Wednesday, February 01, 2017

Scientists confused about photosynthesis - press release makes it worse

Photosynthesis is the series of reactions that capture light energy and use it to make ATP and sometimes reducing equivalents (e.g NADPH). There are many different versions of photosynthesis. One of the simplest is found in purple bacteria where the process results in formation of a proton gradient that's used to drive ATP synthesis.

The ATP produced by this process is used for everything in the cell, including DNA synthesis, protein synthesis, lipid/membrane synthesis, and carbohydrate synthesis. It's used to fix carbon dioxide (CO2) as well.

There are six well-known ways of fixing CO2 but the one most familiar to biochemistry students is the Calvin cycle (Calvin-Benson cycle) used by plants [The Calvin Cycle] [The Calvin Cycle: Regeneration]. That pathway is found in chloroplasts and it uses up a considerable amount of the ATP and NADPH produced by photosynthesis. That's because plants make a lot of cellulose and starch.

The connection between photosynthesis and the Calvin cycle is so evident in plants that students are often given the impression that photosynthesis is defined as the conversion of light energy to sugars. This is obviously false since they are separate pathways and most photosynthetic bacteria devote only a small percentage of their ATP to fixing carbon [see The Photosynthesis Song and a Pet Peeve].

Undergraduates are given the impression that the Calvin cycle is only found in photosynthetic species but this is also false [Carbon Dioxide Fixation in the Dark Ocean].

As a result of this misinformation, students grow up to be scientists who still labor under the misconception that photosynthesis includes the Calvin cycle.

Let's look at a paper that's just been published in Nature Communications.
Kono, T., Mehrotra, S., Endo, C., Kizu, N., Matusda, M., Kimura, H., Mizohata, E., Inoue, T., Hasunuma, T., Yokota, A., Matsumura, H., and Ashida, H. (2017) RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nature Communications 8: artilce number 14007 [doi: 10.1038/ncomms14007]

Abstract: Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate’ (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown.
RuBisCo is the enzyme that fixes CO2 at the beginning of the Calvin cycle [Fixing Carbon: the Rubisco Reaction ] [Fixing Carbon: the Structure of Rubisco]. It's been known for some time that RuBisCO is found in non-photosynthetic species; a point the authors are aware of even though they don't explain it very well. It's been established that these bacteria can fix carbon and make carbohydrates even though can't capture light energy to make ATP.

The paper addresses a variant of the Calvin cycle that occurs in methanogenic archaea. It's interesting, but hardly revolutionary.

You wouldn't know that from reading the press release published by Kobe University: Mechanism for photosynthesis already existed in primeval microbe. Here's part of that press release ...
Photosynthesis, creating oxygen and carbohydrates such as glucose from solar energy, water, and CO2, is indispensable for many species on this planet. However, it is unclear exactly how or when organisms evolved the ability to photosynthesize. These questions have fascinated scientists for a long time.

The research group discovered that Methanospirillum hungatei, a microbe (methanogenic archaeon) which is thought to have existed since before the development of photosynthesis, possess genes similar to those that play a role in photosynthesis. Through analysis of the enzymes synthesized by these genes and by investigating the metabolic substances within the organism, carrying out metabolome analysis to locate the trapped CO2, the team proved that Methanospirillum hungatei uses a primitive pathway that closely resembles the metabolic pathway used in photosynthesis to synthesize carbohydrates such as glucose.
The main problem here is the one biochemistry teachers have created by confusing photosynthesis and the Calvin cycle. They are separate reactions. Each of them can exist without the other.

We have a pretty good idea how photosynthesis (sensu stricto) evolved because there are plenty of simple examples in bacteria. In my textbook, I describe a probable evolutionary pathway to the complex pathway seen in cyanobacteria and plants. That idea has been around for decades.

Similarly, the ability to fix CO2 using Calvin cycle enzymes has been thoroughly studied. It is not news that this pathway is used in nonphotosynthetic bacteria. It is not news that the ability to fix carbon dioxide evolved long before the ability to make ATP by photosynthesis.

We need to stop teaching undergraduates that photosynthesis is coupled to fixation of carbon dioxide and synthesis of carbohydrates. That's an archaic idea that can be traced back to a time when nobody knew anything about photosynthesis in bacteria.

(Even worse, almost half the biochemistry courses in North America don't even teach photosynthesis because it's not on the MCAT. We haven't been teaching it in my own department ever since I stopped teaching introductory biochemistry. The excuse is that we teach in a Medical School and students in our courses aren't interested in plants.)


  1. The misunderstanding here probably goes much deeper than just the case of photosynthesis and the Calvin cycle -- the fundamental problem is that because of phylogenetic chauvinism towards large organisms similar to us on one side and land plants that we can eat on the other, the actual diversity of metabolisms (which is, of course, all microbial) simply doesn't figure into most people's thinking.

    Which means that most people don't actually have a complete understanding of what really the nature of life on this planet (and potentially others) is and how it can support itself.

    I actually don't think you can fix this at the college level and beyond -- it has to be thoroughly drilled in high school, after that it's just too late.

    1. This is manifest in the commonest counter to the Creationist 2nd Law of Thermodynamics gaffe: flux from the sun. And in the common assumption that the earliest life must have been photosynthetic.

    2. Hi Georgi,

      Could you please contact me by email?

  2. I agree with you, but on a general level... Many courses do address this issue, in the case of University of Toronto, microbiology does cover this very topic/misconception you're referring to (specifically MGY377).

  3. Once again -- great post. Should the reactions of photosynthesis and Carbon Dioxide fixation 'ever' be taught as a coupled reaction?? Is it such a bad thing to teach to freshmen in HS that their foods are derived from what land plants do, couple photosynthesis and carbon dioxide fixation?

  4. If you think it's hard to teach photosynthesis to Medical students, try teaching it to Pharmacy students - who aren't swayed by the fact that >40% of the compounds they purvey are derived from plant sources. Groan.

  5. Larry, you have not responded at Facebook, so i ask you here:

    HOW did photosynthesis evolve ?

    You seem to know more than the experts in the field, like Blankenship, which does not have that special knowledge of yours...

  6. I don't think you're going to make much headway at defining (redefining?) photosynthesis as you suggest. From the point of view of ecologists, for example, the importance of photosynthesis (as done by plants) is carbon-fixation and sugar synthesis using light.

    We all do learn early on about the light reaction (trapping light and making ATP & NADPH) and the dark reaction (fixing carbon, making sugars). I think one could make a lot of progress with understanding evolution of the coupled reactions (photosynthesis as commonly understand) by simply stressing that these parts can exist separately, and evolved separately.

    (As you might guess, I am one of the many people who has taught photosynthesis as the whole reaction series, from trapping light to making sugars.)

    1. bwilson295 says,

      From the point of view of ecologists, for example, the importance of photosynthesis (as done by plants) is carbon-fixation and sugar synthesis using light.

      Ecologists don't care about plants making DNA, proteins, and lipid membranes? Why?

      Do ecologists care about algae? Algae don't make much sucrose. They mostly use the ATP from photosynthesis to make proteins.

      What about photosynthetic bacteria? Are they completely ignored by ecologists?

      I had no idea ecologists were so fixated on the Calvin cycle in flowering plants.

  7. Professor Moran is right on target. Out of idle curiosity, has anyone calculated the efficiency of photosynthesis for any organism when the numerator is defined as ATP + NADPH produced and the denominator is defined in terms of light input per surface area?

    A quick search of the internet provides no ready answers