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+--Forum: Cabbages and Kings
+---Topic: The Origins of Photosynthesis started by niiicholas
Posted by: niiicholas on May 28 2002,15:10
I came across a new article on the evolution of photosynthesis; there are a number of articles on this topic, I will post them as I rediscover them, others may have come across interesting stuff also.
Reaction centres: the structure and evolution of biological solar power
Peter Heathcote b, Paul K. Fyfe a and Michael R. Jones a
Trends in Biochemical Sciences 2002, 27:79-87
Reaction centres are complexes of pigment and protein that convert the electromagnetic energy of sunlight into chemical potential energy. They are found in plants, algae and a variety of bacterial species, and vary greatly in their composition and complexity. New structural information has highlighted features that are common to the different types of reaction centre and has provided insights into some of the key differences between reaction centres from different sources. New ideas have also emerged on how contemporary reaction centres might have evolved and on the possible origin of the first chlorophyll–protein complexes to harness the power of sunlight.
[...I'll quote the last part of the review to give a sense of where things are at...]
Common structural blueprint
The crystallographic information summarized in Fig. 4 highlights structural features that are common to all types of reaction centre [3,10,25] . At the heart of each complex is a core domain consisting of an arrangement of two sets of five transmembrane helices. This protein scaffold encases six (bacterio)chlorin and two quinone cofactors that are arranged in two pseudosymmetric membrane-spanning branches. These cofactors catalyse the photochemical transmembrane electron transfer reaction that is the key to the photosynthetic process. Added to this basic structural blueprint are a variety of protein–cofactor structures, such as antenna complexes, the oxygen-evolving complex or Fe–S centres, which represent further adaptations. In particular, in the PSII reaction centre and all known Type I reaction centres, the core electron transfer domain is flanked by two homologous antenna domains, each consisting of a bundle of six membrane-spanning helices binding antenna pigments , and antenna chlorophylls are also bound to the ten-helix core ( Fig. 4). These antenna domains are not present in purple bacteria such as Rhodobacter sphaeroides or green filamentous bacteria such as Chloroflexus.
Which is the oldest reaction centre?
The realization that all reaction centres are based on a common design has provoked much discussion over the evolutionary links between the different complexes and the nature of the ancestral reaction centre. This is a challenging topic because it is clear that chlorophyll-based photosynthesis is a very old process that appeared during the first few hundred million years of evolution . One approach to this problem has been to examine which of the five distinct groups of photosynthetic bacteria represents the oldest photosynthetic lineage, through phylogenetic studies of both photosynthetic and non-photosynthetic proteins. However, such studies have produced conflicting results, with green filamentous bacteria, heliobacteria and purple bacteria all being identified as the oldest lineage in different studies [39–42] . The problem of tracing the evolutionary development of modern day photosystems is not helped by some of the variety and complexity exhibited by photosynthetic organisms, which indicates some interchange of photosynthetic components by lateral gene transfer between groups during the course of evolution [41,43] . At present, it is probably prudent to conclude that the use of this approach requires additional data and a more extensive analysis.
Primordial reaction centre: Type I, Type II or both?
Setting aside the question of which is the oldest photosynthetic organism, several models have been proposed to account for the development of modern day reaction centres from simpler ancestors . Most recently, a new evolutionary scheme for contemporary reaction centres has been proposed that envisages the ancestral reaction centre as homodimeric, with the three-domain antenna–core–antenna organization seen in extant Type I complexes . It is proposed that this ancestral reaction centre had two membrane-spanning electron transfer chains, each terminating in a loosely bound quinone that could dissociate when reduced and move into the membrane pool, and that it occupied a membrane that had already developed a fully functional anaerobic respiratory chain, in accordance with the 'respiration early' hypothesis . Therefore, the ancestral reaction centre proposed had a mixed character, with the three-domain organization and (possibly) symmetric electron transfer characteristic of contemporary Type I reaction centres but a capacity to reduce the intramembrane quinone pool, as seen in contemporary Type II reaction centres .
The future ... and the dim, distant past
The increasingly detailed crystallographic information now available for the cyanobacterial Type I and Type II reaction centres is provoking renewed interest in the detailed mechanism of these elegant transducers of energy. In particular, the first crystallographic glimpses of the machinery for oxygen evolution are both intriguing and exciting, and will trigger much re-evaluation of our current understanding of a reaction that is of obvious importance to aerobes such as ourselves. It is also becoming apparent that a detailed understanding of quinone chemistry of the homodimeric reaction centres from heliobacteria and green sulfur bacteria might help to focus ideas about the nature of the ancestral reaction centre and the evolutionary route that has led to contemporary complexes.
Finally, peering even further back in evolutionary time, an intriguing question that remains relatively unexplored concerns the origins of the ancestral reaction centre. What was the function of this (bacterio)chlorophyll-containing membrane protein before it evolved into a system capable of harnessing light energy? One suggestion is that early organisms used pigment–protein complexes to protect themselves against the ultraviolet (UV) radiation that bathed the surface of the planet before the development of the atmospheric ozone layer . Such proteins might originally have operated by absorbing high-energy UV photons and dissipating the energy through internal conversion between the (bacterio)chlorophyll Soret absorbance transition and the visible-region absorbance bands, before emitting the energy as a much more benign visible or near-infrared photon . Light-activated electron transfer might originally have developed as an extension to this photoprotective function, excited state energy being converted first into the energy of a charge separated state (similar to the P870+HA- state formed in the purple bacterial reaction centre) and subsequently lost as heat as the charge-separated state recombines (as occurs in purple bacterial reaction centres when forward electron transfer from HA- is blocked). Another suggestion is that photosynthetic function evolved from bacteriochlorophyll-containing proteins involved in infrared thermotaxis . Whatever the truth, addressing these questions requires a journey back to an early stage in the evolution of life, and presents a fascinating challenge.
 Baymann F. et al. (2001) Daddy, where did PS(I) come from?
Biochim. Biophys. Acta, 1507:291-310. MEDLINE Cited by
 Nisbet E.G. and Sleep N.H. (2001) The habitat and nature of early life.
Nature, 409:1083-1091. Cited by
 Olsen G.J. et al. (1994) The winds of (evolutionary) change: breathing new life into microbiology.
J. Bacteriol., 176:1-6. MEDLINE Cited by
 Gupta R.S. et al. (1999) Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis.
Mol. Microbiol., 32:893-906. MEDLINE Cited by
 Xiong J. et al. (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis.
Proc. Natl. Acad. Sci. U. S. A., 95:14851-14856. Full text MEDLINE Cited by
 Xiong J. et al. (2000) Molecular evidence for the early evolution of photosynthesis.
Science, 289:1724-1730. Full text MEDLINE Cited by
 Blankenship R.E. (2001) Molecular evidence for the evolution of photosynthesis.
Trends Plant Sci., 6:4-6. Full text Cited by
 Castresana J. et al. (1994) Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
EMBO J., 13:2516-2525. MEDLINE Cited by
 Mulkidjanian A.Y. and Junge W. (1997) On the origin of photosynthesis as inferred from sequence analysis.
Photosynth. Res., 51:27-42.
 Nisbet E.G. et al. (1995) Origins of photosynthesis.
Posted by: Dr.GH on May 29 2002,17:18
These are some of the articles I have in my abiogensis bibliography. I have mentioned to
Ian the notion of a collaboration. While I am waiting for his reply, I am working on an
annotated bibliography. Articles marke with an * are referenced in Wells’ Icons ...
*Castresana, Jose, Matti Saraste
1995 “Evolution of energetic metabolism: the respiration-early hypothesis” Trends in
Biochemical Science 20:443-448
Dismukes, G. C., V. V. Klimov, S. V. Baranov, Yu. N. Kozlov, J. DasGupta, A.
2001 “The Origin of Atmospheric Oxygen on Earth: The Innovation of Oxygenic
Photosynthesis” PNAS-USA vl 98 no. 5: 2170-2175
1993 “Algae and oxygen in Earth's ancient atmosphere” (Tech. Comment) and B.
Runnegar “Responce to Kasting.” Science 259: 835.
Kolber, Z. S., C. L. Van Dover, R. A. Niederman, P. G. Kalkowski
2000 Bacterial photosynthesis in surface waters of the open ocean” letters Nature
Olendzenski, Lorraine, Olga Zhaxybayeva, J. Peter Gogarten
2000 “How Much Did Horizontal Gene Transfer Contribute to Early Evolution?:
Quantifying Archaeal Genes in Two Bacterial Lineages ” (Abstract) General Meeting of
the NASA Astrobiology Institute.
*Schwartz, Robert M., Margret O. Dayhoff
1978 “Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts” Science Vol
Posted by: theyeti on Dec. 12 2002,17:23
< Annu Rev Plant Biol 2002;53:503-21 >
Complex evolution of photosynthesis.
Xiong J, Bauer CE.
The origin of photosynthesis is a fundamental biological question that has eluded researchers for decades. The complexity of the origin and evolution of photosynthesis is a result of multiple photosynthetic components having independent evolutionary pathways. Indeed, evolutionary scenarios have been established for only a few photosynthetic components. Phylogenetic analysis of Mg-tetrapyrrole biosynthesis genes indicates that most anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the purple bacterial lineage may contain the most ancestral form of this pigment biosynthesis pathway. The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits. However, evidence for a cytochrome b origin for the type II reaction center apoproteins is emerging. Based on the combined information for both photopigments and reaction centers, a unified theory for the evolution of reaction center holoproteins is provided. Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes from divergent photosynthetic bacteria.
Posted by: niiicholas on Dec. 12 2002,20:58
Interesting. Here's another one by the same folks:
< A cytochrome b origin of photosynthetic reaction centers: an evolutionary link between respiration and photosynthesis >
J Mol Biol 2002 Oct 4;322(5):1025-37
Xiong J, Bauer CE.
Department of Biology, Texas A&M University, College Station, TX 77843, USA.
The evolutionary origin of photosynthetic reaction centers has long remained elusive. Here, we use sequence and structural analysis to demonstrate an evolutionary link between the cytochrome b subunit of the cytochrome bc(1) complex and the core polypeptides of the photosynthetic bacterial reaction center. In particular, we have identified an area of significant sequence similarity between a three contiguous membrane-spanning domain of cytochrome b, which contains binding sites for two hemes, and a three contiguous membrane-spanning domain in the photosynthetic reaction center core subunits, which contains binding sites for cofactors such as (bacterio)chlorophylls, (bacterio)pheophytin and a non-heme iron. Three of the four heme ligands in cytochrome b are found to be conserved with the cofactor ligands in the reaction center polypeptides. Since cytochrome b and reaction center polypeptides both bind tetrapyrroles and quinones for electron transfer, the observed sequence, functional and structural similarities can best be explained with the assumption of a common evolutionary origin. Statistical analysis further supports a distant but significant homologous relationship. On the basis of previous evolutionary analyses that established a scenario that respiration evolved prior to photosynthesis, we consider it likely that cytochrome b is the evolutionary precursor for type II reaction center apoproteins. With a structural analysis confirming a common evolutionary origin of both type I and type II reaction centers, we further propose a novel "reaction center apoprotein early" hypothesis to account for the development of photosynthetic reaction center holoproteins.
Did I mention that I really like accumulating the refs and links on topics like this in topic-specific UBB threads? Quite a useful thing to have around IMO...
Posted by: niiicholas on April 06 2003,00:06
< ORIGIN OF PHOTOSYNTHESIS >
NISBET, E. G., Dept. of Geology, Royal Holloway, Univ. of London, Egham TW20 0EX United Kingdom, firstname.lastname@example.org.
Oxygenic photosynthesis, coupled tightly with nitrogen fixation, is the manager of the modern atmosphere. When and how did this begin? Carbon isotopes imply that rubisco has controlled the global distribution of carbon in the atmosphere-ocean system for at least 3.5Ga, selectively fractionating carbon into the biosphere from an abundant atmospheric reservoir. Modern biochemical reactions of carbon capture (including nitrogen fixation) already operated very productively by then. Anoxygenic photosynthesis may substantially predate oxygenic. The first life was most likely non-photosynthetic, existing on the redox contrast between the atmosphere-ocean and the mantle.
The biochemistry of key housekeeping enzymes may suggest evolutionary history. Many are metal proteins, especially with Fe-S clusters, including some key proteins in photosynthesis. Nitrogenase uses Fe-Mo, urease uses Ni. The oxygen-evolving complex is Mn-based. Such clues suggest photosynthesis began in and around hydrothermal systems, possibly originally as an accessory, facultative, process. .Support comes from the role of heat shock proteins, essential for assembly of rubisco. A possible speculation is that Haem may have come from an alkaline system, perhaps around ultramafic volcanism.
Perhaps infrared thermotaxis, in a hydrothermally supported organism, allowed the start of anoxygenic photosynthesis, followed by the development of oxygenic photosynthesis in a symbiotic chimaera in a microbial mat. With the evolution of cyanobacteria, capable not only of anoxygenic and oxygenic photosynthesis, but also nitrogen fixation, life could escape the hydrothermal ghetto and occupy the planet. Walker-world intervals (air more reduced than sediment) may have occurred, perhaps many times, but after 3.5Ga, Earth has probably in general had relatively oxidised air, though without abundant free molecular oxygen until the Proterozoic.
Posted by: theyeti on June 05 2003,10:47
Here's a recent article about Chl binding proteins.
< FEMS Microbiol Lett 2003 May 16;222(1):59-68 >
Origin and evolution of transmembrane Chl-binding proteins: hydrophobic cluster analysis suggests a common one-helix ancestor for prokaryotic (Pcb) and eukaryotic (LHC) antenna protein superfamilies.
Garczarek L, Poupon A, Partensky F.
All chlorophyll (Chl)-binding proteins constituting the photosynthetic apparatus of both prokaryotes and eukaryotes possess hydrophobic domains, corresponding to membrane-spanning alpha-helices (MSHs). Hydrophobic cluster analysis of representative members of the different Chl protein superfamilies revealed that all Chl proteins except the five-helix reaction center II proteins and the small subunits of photosystem I possess related domains. As a major conclusion, we found that the eukaryotic antennae likely share a common precursor with the prokaryotic Chl a/b antennae from Chl-b-containing oxyphotobacteria. From these data, we propose a global scheme for the evolution of these proteins from a one-MSH ancestor.
This is interesting because I remember an IDist (math professor at University of South Carolina, can't remember his name) mentioning these antennae as something whose evolution was "implausible".
Posted by: niiicholas on June 06 2003,01:20
Nuts. I had a larger post on RUBISCO inefficiency and whether it is necessary or due to historical constraints, but then lost it. But here is the t.o. post:
< http://groups.google.com/groups?....num%3D1 >
< A google search >
One example of the "constraints" view:
Nature 409, 1083 - 1091 (2001)
The habitat and nature of early life
E. G. NISBET* AND N. H. SLEEP
< Nature google archived >
Is Rubisco a 'qwerty' enzyme?
Where CO2 is in excess, as in the air, Rubisco87 preferentially selects 12C. For 3.5 Gyr, this isotopic signature in organic carbon, and the reciprocal signature in inorganic carbonate, has recorded Rubisco's role in oxygenic photosynthesis as the main link between atmospheric and biomass carbon32. But Rubisco itself may long predate oxygenic photosynthesis, as many non-photosynthetic microaerobic and aerobic bacteria use it. Unlike the many enzymes whose efficiency has been so honed by the aeons as to approach 100% (for example, catalase), Rubisco works either as carboxylase or oxygenase in photosynthesis and photorespiration88. This apparent 'inefficiency', capable of undoing the work of the photosynthetic process, is paradoxical, yet fundamental to the function of the carbon cycle in the biosphere. Without it, the amount of CO2 in the air would probably be much lower.
It is possible that Rubisco is not subject to evolutionary pressures because it has a monopoly. The qwerty keyboard, which is the main present link between humanity and the silicon chip, may be a parallel: legend is that qwerty was designed to slow typists' fingers so that the arms of early mechanical typewriters would not jam. It is among the worst, not the best, of layouts, and only minor evolution occurred (English has Y where German has Z). Perhaps the same applies to Rubisco: if so, genetic engineering to improve Rubisco might lead to a productivity runaway that removes all atmospheric CO2.
However, I think that the "life has pushed CO2 concentration down almost as low as enzymes can push it" might be a better explanation, despite the common mention of the historical constraints explanation in textbooks and webpages:
email@example.com (Laurence A. Moran) wrote in message news:<firstname.lastname@example.org>...
> You might be interested in something from one of my textbooks ...
> "Since extensive searches of Rubisco mutants have not uncovered
> a mutant enzyme that catalyzes only the carboxylation of ribulose-
> 1,5-bis phosphate, photorespiration may be physiologically
> essential or chemically unavoidable."
> In other words, your experiment has already been tried with mutants of
> rubisco. It doesn't seem possible to have the carboxylation reaction
> without the "reverse" oxygenation reaction (what you call "poisoning").
> I suspect that's because the chemical mechanism is a bit sloppy and can't
> distinguish between oxygen and carbon dioxide. (Carbon dioxide and oxygen
> compete for the same active site in the enzyme.)
> It may be possible to engineer a completely different protein that doesn't
> catalyze photorespiration but why bother? You may have noticed that plants
> are doing quite nicely without our help. :-)
Yeah, I wonder about this example. Two points indicate that getting a
"better" rubisco might not be possible:
1) O2 looks like this: O=O
CO2 looks like this: O=C=O
...they are quite similar, nonpolar, and very small, which might
indicate that discrimination is intrinsically difficult.
2) I think (IIRC) that the "confusion" depends much upon the relative
concentrations of the two molecules. Currently O2 is something like
21% of the atm, but CO2 is down at 300-something ppm (but rising fast,
thanks to cars and stuff). So concentration-wise O2 is much much more
common. If you have something like 5% CO2 (something which I've heard
was at least possible back in dino times), competition is much less of
an issue (IIRC).
It is likely that rubisco originated under high-CO2, low-O2
conditions; but it may be that it has adapted as far as possible to
current conditions and it's simply as good as a protein can get in
On the other hand, if someone designs a better rubisco then I'm wrong
and then it is a great anti-ID example.
(Although a better rubisco might suck enough CO2 out of the air to
sink us even further into ice ages than we already are (geologically
speaking). Does Canada really deserve to be buried under a vertical
mile of ice just because they beat us at hockey on Sunday?)
Posted by: niiicholas on Dec. 28 2003,05:28
< PvM found > some good refs:
< Talk.origins references >
< COMPLEX EVOLUTION OF PHOTOSYNTHESIS > in Annual Review of Plant Biology Jun 2002, Vol. 53, pp. 503-521 by Xiong and Bauer
Abstract The origin of photosynthesis is a fundamental biological question that has eluded researchers for decades. The complexity of the origin and evolution of photosynthesis is a result of multiple photosynthetic components having independent evolutionary pathways. Indeed, evolutionary scenarios have been established for only a few photosynthetic components. Phylogenetic analysis of Mg-tetrapyrrole biosynthesis genes indicates that most anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the purple bacterial lineage may contain the most ancestral form of this pigment biosynthesis pathway. The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits. However, evidence for a cytochrome b origin for the type II reaction center apoproteins is emerging. Based on the combined information for both photopigments and reaction centers, a unified theory for the evolution of reaction center holoproteins is provided. Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes from divergent photosynthetic bacteria.
< Clues to the evolution of photosynthesis Sequenced genome of Chlorobium tepidum >
< Bauer Lab >
Posted by: theyeti on May 04 2004,13:49
< FEBS Lett. 2004 Apr 30;564(3):274-80. >
Evolution of photosystem I - from symmetry through pseudosymmetry to asymmetry.
Ben-Shem A, Frolow F, Nelson N.
The evolution of photosystem (PS) I was probably initiated by the formation of a homodimeric reaction center similar to the one currently present in green bacteria. Gene duplication has generated a heterodimeric reaction center that subsequently evolved to the PSI present in cyanobacteria, algae and plant chloroplasts. During the evolution of PSI several attempts to maximize the efficiency of light harvesting took place in the various organisms. In the Chlorobiaceae, chlorosomes and FMO were added to the homodimeric reaction center. In cyanobacteria phycobilisomes and CP43' evolved to cope with the light limitations and stress conditions. The plant PSI utilizes a modular arrangement of membrane light-harvesting proteins (LHCI). We obtained structural information from the two ends of the evolutionary spectrum. Novel features in the structure of Chlorobium tepidum FMO are reported in this communication. Our structure of plant PSI reveals that the addition of subunit G provided the template for LHCI binding, and the addition of subunit H prevented the possibility of trimer formation and provided a binding site for LHCII and the onset of energy spillover from PSII to PSI.