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Photosynthesis genes source still unclear

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From Charles Q. Choi at Inside Science:

However, much remains unknown about when and how cyanobacteria evolved oxygenic photosynthesis. “The whole question of the origin of cyanobacteria has long been a mystery because they kind of just appeared out of the tree of life with this very advanced capability to do oxygenic photosynthesis without any apparent forebears,” said biochemist Robert Blankenship at Washington University in St. Louis, Missouri.

Until recently, all known cyanobacteria were photosynthetic members of class Oxyphotobacteria.

But in 2013, researchers discovered a nonphotosynthetic class of cyanobacteria known as Melainabacteria. Now Fischer and his colleagues have discovered a second class of nonphotosynthetic cyanobacteria, the Sericytochromatia. The researchers suggest that both groups are clearly closely related to photosynthetic cyanobacteria, based on their genomes, but the two groups do not perform photosynthesis themselves.

One possible explanation for the lack of photosynthesis in these two classes of cyanobacteria was that they could once photosynthesize but then lost the ability. More.

The plot deepens.

See also: Can we pinpoint the origin of oxygen photosynthesis?

17 Replies to “Photosynthesis genes source still unclear

  1. 1
    Dionisio says:

    “The plot deepens.”
    And it ain’t look good for Darwin’s fans and their comrades.
    At this point one could sweep and mop the floor with their “just so” stories. But let’s be gracious. Just ignore them.
    🙂

  2. 2
    Dionisio says:

    “New findings suggest current oxygen-producing bacteria borrowed the ability from a possibly extinct lifeform.”

    Huh?

    Still I prefer Cinderella’s story: a pumpkin turned carriage, mice became horses, and a grasshopper was hired as ‘cochero’. At least that makes more sense than the Darwinian fiction.

  3. 3
    Dionisio says:

    “Now the mystery of how that moment happened is deepening: Scientists have found that the genes for such photosynthesis apparently came from a now-extinct mystery source.”

    Perhaps it’s time to call Sherlock Holmes?

  4. 4
    Dionisio says:

    How and when Cyanobacteria evolved the ability to produce oxygen through photosynthesis is poorly understood.

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Oh well, what else is new?

    Is there anything that is well understood these days?

  5. 5
    Dionisio says:

    The phylogenetic relationships of these prokaryotes suggest that the evolution of aerobic respiration likely occurred multiple times.

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Wow! That’s cool! 🙂

  6. 6
    Dionisio says:

    […] the modern photosynthetic system apparently arose through the lateral gene transfer and fusion of two photosynthetic systems […]

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Huh?

    Still I prefer Cinderella’s story: a pumpkin turned carriage, mice became horses, and a grasshopper was hired as ‘cochero’. At least that makes more sense than the Darwinian fiction.

    Complex complexity.

  7. 7
  8. 8
    Dionisio says:

    It is difficult to imagine random changes accomplishing so much.

    But random genetic drift is now widely recognized as one of the most important mechanisms of evolution.

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Huh?

    Still I prefer Cinderella’s story: a pumpkin turned carriage, mice became horses, and a grasshopper was hired as ‘cochero’. At least that makes more sense than the Darwinian fiction.

    Complex complexity.

  9. 9
    Dionisio says:

    The Cyanobacteria are one of the most important microbial groups on Earth; however, much remains to be learned about their diversity and evolution.

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Complex complexity.

  10. 10
    Dionisio says:

    […] the last common ancestor of the Cyanobacteria did not use oxygen […]

    […] the three classes acquired aerobic respiration independently after their divergence […]

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    Complex complexity.

  11. 11
    Dionisio says:

    There is a substantial and ongoing debate regarding the timing of both the origin of oxygenic photosynthesis and the appearance of oxygen on Earth, with different geological, geochemical, and paleontological data yielding interpretations that span 1.5 billion years of Earth’s history […]

    On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
    Rochelle M. Soo, James Hemp, Donovan H. Parks, Woodward W. Fischer, Philip Hugenholtz
    Science Vol. 355, Issue 6332, pp. 1436-1440
    DOI: 10.1126/science.aal3794

    What else is new?

    Isn’t that called “speculation”?

  12. 12
    Dionisio says:

    No politely dissenting interlocutors in this thread?
    🙂

  13. 13
    Otangelo Grasso says:

    Photosynthesis

    http://reasonandscience.heaven.....osynthesis

    At the base of virtually every food chain on Earth, today is a photosynthetic organism – a tree, a plant, an algal cell or a cyanobacterium. Virtually every living thing on the planet today is ultimately powered by sunshine. Every mouthful of every meal has its origins in the Sun, from the fruit and vegetables created by plants that absorb sunlight directly, to the meat and fish that deliver their sunshine second- or third-hand as part of the complex food chain. It appears today as if the Sun is a truly fundamental ingredient for life, a provider without which life couldn’t exist. Yet this intimate relationship with our nearest star is not a simple one. The Sun is a far from benevolent companion. Its radiant rain has a dark side that is as dangerous as it is nourishing, and early in the development of life on Earth it is likely that the Sun was a presence to be avoided rather than cherished. To understand how life transformed its relationship with light, we have to go back to a time when life sheltered in the darkness. For many biologists, life on Earth didn’t begin in the light, but rather in the darkness of the deep oceans. The transformation of light from threat to food required one of life’s most extraordinary inventions: oxygenic photosynthesis. The evolution of this biological process ultimately resulted in the capture of carbon and the release of large amounts of oxygen into the atmosphere, which in turn played a key role in triggering the explosive evolution of life from the simple to the complex and conscious. Photosynthesis uses carbon dioxide and water to produce sugars and oxygen in a process powered by the energy of the Sun. The purpose of photosynthesis, if you are a plant, is twofold. One is clearly visible in the famous equation: it is to make sugars, which is done by forcing electrons onto carbon dioxide. The other, which is hidden in the detail, is to capture energy from the Sun and store it in a usable form. All life on Earth stores energy in the same way, as a molecule called adenosine triphosphate, or ATP. This suggests strongly that ATP is a very ancient ‘invention’, and the details of its production and function could provide clues as to life’s origin.

    The molecular machinery of oxygenic photosynthesis in constructed from three distinct components known as photosystem I, photosystem II, and the Oxygen Evolving Complex, linked together by two electron transport chains. This linked molecular machine is known as the Z scheme. Photosystem I takes electrons and, using energy from the Sun collected by the pigment chlorophyll, forces them onto carbon dioxide to make sugars. Photosystem II functions in a different way. It uses another form of chlorophyll and, rather than forcing its energised electrons onto carbon dioxide, it cycles them around a circuit somewhat like a battery, siphoning off a little of the Sun’s captured energy and storing it in the form of ATP. In order to make sugars and ATP, therefore, the plant needs sunlight, carbon dioxide and a supply of electrons. It doesn’t ‘care’ where those electrons come from. The plant may not care, but we certainly do, because plants get their electrons from water, splitting it apart in the process and releasing a waste gas (oxygen) into the atmosphere. This is the source of all the oxygen in the atmosphere of our planet, and so understanding the evolution of the Z scheme is of paramount importance if we are to understand how Earth came to be a home for complex animals like us.

    In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose and fixed carbon to make glucose, its food of the organism as end products. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and oxygen, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, and no advanced life would be possible on earth.

    So, photosynthesis is an interdependent system that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage — all happened by a series of natural events that we can call ad hoc mistakes “formed in one particular moment without ability to consider any application,” to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to “feed” ATP synthase nano motors to produce ATP, and so on? Such independent structures would have not aided survival.

    Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment–would they ever “get together” since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where every small step needs to provide a survival advantage.

    Essential parts of oxygenic photosynthesis

    The photosynthesis pathway is interdependent and irreducible. Take any of the individual parts out, and the process ceases to function. Neither do most individual parts and proteins have no function , unless in this remarkable pathway.
    We can, therefore, infer that design explains best the origin of photosynthesis through a creator.

    1. Lipid bilayer membranes are critical to the early stages of energy storage, such that photosynthesismust be viewed as a process that is at heart membrane-based. 4
    2. Chlorophyll is an essential component of photosynthesis, which helps plants get energy from light. 1
    3. The light harvesting complexes, also called antenna complexes, are essential for collecting sunlight and regulating photosynthesis 2
    4. Photosystem II (PSII) is a key component of photosynthesis 2
    5. The oxygen evolving is responsible for catalyzing the oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. 3
    6. The cytochromeb6 f complex is an essential player in noncyclic and cyclic electron flow 4
    7. Plastocyanin is an essential member of photosynthetic electron transport and functions near PS I. 5
    8. PSI is necessary to provide the energy to reduce NADP+ to NADPH 6
    9. Ferredoxin (Fd) proteins are required for the electron transfer process from the bound Fe–S centers in the Photosystem I reaction center to NADP+. 4
    10. Ferredoxin—NADP(+) reductase same as 9
    11. In plants and photosynthetic bacteria ATP synthase is essential for solar energy conversion and carbon fixation.

    1) http://www.newworldencyclopedi.....hlorophyll
    2) http://www.nature.com/nature/j.....01344.html
    3) http://www.sciencedirect.com/s.....4507001877
    4) Blankenship: Molecular mechanisms of photosynthesis
    5) http://www.esalq.usp.br/lepse/.....-Katoh.pdf
    6) http://www.nature.com/nsmb/jou.....1_577.html
    7) http://www.atpsynthase.info/Basics.html

    Fun and games with Otangelo Grasso about photosynthesis
    http://sandwalk.blogspot.com.b.....rasso.html

  14. 14
    Dionisio says:

    Otangelo Grasso @13:

    “The photosynthesis pathway is interdependent and irreducible. Take any of the individual parts out, and the process ceases to function. Neither do most individual parts and proteins have no function , unless in this remarkable pathway.”

    Very interesting. Thanks.

  15. 15
    gpuccio says:

    Otangelo Grasso:

    Well, Larry Moran seems happy that “the cytochrome bc complex and ATP synthase pre-date photosynthesis”.

    They are obviously simple structures that can be easily explained away! 🙂

  16. 16
  17. 17
    Dionisio says:

    gpuccio:

    Is this paper somehow related to one of the topics you mentioned @15?

    Genetic Evidence for Cytochrome b Qi Site Inhibition by 4(1H)-Quinolone-3-Diarylethers and Antimycin in Toxoplasma gondii.

    Alday PH1, Bruzual I2, Nilsen A2, Pou S2, Winter R2, Ben Mamoun C3, Riscoe MK2, Doggett JS

    Antimicrob Agents Chemother. 2017 Jan 24;61(2). pii: e01866-16. doi: 10.1128/AAC.01866-16. Print 2017 Feb.

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