in the dark and photosynthesis in the light. On the population level, this separation is not always complete, since the two processes can overlap during transitions from dark to light. How do single cells avoid inactivation of nitrogenase during these periods?



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2 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 4:56 pm

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The circadian rythm is as old as life, existing in Cianobacteria. According to Wiki : The variations of the timing and duration of biological activity in living organisms occur for many essential biological processes. These occur (a) in animals (eating, sleeping, mating, hibernating, migration, cellular regeneration, etc.), (b) in plants (leaf movements, photosynthetic reactions, etc.), and in microbial organisms such as fungi and protozoa. They have even been found in bacteria, especially among the cyanobacteria (aka blue-green algae, see bacterial circadian rhythms). The most important rhythm in chronobiology is the circadian rhythm, a roughly 24-hour cycle shown by physiological processes in all these organisms. How could such sophisticated mechanisms be result of natural , unguided mechanisms ? hard to believe...

http://en.wikipedia.org/wiki/Circadian_rhythm

A circadian rhythm is any biological process that displays an endogenous, entrainable oscillation of about 24 hours. These rhythms are driven by a circadian clock, and rhythms have been widely observed in plants, animals, fungi and cyanobacteria. The term circadian comes from the Latin circa, meaning "around" (or "approximately"), and diem or dies, meaning "day". The formal study of biological temporal rhythms, such as daily, tidal, weekly, seasonal, and annual rhythms, is called chronobiology. Although circadian rhythms are endogenous ("built-in", self-sustained), they are adjusted (entrained) to the local environment by external cues called zeitgebers, commonly the most important of which is daylight.
http://www.evolutionnews.org/2012/09/circadian_rhyth063881.html

"Over the past decade, remarkable progress has been made in elucidating the molecular genetics of these single-cell oscillators," he writes. "More recently, structural biology has begun to contribute a detailed picture of our clock components." The ghost of William Paley studying components of a watch found on a heath rises at the sound of statements like this. (Emphasis added in all quotations.)

Crane was commenting on work by Huang et al., in the same issue of Science. (see our June 5 article). They identified two proteins that are part of the "autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete." The proteins form a complex that "controls the expression of numerous genes, including those that code for the oscillator proteins of the clock itself." These proteins, CLOCK and BMAL1, are "made up of two domains that are found throughout biology, serving a range of functions." Moreover, they contain numerous interfaces to other proteins. Speaking of a particular association with PAS proteins, Crane made this Paley-supporting analogy:
- See more at: http://www.evolutionnews.org/2012/09/circadian_rhyth063881.html#sthash.HH0gtAH0.dpuf

http://www.sciencemag.org/content/337/6091/165.summary

Much of human physiology and behavior is influenced by circadian rhythms. Whether you burned the midnight oil, rose at the crack of dawn, or enjoyed your rest last night, tiny clocks in your cells have been trying to keep you on schedule. Over the past decade, remarkable progress has been made in elucidating the molecular genetics of these single-cell oscillators. More recently, structural biology has begun to contribute a detailed picture of our clock components.

http://jxb.oxfordjournals.org/content/63/6/2259.abstract

The focus of the contribution is on a mathematical description of the metabolic network of Synechocystis sp. PCC 6803 and its analysis using constraint-based methods. A particular challenge is to integrate the description of the metabolic network with other cellular processes, such as the circadian clock, the photosynthetic light reactions, carbon concentration mechanism, and transcriptional regulation—aiming at a predictive model of a cyanobacterium in silico.


http://en.wikipedia.org/wiki/Chronobiology

The variations of the timing and duration of biological activity in living organisms occur for many essential biological processes. These occur in animals (eating, sleeping, mating, hibernating, migration, cellular regeneration, etc.), in plants (leaf movements, photosynthetic reactions, etc.), and in microbial organisms such as fungi and protozoa. They have even been found in bacteria, especially among the cyanobacteria (aka blue-green algae, see bacterial circadian rhythms). The most important rhythm in chronobiology is the circadian rhythm, a roughly 24-hour cycle shown by physiological processes in all these organisms.

transcriptional feedback mechanism

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002966

Abstract

Molecular genetic studies in the circadian model organism Synechococcus have revealed that the KaiC protein, the central component of the circadian clock in cyanobacteria, is involved in activation and repression of its own gene transcription. During 24 hours, KaiC hexamers run through different phospho-states during daytime. So far, it has remained unclear which phospho-state of KaiC promotes kaiBC expression and which opposes transcriptional activation. We systematically analyzed various combinations of positive and negative transcriptional feedback regulation by introducing a combined TTFL/PTO model consisting of our previous post-translational oscillator that considers all four phospho-states of KaiC and a transcriptional/translational feedback loop. Only a particular two-loop feedback mechanism out of 32 we have extensively tested is able to reproduce existing experimental observations, including the effects of knockout or overexpression of kai genes. Here, threonine and double phosphorylated KaiC hexamers activate and unphosphorylated KaiC hexamers suppress kaiBC transcription. Our model simulations suggest that the peak expression ratio of the positive and the negative component of kaiBC expression is the main factor for how the different two-loop feedback models respond to removal or to overexpression of kai genes. We discuss parallels between our proposed TTFL/PTO model and two-loop feedback structures found in the mammalian clock.
Author Summary

Many organisms possess a true circadian clock and coordinate their activities into daily cycles. Among the simplest organisms harboring such a 24 h-clock are cyanobacteria. Interactions among three proteins, KaiA, KaiB, KaiC, and cyclic KaiC phosphorylation govern the daily rhythm from gene expression to metabolism. Thus, the control of the kaiBC gene cluster expression is important for regulating the cyanobacterial clockwork. A picture has emerged in which different KaiC phospho-states activate and inhibit kaiBC expression. However, the mechanism remains to be solved. Here, we investigated the impact of each KaiC phospho-state on kaiBC expression by introducing a model that combines the circadian transcription/translation rhythm with the KaiABC-protein oscillator. We tested 32 combinations of positive and negative transcriptional regulation. It turns out that the kaiBC expression and KaiC phosphorylation dynamics in wild type and kai mutants can only be described by one mechanism: threonine and double phosphorylated KaiC hexamers activate kaiBC expression and the unphosphorylated state suppresses it. Further, we propose that the activator-to-repressor abundance ratio very likely determines the kaiBC expression dynamics in the simulated kai mutants. Our suggested clock model can be extended by further kinetic mechanisms to gain deeper insights into the various underlying processes of circadian gene regulation.

http://www.nature.com/ncomms/2013/131205/ncomms3897/fig_tab/ncomms3897_F1.html

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3 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 4:58 pm

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Phycobiliprotein

Phycobiliproteins are water-soluble proteins present in cyanobacteria and certain algae (rhodophytes, cryptomonads, glaucocystophytes) that capture light energy, which is then passed on to chlorophylls during photosynthesis. Phycobiliproteins are formed of a complex between proteins and covalently bound phycobilins that act as chromophores (the light-capturing part). They are most important constituents of the phycobilisomes.

Phycobilisomes







Chromophores

A chromophore is the part of a molecule responsible for its colour. The colour arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state.

In biological molecules that serve to capture or detect light energy, the chromophore is the moiety that causes a conformational change of the molecule when hit by light.

In the conjugated chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds,

The excited (energized) molecule can pass the energy to another molecule or release it in the form of light or

Some of these are metal complex chromophores, which contain a metal in a coordination complex with ligands. Examples are chlorophyll, which is used by plants for photosynthesis.

metal complex chromophores

a metal is complexed at the center of a tetrapyrrole macrocycle ring: magnesium complexed in a chlorin-type ring in the case of chlorophyll.

Chlorin

Magnesium-containing chlorins are called chlorophylls, and are the central photosensitive pigment in chloroplasts.

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4 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 4:59 pm

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Contradictory Phylogenies for Cyanobacteria

The cyanobacteria are interesting for a number of reasons. They have a complex photosynthesis pathway with two separate phostosystems and an oxygen evolving complex. That means they can use water as an electron donor and NADP⊕ as an electron acceptor.

Cyanobacteria probably played an important role in creating an atmosphere with significant levels of oxygen but, contrary to some speculation, they almost certainly arose fairly late in the history of life (i.e. after 500 million years). Cyanobacteria make up a significant proportion of life in the ocean. Primitive cyanobacteria gave rise to chloroplasts in modern plants and algae.

For all of these reasons, cyanobacteria phlylogeny is important. I've been interested in the literature for 25 years, ever since I realized that my favorite genes (HSP70) had chloroplast versions that were similar to the cyanobacteria homologs.

Two groups have recently published phylogenies based on whole genome sequences of cyanobacteria. The first one out was published in PNAS last January but I wasn't aware of it until Jonathan Eisen mentioned it on his blog [New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria]. The paper is by Shih et al. (2013).

The authors sequenced 54 new species of cyanobacteria. They deliberately selected new species that would represent the diversity of the phylum. They selected 31 "conserved" proteins and constructed a tree of cynaobacteria using the concatenated sequences. You can read what Jonathan Eisen has to say about these 31 genes and the problems with sequence alignments at: Bacteria Phylogeny: Facing Up to the Problems. Their tree is quite similar to those made using 16S RNA sequences.

The second paper was just published in Genome Biology and Evolution (Dagan et al., 2013). The senior author is Bill Martin. The only reason I know about this paper is because we were given a free copy of the journal at SMBE2013.1

The second group sequenced six new species of cyanobacteria. They selected a set of 324 genes common to all 51 species in their dataset and constructed a tree from the concatenated sequences. They generated a Maximum Likelihood (ML) tree but they report that the Neighbor Joining tree (NJ) is identical and has stronger support. The NJ tree was published. (That's satisfying because I don't trust ML trees.)


The two phylogenies don't agree. The two papers agree that Gleobacter violaceus is the deepest rooting branch followed by two strains of Synechococcus (JA 3-3Ab and JA2-3b). Both groups recognize the main clades such as the grouping of the abundant small marine organims (Proclorococcus) and various other Synechococcus species (SynPro). The biggest difference is that Dagan et al. (2013) divide all other cyanobacteria into two deeply divergent clades. One contains the SynPro group and the other contains all remaining species of cyanobacteria.

There are other differences. In general, the Shih et al. tree is more complicated than the Degan et al. tree, which tends to have larger monophyletic groups. I'm sure that the Martin group would attribute this to errors caused by lateral gene transfer, which they tried to control for.

It's puzzling that two highly respected groups come up with different phylogenies. This has implications when trying to decipher the origin of chloroplast genomes but that's a topic for another post.

Photo Credit: Fischerella sp. from Cyanobacteria. This is one of the new species sequenced by both groups.

1. This makes me realize that I'm relying heavily on news reports and blogs to alert me to important papers. The only journals I read are Science and Nature and I've all but given up scanning the tables of content of other journals.

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
[doi: 10.1093/gbe/evs117]

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Shih, P.M., Wu, D., Latifi, A., Axen, S.D., Fewer, D.P., Talla, E., Calteau, A., Cai, F., de Marsac, N.T. and Rippka, R. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Nat. Acad. Sci. (USA) 110:1053-1058. [doi: 10.1073/pnas.1217107110]

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5 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 5:00 pm

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Cyanobacteria, the ancient algae that could



I did two seemingly unremarkable things today. I walked by a local algae covered pond and I breathed the air while doing so. But are those things so unremarkable? Perhaps not. In fact the very act of respiration that I performed while doing that walk is only possible because of the ancient ancestors of the algae that covered the pond.

Earth was not always as we know it now. Of course this is not news to anyone familiar with dinosaurs. But while giant animals roaming the landscape might seem like an Earth that is pretty different from what we know the very ancient Earth was a place we'd never even recognize.

Ancient Earth in the time of the Archean (2.5 - 4 billion years ago) was a planet so different from what we know now—with no life at all on land, green oceans instead of blue ones, a sky that would have been tinted red all day long and the Moon would have been much larger in the sky—that it would seem like an alien planet if you were able to time travel back to it. It'd also be deadly as the atmosphere itself would have quickly suffocated you.

It would have suffocated you because there would have been no oxygen available to breathe.

And why is it that there was no oxygen? How is it that the same planet once lacked one of the most important elements to our metabolism?



Well, don't worry, it isn't that oxygen was suddenly gifted to the planet by alien planetary engineers, a wizard or trickster gods. The oxygen was always there. It was just locked up in various chemical bonds that prevented free oxygen O2, from being available. And free oxygen is what is needed for aerobic respiration in animals.

So the oxygen was there, but not available. How is that the case? Well this is because of the atomic structure of oxygen itself. It is primarily because of the number of electrons that oxygen has and the behavior of the valence shell.

What is a valence shell? Well the valence shell is the outermost electron shell which is a layer surrounding the atomic nucleus where the electrons of the atom reside. There are different layers of electron shells at differing altitudes (so to speak) above the nucleus depending on how many electrons that particular atom contains. The lowest level electron shell will contain a maximum of 2 electrons, the next layer will hold up to 8 electrons, the one above that will hold up to 18. This continues on and on but for the purposes of this article we only need be concerned with the first two electron shells.

The outermost electron shell—the Valence Shell—determines the chemical properties of the element and is thus very important. As I previously explained the shell has a maximum number of electrons it can hold. But the total number of electrons in the element includes electrons that inhabit a lower orbit. So an element, like oxygen, with 8 electrons has two electrons that will preferentially inhabit a lower orbit leaving the outer shell with six electrons and two of them will be seeking a partner.

To understand this you must realize that the electrons in the valence shell will partner up and to kind of visualize this you need to first see this diagram of how oxygen looks with its electrons arranged into their shells based on their own preferences.



This means Oxygen has two electrons on the outer shell that will be seeking new electrons to pair up with. Oxygen, therefore, will be seeking other elements looking to give up electrons either by sharing them (known as a covalent bond) or gifting them entirely and becoming positive ions.

Oxygen will do either. You see elements that are close to having a full valence shell but are just short will be highly reactive. As are elements that have a valence shell that only contain one or two electrons. To see this in action just expose an alkali metal (which has only one electron in its valence shell) to concentrated oxygen (which voraciously seeks out the electrons of other elements) and watch how it causes an exothermic reaction that is literally explosive.


Yeah that was pure sodium being dropped into water. The desire of oxygen to react with the alkali metal is so fierce that it rips itself from its covalent bond with hydrogen and absorbs the extra electrons that each sodium atom wants to get rid of.

So what does this have to do with why earth had no breathable oxygen? Well oxygen is so reactive that it almost always finds elements such as the ones previously described and bonds with them. Gifting us with a planet full of things like water (oxygen + hydrogen), Carbon Dioxide (carbon + oxygen) or rust (iron + oxygen).

Free oxygen just wasn't around because all of it was locked up in those existing chemical compounds.

And that was when the ancient ancestor to pond scum came along: cyanobacteria.

Cyanobacteria actually represented a huge step forward in evolution. Prior to the advent of cyanobacteria all previously existing life forms utilized a primitive form of photosynthesis that used H2S to donate electrons for the photosynthetic process instead of water. This meant these organisms only produced sulfur as a byproduct of their photosynthesis.

And then a mutant came along, cyanobacteria, that did use water to donate electrons and the byproduct of its photosynthesis was free oxygen!

Now it wasn't all free sailing after that. The ancient Earth was a place very unused to the presence of free oxygen. The first thing that happened was that all the dissolved iron in the oceans reacted with the new abundance of free oxygen turning into rust. This left the oceans relatively iron free, and blue, for the first time in the planet's history. After that oxygen accumulated in the atmosphere. That is until the level of oxygen rose so high it collapsed the ecosystem which was still dominated by the ancient bacteria that used anaerobic photosynthesis. This resulted in a series of extinction events called The Oxygen Catastrophe.

But, eventually the ecosystem stabilized. Cyanobacteria gave rise to new mutants that eventually gave us plant life. Eventually the rise of respirating animals would come along that would use free oxygen to synthesize Adenosine triphosphate from glucose the main energy driver in the cells of animals.

So there you go. Breathing oxygen; more remarkable given our planet's history than you might have thought. And something that would be impossible if not for ancient blue-green algae 3.5 billion years ago.

You'll never look at pond scum the same way again.

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6 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 5:00 pm

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Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

Abstract

Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.




Cyanobacterial species tree and the distribution of secondary metabolite biosynthesis. (A) Maximum-likelihood phylogeny of cyanobacteria included in this study (outgroup shown in SI Appendix, Fig. S1). Branches are color coded according to morphological subsection. Taxa names in red are genomes sequenced in this study. Nodes supported with a bootstrap of ≥70% are indicated by a black dot. Morphological transitions that were investigated are denoted by blue triangles, annotated by events 1–8. Phylogenetic subclades are grouped into seven major subclades (A–G), some of which are made up of smaller subgroups. SI Appendix, Table S1 provides reference information for genomes used in this analysis. (B) Distribution of the nonribosomal peptide and polyketide gene clusters.

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7 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 5:01 pm

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Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes

Abstract

Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.

Introduction


The role of cyanobacteria in natural product research

Cyanobacteria flourish in diverse ecosystems and play an enormous role in the biogeochemical cycles on earth. They are found in marine, freshwater and terrestrial environments and even populate such extreme habitats as the Antarctic or hot springs [1]. Due to their capability to fix nitrogen from the atmosphere some species are attractive partners in symbioses. Other cyanobacteria show a strong tendency for mass developments during summer months, so-called blooms. Cyanobacteria do not belong to the established sources of natural products and are only incidentally screened by pharmaceutical industries. . Many bioactive metabolites possess a peptide or a macrolide structure, or a combination of both types [6-8]. Other metabolites belong to the alkaloid class of compounds. In the last two decades, biosynthesis gene clusters were assigned to an increasing number of these cyanobacterial natural products [7,9]. Part of the genetic analyses was assisted by biochemical studies of the enzymes. These studies revealed a truly fascinating variety of enzymatic features, including many that are not or only rarely seen in other microorganisms. The potential of cyanobacteria for natural product research thus goes far beyond the exploitation of the bioactivity of the products. Knowledge about the biochemistry of unique enzymes is particularly valuable for synthetic biology approaches towards libraries of new compounds or for rational biotransformation of existing leading compounds.

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8 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 5:03 pm

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Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase

http://www.annualreviews.org/doi/full/10.1146/annurev.micro.62.081307.162737

The iron-molybdenum cofactor (FeMo-co), located at the active site of the molybdenum nitrogenase, is one of the most complex metal cofactors known to date. During the past several years, an intensive effort has been made to purify the proteins involved in FeMo-co synthesis and incorporation into nitrogenase. This effort is starting to provide insights into the structures of the FeMo-co biosynthetic intermediates and into the biochemical details of FeMo-co synthesis.

Most biological nitrogen fixation is carried out by the activity of the molybdenum nitrogenase, which is found in all diazotrophs.

The molybdenum nitrogenase enzyme complex has two component proteins encoded by the nifDK and the nifH genes


Nitrogen Fixation: The Mechanism of the Mo-Dependent Nitrogenase

http://informahealthcare.com/doi/pdf/10.1080/10409230391036766

This review focuses on recent developments elucidating the mechanism of the
Mo-dependent nitrogenase. This enzyme, responsible for the majority of biological nitrogen
fixation, is composed of two component proteins called the MoFe protein and the Fe protein.
Recent progress in understanding the mechanism of this enzyme has focused on elucidating the
structures of the active site metal clusters and of the proteins, understanding substrate interactions
with the active site, defining the flow of electron transfer between the metal clusters, and defining
the various roles of MgATP hydrolysis.

http://www.ias.ac.in/jbiosci/nov2013/733.pdf

Our investigation provides ample support to the fact that NifH
protein and BchL share robust structural similarities and have
probably deviated from a common ancestor followed by divergence
in functional properties possibly due to gene duplication


http://chemwiki.ucdavis.edu/Wikitexts/UC_Davis/UCD_Chem_124A%3A_Berben/Nitrogenase/Nitrogenase_2

There are at least three different types of nitrogenase known including both Vanadium (V) nitrogenase and iron (Fe) nitrogenase2, 5 . These forms of nitrogenase are often found in bacteria.3 The commonly studied and used form of the metalloenzyme is the molybdenum (Mo) nitrogenase.2 It involves a Fe protein and MoFe protein.6 The Fe protein is composed of a [4Fe-4S] cluster and MgATP proteins that help send electrons to the MoFe protein.7 Meanwhile, the MoFe protein consists of a FeMo active site and P-cluster [8Fe-7S] metals that serve as an intermediate for transferring electrons.7 Equation (1) illustrates the complete reaction of the reduction of N2 .



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9 Re: Cyanobacteria, amazing evidence of design on Sat Mar 01, 2014 5:07 pm

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Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways

Abstract

Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.

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http://www.evolutionnews.org/2014/02/explaining_life082691.html

Stephen Meyer likes to quote the characterization of a form of madness as "reasoning correctly from false premises." That seems like an apt description of some ruminations on the mystery of how complex life arose on Earth. As ENV notes in our cover story, oxygen is the current favorite solution to the enigma. We're told that, leading up to Cambrian explosion, the atmosphere and the vast ocean were increasingly infused with oxygen, thus vitally setting the stage for life.

There's a big problem, though, as anyone who's read Dr. Meyer's book Darwin's Doubt will know. What makes the Cambrian explosion so mysterious is an infusion of information in the biosphere. Oxygen doesn't help with that at all. But reasoning from the premise that oxygen somehow does help -- as it would in, for example, feeding a fire -- you naturally want to know where the oxygen came from, and when and why.

And good news, that is just the question that an article in Current Biology, "A Neoproterozoic Transition in the Marine Nitrogen Cycle," seeks to answer:

   The Neoproterozoic (1000-542 million years ago, Mya) was characterized by profound global environmental and evolutionary changes, not least of which included a major rise in atmospheric oxygen concentrations [1,2], extreme climatic fluctuations and global-scale glaciation [3], and the emergence of metazoan life in the oceans [4,5]. We present here phylogenomic (135 proteins and two ribosomal RNAs, SSU and LSU) and relaxed molecular clock (SSU, LSU, and rpoC1) analyses that identify this interval as a key transition in the marine nitrogen cycle. Specifically, we identify the Cryogenian (850-635 Mya) as heralding the first appearance of both marine planktonic unicellular nitrogen-fixing cyanobacteria and non-nitrogen-fixing picocyanobacteria (Synechococcus and Prochlorococcus [6]). Our findings are consistent with the existence of open-ocean environmental conditions earlier in the Proterozoic adverse to nitrogen-fixers and their evolution -- specifically, insufficient availability of molybdenum and vanadium, elements essential to the production of high-yielding nitrogenases. As these elements became more abundant during the Cryogenian [7,8], both nitrogen-fixing cyanobacteria and planktonic picocyanobacteria diversified. The subsequent emergence of a strong biological pump in the ocean implied by our evolutionary reconstruction may help in explaining increased oxygenation of the Earth's surface at this time, as well as tendency for glaciation.

More simply:

   Plankton in the Earth's oceans received a huge boost when microorganisms capable of creating soluble nitrogen 'fertilizer' directly from the atmosphere diversified and spread throughout the open ocean. This event occurred at around 800 million years ago and it changed forever how carbon was cycled in the ocean.

Other research, reported in PNAS, casts doubt on how essential oxygen was in the first place. Sponges, for one, can get by without much. But even granting that low oxygen would absolutely impede the rise of animal life, O2 is only a precondition for the explosion of diverse creatures about 530 million years ago. An atmosphere rich in oxygen may correlate with the emergence of animals in the oceans, with the sudden bloom that followed the Great Oxygenation Event or Great Oxygenation Transition, but there's no way you can call it the cause.

Speculating about how nitrogen "fertilization" could have lead to what University of Bristol researcher Patricia Sanchez-Baracaldo calls life's "great leap forward" is to reason correctly from a false premise. It's madness. Information, a product of mind not of atmospheric O2, is the key. But in all these discussions that fact is persistently obscured.

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11 Re: Cyanobacteria, amazing evidence of design on Thu Mar 13, 2014 8:21 pm

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http://mmbr.asm.org/content/56/2/340.full.pdf

The existence in the same organism of cyanobacterias of two conflicting metabolic systems, oxygen evolving photosynthesis and oxygen-sensitive nitrogen fixation, is  a puzzling paradox.



http://mmbr.asm.org/content/74/4/529.full

In cyanobacteria, the O2 problem is enhanced by the photosynthetic production of this gas. Many filamentous cyanobacteria solve the issue by cell differentiation. Under aerobic growth conditions, their vegetative cells perform photosynthetic O2 evolution and CO2 fixation, whereas nitrogenase resides in specialized cells, the heterocysts (66). These differentiate from vegetative cells by cell division and extensive metabolic changes (133, 162). Photosystem II (PSII) is largely degraded in heterocysts so that they cannot perform the photosynthetic water-splitting reaction. They are also unable to fix CO2 photosynthetically. Vegetative cells provide photosynthetically fixed carbon, which may be exported as sucrose to the heterocysts (52). In turn, heterocysts provide nitrogen, likely as glutamine formed via ammonia generated by N2 fixation and both glutamine synthetase and glutamate synthase (219). Alternatively, glutamine may be converted to arginine which is then incorporated into the cyanophycin granule. This may be degraded by cyanophycinase in a dynamic way depending on the N demand of heterocysts and vegetative cells (86).

Heterocysts possess a thick cell envelope composed of long-chain, densely packed glycolipids providing a barrier to gas exchange (9). The main diffusion pathway for O2 and N2 might be through the terminal pores (“microplasmodesmata”) (83) that connect heterocysts with vegetative cells. Walsby (230) suggested that transmembrane proteins make the narrow pores permeable enough and might provide a means of regulating gas exchange. Residual O2 reaching the inside of the heterocysts might be immediately consumed by their high respiratory activity and also other reactions in these cells. In this way, heterocysts provide an anaerobic environment which allows nitrogenase to function.



The existence in the same organism of cyanobacterias of two conflicting metabolic systems, oxygen evolving photosynthesis and oxygen-sensitive nitrogen fixation, is a puzzling paradox. Explanations are pure guesswork.

Researchers have long been puzzled as to how the cyanobacteria could make all that oxygen without poisoning themselves. To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet? The explanations are fantasious at best

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12 MOLECULAR MECHANISMS OF PHOTOSYNTHESIS on Wed Mar 19, 2014 10:20 am

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MOLECULAR MECHANISMS OF PHOTOSYNTHESIS


Cyanobacteria are remarkably complex cells in terms of photosynthetic
capability, and they certainly do not occupy an early branching position on the tree of
life. It is inconceivable that the cyanobacteria were the first photosynthetic cells, as they
contain most of the innovations that characterize the most advanced forms of photosynthesis.
Anoxygenic photosynthetic bacteria are by any measure much more primitive as
regards the structure of their photosynthetic apparatus and their lack of the pinnacle of
photosynthetic capability, the oxygen-evolving complex

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13 Re: Cyanobacteria, amazing evidence of design on Fri Apr 11, 2014 12:57 pm

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http://blog.drwile.com/?p=12333#more-12333

The image you see above is of a tiny bacterium from genus Prochlorococcus. It is part of a phylum of bacteria called Cyanobacteria, and the members of this phylum are an incredibly important part of the world’s ecosystems. They live in water, converting sunlight and carbon dioxide into sugar and oxygen via photosynthesis. Estimates indicate that cyanobacteria are responsible for producing about 20 to 30 percent of the earth’s oxygen supply.

Prochlorococcus are particularly important cyanobacteria. They are thought to be the most abundant photosynthetic organism on earth, with an estimated worldwide population of an octillion (1,000,000,000,000,000,000,000,000,000).1 More importantly, they tend to live in parts of the ocean that are nutrient-poor. Their photosynthesis helps to alleviate this problem, of course, making them a food source for other organisms that might try to live there.

Dr. Sallie Chisholm at the Massachusetts Institute of Technology (MIT) first described the organisms in 1988 and has continued to study them over the years. She and her colleagues were recently looking at them under an electron microscope and noticed what she described as, “these pimples – we call them ‘blebs’ – on the surface.”2 Dr. Steven J. Biller, a microbiologist who is also at MIT, recognized the blebs as vesicles, which are tiny “sacs” made by nearly every cell in nature. Since the vesicles were found on the surface of the cell, the scientists decided the bacteria were using them to get rid of whatever was inside the vesicles.

They studied the water from their laboratory samples and found that it was, indeed, rich with vesicles that had been released by the Prochlorococcus, and they were surprised by what they found inside.

The vesicles contained components of the bacterial cell membrane, which is not surprising, given that they had to “pinch off” from the surface of the cell. However, they also contained a wide variety of proteins as well as some DNA. That’s the surprising part, because remember, these bacteria live in parts of the ocean where nutrients are scarce. Well, the proteins in the vesicles are nutrients. So these bacteria voluntarily give up nutrients and put them in the surrounding water. As Chisholm and her colleagues state:3

It is perhaps surprising that Prochlorococcus, or other microbes growing in the nutrient-poor oligotrophic oceans, would continually export nutrients in the form of membrane vesicles. Prochlorococcus, for example, has adaptations that reduce its phosphorus and nitrogen requirements, including the use of sulfolipids instead of phospholipids and a proteome with relatively low nitrogen demand. Vesicle release seems inconsistent with the need to make efficient use of limited resources that presumably underlies these adaptations.

To make sure that the voluntary release of these limited resources wasn’t an artifact of the bacteria being cultured in the laboratory, the authors examined ocean water from two different regions that have large Prochlorococcus populations, and they found that the water was full of these nutrient-rich vesicles. Based on their limited observations, they estimate that as many as 10,000 to 100,000 tons of useful chemicals might be dumped into the ocean every day by these generous bacteria.

Why would the bacteria do something like this? The authors say that they can only speculate. Perhaps they are “feeding” other organisms that help to promote their growth. It is known that Prochlorococcus can do better in the presence of certain other organisms, so perhaps they are producing a good environment to promote the growth of those organisms. It’s also possible that these vesicles act as decoys, fooling viruses into attacking the vesicles instead of the bacteria themselves. Finally, it is possible that they are being used to distribute useful chunks of DNA to other Prochlorococcus and all organisms that benefit their growth.

I would add one more possibility that the authors didn’t consider. Since they grow in nutrient-poor conditions, it is possible that these bacteria comprise one of the many negative-feedback mechanisms that the Creator folded into His creation. They could be designed to seed nutrient-poor areas of the ocean with nutrients so as to promote the viability of the ecosystem as a whole. If further research shows that the vesicles benefit a wide variety of organisms (even the ones that don’t necessarily help the Prochlorococcus), that would probably be the most likely explanation.

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14 Re: Cyanobacteria, amazing evidence of design on Mon Oct 19, 2015 7:17 am

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http://belligerentdesign-asyncritus.blogspot.com.br/2010/01/cyanobacteria-evolutions-ignored.html

http://forum.religious-science.com/showthread.php?442-The-Cyanobacteria-Evolution-s-worst-nightmare

The Cyanobacteria - Evolution's worst nightmare

I had not realised just how titanic a problem the cyanobacteria present to the theory of evolution. It is obvious that the Creator knew what was required for the continuance and maintenance of His Creation, and took all reasonable steps,requiring stupendous intelligence to make sure the Creation got what it needs now, and needed then.

Here is the story of those marvellous little organisms, the Cyanobacteria. Present from the beginning, and exactly the same today as they were then, they furnish us with absolute proof that evolution simply does not work. It doesn’t explain their origin, it hasn’t got the time available for them to originate by the chance combination of nucleotides or whatever, and it cannot explain their stability of design.

Apart from viruses and phages, they are the ‘simplest’ organisms known. And yet, despite their early origin, they possess those most complex substances, DNA, RNA, proteins and most impossible of all for evolution to explain, chlorophyll. Where did all this complexity come from so early on? The quotes show that they appeared fully formed, and highly complex 3.3 to 3.5 BILLION years ago. The oldest rocks are only 3.8 billion years old – so there isn’t a gap there big enough to allow an evolutionary rat to squeeze through.


1 Their Extreme Age

"One of the earliest types of bacteria were the cyanobacteria. Fossil evidence indicates that bacteria shaped like these existed approximately 3.3 billion years ago and were the first oxygen-producing evolving phototropic organisms..."

They have the distinction of being the oldest known fossils, more than 3.5 billion years old, in fact! It may surprise you then to know that the cyanobacteria are still around; they are one of the largest and most important groups of bacteria on earth.

The oldest known fossils are cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old. This may be somewhat surprising, since the oldest rocks are only a little older: 3.8 billion years old.


2 Their absolute perfection

Cyanobacteria are among the easiest microfossils to recognize. Morphologies in the group have remained much the same for billions of years, and they may leave chemical fossils behind as well, in the form of breakdown products from pigments.

They photosynthesize like all other autotrophic bacteria and are just as efficient.

3 Their Complexity

The cyanobacteria are PROKARYOTES, not eukaryotes like the algae.

They contain chlorophyll, enclosed in chloroplasts.

Although they are truly prokaryotic, cyanobacteria have an elaborate and highly organized system of internal membranes which function in photosynthesis. Chlorophyll a and several accessory pigments (phycoerythrin and phycocyanin) are embedded in these photosynthetic lamellae, the analogs of the eukaryotic thylakoid membranes. The photosynthetic pigments impart a rainbow of possible colors: yellow, red, violet, green, deep blue and blue-green cyanobacteria are known.


4 Their critical role in life support

The oxygen atmosphere that we depend on was generated by numerous cyanobacteria during the Archaean and Proterozoic Eras. Before that time, the atmosphere had a very different chemistry, unsuitable for life as we know it today.

They were responsible for the initial conversion of the earth's atmosphere from an anoxic state to an oxic state (that is, from a state without oxygen to a state with oxygen) during the period 2.7 to 2.2 billion years ago. Being the first to carry out oxygenic photosynthesis, they were able to produce oxygen while sequestering carbon dioxide in organic molecules, playing a major role in oxygenating the atmosphere.

Cyanobacteria also play a major role in the nitrogen cycle. They are able to convert atmospheric nitrogen into its organic form. All plants use organic nitrogen as a nutrient to promote growth. Without this source of nitrogen, the plants would die. Cyanobacteria are one of the few types of organisms that are able to make this conversion from atmospheric to organic nitrogen.


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Cyanobacteria use their whole bodies as eyeballs 1

http://reasonandscience.heavenforum.org/t1551-cyanobacteria#4719

HEY LOOK  The spherical bacteria Synechocystis (shown here in false color) can use their single-celled bodies almost like eyeballs. A light shining up from the bottom of this image passes through the cells and focuses on the far side (white arrows highlight examples of focused light). A laser light source in the center (red dot) helped test which way the cells move in reaction to bright spots of light. 
N. Schuergers et al/eLife 2016
After all those years of people looking into microscopes at bacteria, it turns out that some of the bacteria are (sort of) looking back.
Synechocystisbacteria focus light in a roughly eyeball-like process, says Conrad Mullineaux of Queen Mary University of London.  Light shining through their spherical cells focuses on the opposite side, where light-sensitive substances react, he and colleagues report February 9 in eLife
Biologists knew cyanobacteria move toward light, but this method of detecting it was a surprise. Human vision differentiates between two points about 1,000 times better than do the cyanobacteria, but Mullineaux calculates that the bacterial resolution should be enough for Synechocystis to pick out the outline of his head and shoulders bending over them. 


Cyanobacteria use micro-optics to sense light direction 2

Many prokaryotes move directionally in response to a chemical or physical stimulus. However, it is generally assumed that bacteria are too small for direct sensing of a concentration gradient across the cell: instead they probe changes in stimulus concentration over time, as in the classic paradigm of flagella-mediated chemotaxis in Escherichia coli (reviewed by Wadhams and Armitage, 2004). When moving through a spatial concentration gradient of an attractant,E. coli cells experience temporal concentration changes, which they sense by employing a biochemical memory that directs a “biased random walk”. Swimming along a straight path (run) alternates with random changes of direction (tumble). Tumbles become less frequent when cells sense a temporal increase in attractant concentration, introducing a bias to movement up a concentration gradient (Berg and Brown, 1972).
For phototrophic prokaryotes, light is the main source of energy but also potentially harmful, depending on intensity and wavelength. Unsurprisingly, many phototrophs can alter their movement in response to the light environment (reviewed in Häder, 1987). Bacterial phototaxis was first noted in 1883 (Engelmann, 1883) and has been characterized in free-swimming phototrophs including purple bacteria and Halobacterium spp. (Hildebrand and Dencher, 1975Alam and Oesterhelt, 1984). Cyanobacteria, which are oxygenic phototrophs, do not swim with flagella. Instead, various species exhibit “twitching” or “gliding” motility over moist surfaces (Pringsheim, 1968). This movement can be directed towards a light source, thus constituting true phototaxis (Choi et al., 1999Bhaya, 2004Yoshihara and Ikeuchi, 2004).
The model unicellular cyanobacterium Synechocystis sp. PCC 6803 (hereafterSynechocystis) has spherical cells about 3 µm in diameter and moves using Type IV pili (T4P) (Bhaya et al., 2000Yoshihara et al., 2001). The location of the T4P extension motor PilB1 implies that pili are extended at the leading edge of the cell, and therefore that movement is generated by pilus retraction (Schuergers et al., 2015Wilde and Mullineaux, 2015), as has been shown in other bacteria (Merz et al., 2000). It has recently been established that the motility of a filamentous cyanobacterium is also T4P-dependent, suggesting that this form of motility is widespread in cyanobacteria (Khayatan et al., 2015). One likely exception is marine Synechococcus spp., which swims and exhibits chemotaxis without obvious surface appendages (Willey and Waterbury, 1989Ehlers and Oster, 2012) apart from short spicules found in one of the motile Synechococcusstrains (Samuel et al., 2001).
Synechocystis T4P-dependent phototaxis can be observed microscopically at the single cell level and macroscopically through the migration of cell colonies. Genetic studies have identified a number of photoreceptors that influence phototactic behavior under different light regimes (Bhaya, 2004). WhileSynechocystis harbors signal transduction systems for pilus biogenesis that are homologous to the chemotaxis system in E. coli, it lacks the CheR methyltransferase and the CheB methylesterase that are required in most chemotactic bacteria to sense temporal changes in attractant concentration (Wuichet and Zhulin, 2010). This suggests a different mode of directional control.
Previous studies of Synechocystis single cell phototaxis (Choi et al., 1999Chau et al., 2015) have not addressed the question of how an individual cell might be able to perceive the direction of illumination. Here, we establish that individualSynechocystis cells can directly and accurately perceive the position of a unidirectional light source, and control their motility so as to move towards it. We then show that Synechocystis cells act as microlenses, and that the light intensity gradient across the cell due to this lensing effect is far greater than the effects of shading due to light absorption or reflection. Finally, we use highly-localized laser excitation to show that specific excitation of one side of the cell triggers movement away from the light, indicating that positive phototaxis results from movement away from an image of the light source focused on the opposite side of the cell. Essentially, the cell acts as a microscopic eyeball.

1) https://www.sciencenews.org/blog/science-ticker/cyanobacteria-use-their-whole-bodies-eyeballs
2) http://elifesciences.org/content/5/e12620

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16 Re: Cyanobacteria, amazing evidence of design on Fri Apr 14, 2017 8:24 pm

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Recently, i described, how Human made solar pannels, a rather recent invention  finds its equivalent  in chlorophyll pigments, which have the same function,
, capturing solar energy, and used by cyanobacteria in the photosynthesis pathway. Cyanobacteria are supposedly one of the oldest organisms on earth, to transform solar energy in chemical energy. As waste product in the process, they prodcue oxygen. Thats, why we are here.

Why the biosynthesis pathway of Chlorophyll must be intelligently designed
http://reasonandscience.heavenforum.org/t1546-why-the-biosynthesis-pathway-of-chlorophyll-must-be-intelligently-designed

Scientists sometimes discover mechanical processes that change the world itself, that give more opportunities for others to thrive and grow.
Such a discovery was made by Fritz Haber and Carl Bosch in 1909. The unearthing of their eponymous process changed the world forever in ways that improved millions of lives. That is the legacy of the Haber–Bosch process.
The method was the first creation of an artificial nitrogen fixation system, that was able to convert atmospheric nitrogen into ammonia. This, in turn, became the first chemical fertilizer that helped crops grow across Europe.
It was so successful and useful in agriculture that today the vast majority of nitrogen in our bodies come from the Haber-Bosch process.
But there are downsides to high levels of forced nitrogen fixation. And it can be costly in some ways to run, making it less accessible for third world countries as a method. This leaves them with less crop growth and a food supply shortage.
It’s not surprising then that scientists have been searching for alternatives to the regular process, a way to produce the ammonia more directly via bacteria.
Specifically, the researchers have been isolating the enzymes that bacteria use for nitrogen fixation, enzymes called nitrogenases. They are able to cleave the hearty molecular bond between nitrogen atoms and reduce them into ammonia.
A drawback of the system is that the enzymes can only function in an oxygen free environment, meaning that the scientists had to devise a fuel cell container that could catalyze the reduction and function properly.
One positive side benefit from their twin cell containers is that the process derives electricity from the reduction, due to free electrons in the cycle, and doesn’t need to be manually charged like the Haber-Bosch process does.
The only thing preventing larger scale production of the fuel cells is the lack of cheap ATP to facilitate it. The researchers are currently looking into a way to avoid the necessity of ATP for the chemical reaction to occur.
The greatest benefit from the fuel cell design is that it both produces a small amount of ammonia over time, but also a positive amount of electricity, doubling as a fuel and energy producer.
Hopefully once completed, multiple uses can be found for such a multi-purpose device. And without the current 1% of global electricity per year that the Haber-Bosch process requires.
http://bioscriptionblog.com/2017/02/08/innovations-overturn-haber-bosch-ammonia/

Beside photosynthesis, another remarkable feature of cyanobacteria is fixation of nitrogen in the atmosphere into ammonia. YOu can read about their amazing feats here:

Cyanobacterias, amazing evidence of design
http://reasonandscience.heavenforum.org/t1551-cyanobacteria-amazing-evidence-of-design

and about how they transform nitrogen in the atmosphere into ammonia through nitrogenase enzymes here:

The Nitrogenase enzyme,  the molecular sledgehammer  
http://reasonandscience.heavenforum.org/t1585-nitrogenase#2406

In their active site, these enzymes require Iron-Molybdenum Cofactors. How these are synthesized, and their ULTRACOMPLEX process, which is astounding, you can read here:

Molybdenum, essential for life
http://reasonandscience.heavenforum.org/t2430-molybdenum-essential-for-life

God is truly the Grand-master of creation, and we can never fully comprehend and scrutinize all his inventions and his intelligence seems to have no limits !! What tremendous creator HE is, and what tremendous God we have.

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17 Re: Cyanobacteria, amazing evidence of design on Fri Apr 14, 2017 8:24 pm

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Admin
Recently, i described, how Human made solar pannels, a rather recent invention  finds its equivalent  in chlorophyll pigments, which have the same function,
, capturing solar energy, and used by cyanobacteria in the photosynthesis pathway. Cyanobacteria are supposedly one of the oldest organisms on earth, to transform solar energy in chemical energy. As waste product in the process, they prodcue oxygen. Thats, why we are here.

Why the biosynthesis pathway of Chlorophyll must be intelligently designed
http://reasonandscience.heavenforum.org/t1546-why-the-biosynthesis-pathway-of-chlorophyll-must-be-intelligently-designed

Scientists sometimes discover mechanical processes that change the world itself, that give more opportunities for others to thrive and grow.
Such a discovery was made by Fritz Haber and Carl Bosch in 1909. The unearthing of their eponymous process changed the world forever in ways that improved millions of lives. That is the legacy of the Haber–Bosch process.
The method was the first creation of an artificial nitrogen fixation system, that was able to convert atmospheric nitrogen into ammonia. This, in turn, became the first chemical fertilizer that helped crops grow across Europe.
It was so successful and useful in agriculture that today the vast majority of nitrogen in our bodies come from the Haber-Bosch process.
But there are downsides to high levels of forced nitrogen fixation. And it can be costly in some ways to run, making it less accessible for third world countries as a method. This leaves them with less crop growth and a food supply shortage.
It’s not surprising then that scientists have been searching for alternatives to the regular process, a way to produce the ammonia more directly via bacteria.
Specifically, the researchers have been isolating the enzymes that bacteria use for nitrogen fixation, enzymes called nitrogenases. They are able to cleave the hearty molecular bond between nitrogen atoms and reduce them into ammonia.
A drawback of the system is that the enzymes can only function in an oxygen free environment, meaning that the scientists had to devise a fuel cell container that could catalyze the reduction and function properly.
One positive side benefit from their twin cell containers is that the process derives electricity from the reduction, due to free electrons in the cycle, and doesn’t need to be manually charged like the Haber-Bosch process does.
The only thing preventing larger scale production of the fuel cells is the lack of cheap ATP to facilitate it. The researchers are currently looking into a way to avoid the necessity of ATP for the chemical reaction to occur.
The greatest benefit from the fuel cell design is that it both produces a small amount of ammonia over time, but also a positive amount of electricity, doubling as a fuel and energy producer.
Hopefully once completed, multiple uses can be found for such a multi-purpose device. And without the current 1% of global electricity per year that the Haber-Bosch process requires.
http://bioscriptionblog.com/2017/02/08/innovations-overturn-haber-bosch-ammonia/

Beside photosynthesis, another remarkable feature of cyanobacteria is fixation of nitrogen in the atmosphere into ammonia. YOu can read about their amazing feats here:

Cyanobacterias, amazing evidence of design
http://reasonandscience.heavenforum.org/t1551-cyanobacteria-amazing-evidence-of-design

and about how they transform nitrogen in the atmosphere into ammonia through nitrogenase enzymes here:

The Nitrogenase enzyme,  the molecular sledgehammer  
http://reasonandscience.heavenforum.org/t1585-nitrogenase#2406

In their active site, these enzymes require Iron-Molybdenum Cofactors. How these are synthesized, and their ULTRACOMPLEX process, which is astounding, you can read here:

Molybdenum, essential for life
http://reasonandscience.heavenforum.org/t2430-molybdenum-essential-for-life

God is truly the Grand-master of creation, and we can never fully comprehend and scrutinize all his inventions and his intelligence seems to have no limits !! What tremendous creator HE is, and what tremendous God we have.

View user profile http://elshamah.heavenforum.com

18 Re: Cyanobacteria, amazing evidence of design on Fri Jun 02, 2017 4:58 pm

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Surprising New Species Of Light-harvesting Bacterium Discovered In Yellowstone
https://www.sciencedaily.com/releases/2007/07/070726142026.htm

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19 Re: Cyanobacteria, amazing evidence of design on Wed Jun 28, 2017 5:52 am

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The rapid production of new kinds of metabolites by Prochlorococcus cyanobacteria's challenges evolution theory 1

http://reasonandscience.heavenforum.org/t2568-the-rapid-production-of-new-kinds-of-metabolites-by-prochlorococcus-cyanobacteria-s-challenges-evolution-theory

It's one of the tiniest organisms on Earth, but also one of the most abundant.

The marine cyanobacterium Prochlorococcus is the smallest and most abundant photosynthetic organism on Earth. 4 . It is the smallest (the cell diameter is 0.5–0.7μm)2 and most abundant photosynthetic organism on the planet, with an estimated global population of ~10^27 cells.  Prochlorococcus has the smallest genome of any free-living phototroph; some isolates have genomes as small as 1.65Mbp, with only ~1,700 genes. It is the only type of marine phytoplankton that uses the divinyl form of chlorophyll a and chlorophyll b to harvest light energy, which causes a slight red shift in its absorption spectra.   This unique pigmentation has made it possible to determine that Prochlorococcus accounts for 50% of the total chlorophyll in vast stretches of the surface oceans.  Collectively, this cyanobacterium produces an estimated 4 gigatons of fixed carbon each year, which is approximately the same net primary productivity as global croplands.

Meet the obscure microbe that influences climate, ocean ecosystems, and perhaps even evolution 5
Prochlorococcus is the smallest, most abundant photosynthesizing cell in the ocean—responsible for 5% of global photosynthesis.  Its many different versions, or ecotypes, thrive from the sunlit sea surface to a depth of 200 meters, where light is minimal.  Collectively the "species" boasts an estimated 80,000 genes—four times what humans have, and plenty to deal with whatever the world's oceans throw at it. "It's a beautiful little life machine and like a superorganism," Chisholm says. "It's got a story to tell us."




When the U.S. Department of Energy's Joint Genome Institute first began sequencing microbes in 2003, Chisholm convinced it to sequence two Prochlorococcus strains—this at a time when sequencing a single microbe was a big deal—so she could assess genetic differences between the forms adapted to low and high light levels. "That was very greedy of me," she smiles. Her team found the high light–adapted ecotype's genome was very streamlined—1.7 million bases with just 1700 genes. "It's one of, if not the, simplest self-sustaining organism we know of," says Chisholm's postdoc Jamie Becker. The low-light version's genome has 2.4 million bases, with 2275 genes, including some that may enable the microbe to work best in low light and avoid damage from the sun should it wind up at the surface somehow.

Together, her lab found that each of the main Prochlorococcus ecotypes has its own genomic "island," a patch of genes that confers specific adaptations to an environment. One island helps the microbe survive in very low-phosphorus waters, for example. Bacteriophages, viruses that infect bacteria and can either pick up or deposit genetic material, may move these islands and other genes between ecotypes, Chisholm's postdoc Debbie Lindell proposed in 2004, thereby ensuring the microbes can adapt to changing conditions.

The worldwide sampling showed that the five primary ecotypes didn't begin to capture Prochlorococcus's diversity. Sequencing revealed hundreds of strains coexisting even in just a milliliter of seawater, each with more than 100 distinctive genes. And when it became possible to sequence genomes from single cells—a technique Chisholm's lab pioneered for marine microbes—each strain turned out to encompass still more genetic variation. "It's not one bug, it's a whole family of things that grade into each other," says Olson, now at WHOI.

Although each cell has only about 2000 genes, Prochlorococcus as a whole has a "pan-genome" of perhaps 80,000 genes, Chisholm and her colleagues estimate. "That's a ton of information for these little guys," she says, and it must be the secret of Prochlorococcus's success. Its enormous genomic repertoire enables it to cope with conditions across a vast swath of the oceans, dominating warm seas from 40° North to 40° South

These waters contain an estimated 3 billion billion billion Prochlorococcus cells, collectively weighing as much as 220 million Volkswagen Beetles. That abundance makes the microbe a heavyweight in ocean food webs and climate. It is a key source of food in the nutrient-poor regions of the ocean where it flourishes.  "Prochlorococcus makes organic matter that other microorganisms eat." And because of its role in the carbon cycle, the microbe significantly regulates levels of climate-warming carbon dioxide (CO2)  

She continues to be driven to unravel the story of Prochlorococcus. In 2014, for example, electron micrographs taken in her lab revealed tiny vesicles budding off Prochlorococcus cells; later, her postdoc Steven Biller showed that each cell releases two to five lipid-membrane bubbles filled with DNA and RNA per generation—possible food sources for other plankton, decoys for viruses, gene-transfer vehicles, or even messengers that communicate with other microbes.

And now, Prochlorococcus can add one more superlative to its list of attributes: It evolves new kinds of metabolites called lanthipeptides, more abundantly and rapidly than any other known organism. While most bacteria contain genes to pump out one or two versions of this peptide, Prochlorococcus varieties can each produce more than two dozen different peptides (molecules that are similar to proteins, but smaller). And though all of Earth's Prochlorococcus varieties belong to just a single species, some of their localized varieties in different regions of the world's oceans each produce a unique collection of thousands of these peptides, unlike those generated by terrestrial bacteria.

Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that display a wide variety of biological activities, from antimicrobial to antiallodynic. lanthipeptide biosynthetic enzymes are also present in some archaea and in higher eukaryotes including mammals, lanthipeptide detection and isolation is thus far restricted to bacteria. The increase in the number of characterized lanthipeptides as a result of the bacterial genome sequencing projects has led to the realization that their functions are not limited to antimicrobial activities but also include antifungal, morphogenetic, antiviral, antinociceptive and antiallodynic functions. Lanthipeptide biosynthetic gene clusters are particularly found in the genomes of many genera of Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. 3


"No one had seen the true extent of the diversity in these molecules" until this new study, Cubillos-Ruiz says. The first hints of this unexpected diversity surfaced in 2010, when Bo Li and Daniel Sher, members of van der Donk's and Chisholm's labs respectively, found that one variety of Prochlorococcus could produce as many as 29 different lanthipeptides. But the big surprise came when Cubillos-Ruiz looked at other populations and found that the same organisms, in a different location, produced similarly great numbers of the peptides, "and all of them were completely different," he says.

After considerable study examining the genomes of many Prochlorococcus cultures and pieces of DNA from the wild, the researchers determined that the way the extraordinary numbers of lanthipeptides evolve is, in itself, something that hasn't been observed before. While most evolution takes place through tiny incremental changes, while preserving the vast majority of the genetic structure, the genes that enable Prochlorococcus to produce these lanthipeptides do just the opposite. They somehow undergo dramatic, wholesale changes all at once, resulting in the production of thousands of new varieties of these metabolites.

Cubillos-Ruiz, who is now a postdoc at MIT's Institute For Medical Engineering and Science, says the way these genes were changing "wasn't following classic phylogenetic rules," which dictate that changes should happen slowly and incrementally to avoid disruptive changes that impair function. But the story is a bit more complicated than that: The specific genes that encode for these lanthipeptides are composed of two parts, joined end to end. One part is actually very well-preserved across the lineages and different populations of the species. It's the other end that goes through these major shakeups in structure. "The second half is amazingly variable," he says. "The two halves of the gene have taken completely different evolutionary pathways, which is uncommon."

The actual functions of most of these thousands of peptides, which are known as prochlorosins, remain unknown, as they are very difficult to study under laboratory conditions. Similar compounds produced by terrestrial bacteria can serve as chemical signaling devices between the organisms, while others are known to have antimicrobial functions, and many others serve purposes that have yet to be determined. Because of the known antimicrobial functions, though, the team thinks it will be useful to screen these compounds to see if they might be candidates for new antibiotics or other useful biologic products.
This evolutionary mechanism in Prochlorococcus represents "an intriguing mode of evolution for this kind of specialized metabolite," Cubillos-Ruiz says. While evolution usually favors preservation of most of the genetic structure from the ancestor to the descendants, "in this organism, selection seems to favor cells that are able to produce many and very different lanthipeptides. So this built-in collective diversity appears to be part of its function, but we don't yet know its purpose. We can speculate, but given their variability it's hard to demonstrate." Maybe it has to do with providing protection against attack by viruses, he says, or maybe it involves communicating with other bacteria.

"Prochlorococcus is trying to tell us something, but we don't yet know what that is," says Chisholm, who has joint appointments in MIT's departments of Civil and Environmental Engineering and Biology. "What [Cubillos-Ruiz] uncovered through this molecule is an evolutionary mechanism for diversity." And that diversity clearly must have very important survival value, she says: "It's such a small organism, with such a small genome, devoting so much of its genetic potential toward producing these molecules must mean they are playing an important role. The big question is: What is that role?"
In fact, this kind of process may not be unique—it may be just that Prochlorococcus, an organism that Chisholm and her colleagues initially discovered in 1986 and have been studying ever since, has provided the wealth of data needed for such an analysis. "This might be happening in other kinds of bacteria," Cubillos-Ruiz says, "so maybe if people start looking into other environments for that kind of diversity," it may turn out not to be unique. "There are some hints it happens in other [biological] systems too," he says.

Christopher Walsh, emeritus professor of biological chemistry and molecular pharmacology at Harvard University, who was not involved in this work, says "The dramatic diversity of prochlorosins assembled by a single enzyme … raises surprising questions about how evolution of thousands of cyclic peptide structures can be accomplished by alterations that favor large changes rather than incremental ones."

Evolutionary radiation of lanthipeptides in marine cyanobacteria 2

Lanthipeptides in marine picocyanobacteria are undergoing a rapid evolutionary process of structural diversification. It appears that the prochlorosin biosynthesis pathway has evolved such that it can generate a suite of structurally diverse natural products by using the combination of a substrate-tolerant lanthionine synthetase and a collection of precursor peptide substrates encoded in a highly dynamic family of multicopy genes poised for rapid expansion and diversification. 

This type of diversity-prone selection contrasts with the evolutionary path of other lanthipeptides such as lantibiotics, which display antimicrobial activity



Schematic organization of a P. marinus SS120 cell showing the main metabolic pathways and transporters. Gene identifiers are shown by numbers in blue. Genes with uncertain annotation are shown with a question mark. Reactions for which no candidate enzyme was confidently predicted are indicated by dashed arrows. Pathways that involve multiple reactions are shown by double arrows. Final biosynthetic products are indicated as follows: light blue, amino acids; dark yellow, nucleotides; brown, sugars; pink, cofactors. Chl cycle is based on ref. 37. Cyt, cytochrome; Flvd, flavodoxin; FNR, ferredoxin:NADP+ oxidoreductase; PQ, plastoquinone. 6


1. https://phys.org/news/2017-06-marine-bacteria-evolution-specialized-molecules.html
2. http://www.pnas.org/content/early/2017/06/16/1700990114.full
3. http://pubs.acs.org.sci-hub.cc/doi/pdf/10.1021/acs.chemrev.6b00591
4. http://www.nature.com.ololo.sci-hub.cc/nrmicro/journal/v13/n1/full/nrmicro3378.html
5. http://www.sciencemag.org/news/2017/03/meet-obscure-microbe-influences-climate-ocean-ecosystems-and-perhaps-even-evolution
6. http://www.pnas.org/content/100/17/10020.full

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