Daddy, where did (PS)I come from?

Anoxygenic photosynthesis with emphasis on green sulfur bacteria and a perspective for hydrogen sulfide detoxification of anoxic environments

The bacterial light-dependent energy metabolism can be divided into two types: oxygenic and anoxygenic photosynthesis. Bacterial oxygenic photosynthesis is similar to plants and is characteristic for cyanobacteria. Bacterial anoxygenic photosynthesis is performed by anoxygenic phototrophs, especially green sulfur bacteria (GSB; family Chlorobiaceae) and purple sulfur bacteria (PSB; family Chromatiaceae). In anoxygenic photosynthesis, hydrogen sulfide (H2S) is used as the main electron donor, which differs from plants or cyanobacteria where water is the main source of electrons. This review mainly focuses on the microbiology of GSB, which may be found in water or soil ecosystems where H2S is abundant. GSB oxidize H2S to elemental sulfur. GSB possess special structures-chlorosomes-wherein photosynthetic pigments are located. Chlorosomes are vesicles that are surrounded by a lipid monolayer that serve as light-collecting antennas. The carbon source of GSB is carbon dioxide, which is assimilated through the reverse tricarboxylic acid cycle. Our review provides a thorough introduction to the comparative eco-physiology of GSB and discusses selected application possibilities of anoxygenic phototrophs in the fields of environmental management, bioremediation, and biotechnology.

Illuminating the coevolution of photosynthesis and Bacteria

Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.

Comparison of tryptophan fluorescence lifetimes in cyanobacterial photosystem I frozen in the light and in the dark

The dependence on temperature of tryptophan fluorescence lifetime in trimeric photosystem I (PSI) complexes from cyanobacteria Synechocystis sp. PCC 6803 during the heating of pre-frozen to - 180 °C in the dark or in the light-activated preparations has been studied. Fluorescence lifetime in samples frozen in the light was longer than in samples frozen in the dark. For samples in 65% glycerol at λ_reg = 335 nm and at 20 °C, the lifetime of components were as follows: τ₁ ≈ 1.2 ns, τ₂ ≈ 4.9 ns, and τ₃ ≈ 20 ns. The contribution of the first component was negligible. To analyze the contribution of components 2 and 3 derived from frozen-thawed samples, two temperature ranges from - 180 to - 90 °C and above - 90 °C are considered. In doing so, the contributions of these components appear antiphase course to each other. The dependence on temperature of these contributions is explained by the influence of the microconformational protein dynamics on the tryptophan fluorescence lifetime. In the present work, a comparative analysis of temperature-dependent conformational dynamics and electron transfer in cyanobacterial PSI (Schlodder et al., in Biochemistry 37:9466-9476, 1998) and Rhodobacter sphaeroides reaction center complexes (Knox et al., in J Photochem Photobiol B 180:140-148, 2018) was also carried out.

Early Archean origin of heterodimeric Photosystem I

When and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

A physiological perspective on the origin and evolution of photosynthesis

The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.

Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins

The evolution and diversification of different types of photosynthetic reaction centers (RCs) remains an important unresolved problem. We report here novel sequence features of the core proteins from Type I RCs (RC-I) and Type II RCs (RC-II) whose analyses provide important insights into the evolution of the RCs. The sequence alignments of the RC-I core proteins contain two conserved inserts or deletions (indels), a 3 amino acid (aa) indel that is uniquely found in all RC-I homologs from Cyanobacteria (both PsaA and PsaB) and a 1 aa indel that is specifically shared by the Chlorobi and Acidobacteria homologs. Ancestral sequence reconstruction provides evidence that the RC-I core protein from Heliobacteriaceae (PshA), lacking these indels, is most closely related to the ancestral RC-I protein. Thus, the identified 3 aa and 1 aa indels in the RC-I protein sequences must have been deletions, which occurred, respectively, in an ancestor of the modern Cyanobacteria containing a homodimeric form of RC-I and in a common ancestor of the RC-I core protein from Chlorobi and Acidobacteria. We also report a conserved 1 aa indel in the RC-II protein sequences that is commonly shared by all homologs from Cyanobacteria but not found in the homologs from Chloroflexi, Proteobacteria and Gemmatimonadetes. Ancestral sequence reconstruction provides evidence that the RC-II subunits lacking this indel are more similar to the ancestral RC-II protein. The results of flexible structural alignments of the indel-containing region of the RC-II protein with the homologous region in the RC-I core protein, which shares structural similarity with the RC-II homologs, support the view that the 1 aa indel present in the RC-II homologs from Cyanobacteria is a deletion, which was not present in the ancestral form of the RC-II protein. Our analyses of the conserved indels found in the RC-I and RC-II proteins, thus, support the view that the earliest photosynthetic lineages with living descendants likely contained only a single RC (RC-I or RC-II), and the presence of both RC-I and RC-II in a linked state, as found in the modern Cyanobacteria, is a derivation from these earlier phototrophs.

Probing the Electronic Structure of Bacteriochlorophyll Radical Ions-A Theoretical Study of the Effect of Substituents on Hyperfine Parameters

In reaction centers (RCs) of photosynthesis, a light-induced charge separation takes place creating radical cations and anions of the participating cofactors. In photosynthetic bacteria, different bacteriochlorophylls (BChl) are involved in this process. Information about the electronic structure of the BChl radical cations and anions can be obtained by measuring the electron spin density distribution via the electron-nuclear hyperfine interaction using EPR and ENDOR techniques. In this communication, we report isotropic hyperfine coupling constants (hfcs) of the BChl b and g radical cations and anions, calculated by density functional theory, and compare them with the more common radical ions of BChl a and with available experimental data. The observed differences in the computed hyperfine data are discussed in view of a possible distinction between these species by EPR/ENDOR methods. In addition, ¹⁴ N nuclear quadrupole coupling constants (nqcs) computed for BChl a, b, g, and also for Chl a in their charge neutral, radical cation and radical anion states are presented. These nqcs are compared with experimental values obtained by ESEEM spectroscopy on several different radical ions.

Controlling electron transfer between the two cofactor chains of photosystem I by the redox state of one of their components

Two functional electron transfer (ET) chains, related by a pseudo-C2 symmetry, are present in the reaction center of photosystem I (PSI). Due to slight differences in the environment around the cofactors of the two branches, there are differences in both the kinetics of ET and the proportion of ET that occurs on the two branches. The strongest evidence that this is indeed the case relied on the observation that the oxidation rates of the reduced phylloquinone (PhQ) cofactor differ by an order of magnitude. Site-directed mutagenesis of residues involved in the respective PhQ-binding sites resulted in a specific alteration of the rates of semiquinone oxidation. Here, we show that the PsaA-F689N mutation results in an ∼100-fold decrease in the observed rate of PhQA(-) oxidation. This is the largest change of PhQA(-) oxidation kinetics observed so far for a single-point mutation, resulting in a lifetime that exceeds that of the terminal electron donor, P700(+). This situation allows a second photochemical charge separation event to be initiated before PhQA(-) has decayed, thereby mimicking in PSI a situation that occurs in type II reaction centers. The results indicate that the presence of PhQA(-) does not impact the overall quantum yield and leads to an almost complete redistribution of the fractional utilization of the two functional ET chains, in favor of the one that does not bear the charged species. The evolutionary implications of these results are also briefly discussed.

Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution?

Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna proteins originated from the remodeling of an entire Type I reaction center protein and not from the partial gene duplication of a Type I reaction center gene. Third, I highlight how Photosystem II and Photosystem I reaction center proteins interact with small peripheral subunits in remarkably similar patterns and hypothesize that some of this complexity may be traced back to the most ancestral reaction center. Fourth, I outline the sequence of events that led to the origin of the Mn4CaO5 cluster and show that the most ancestral Type II reaction center had some of the basic structural components that would become essential in the coordination of the water-oxidizing complex. Finally, I collect all these ideas, starting at the origin of the first reaction center proteins and ending with the emergence of the water-oxidizing cluster, to hypothesize that the complex and well-organized process of assembly and photoactivation of Photosystem II recapitulate evolutionary transitions in the path to oxygenic photosynthesis.

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India

The draft genome assembly of Hassallia byssoidea strain VB512170 with a genome size of ~13 Mb and 10,183 protein-coding genes in 62 scaffolds is reported here for the first time. This is a terrestrial hydrophobic cyanobacterium isolated from monuments in India. We report several copies of luciferase and antibiotic genes in this organism.

Evolutionary origins of the photosynthetic water oxidation cluster: bicarbonate permits Mn(2+) photo-oxidation by anoxygenic bacterial reaction centers

The enzyme that catalyzes water oxidation in oxygenic photosynthesis contains an inorganic cluster (Mn4 CaO5 ) that is universally conserved in all photosystem II (PSII) protein complexes. Its hypothesized precursor is an anoxygenic photobacterium containing a type 2 reaction center as photo-oxidant (bRC2, iron-quinone type). Here we provide the first experimental evidence that a native bRC2 complex can catalyze the photo-oxidation of Mn(2+) to Mn(3+) , but only in the presence of bicarbonate concentrations that allows the formation of (bRC2)Mn(2+) (bicarbonate)1-2 complexes. Parallel-mode EPR spectroscopy was used to characterize the photoproduct, (bRC2)Mn(3+) (CO3 (2-) ), based on the g tensor and (55) Mn hyperfine splitting. (Bi)carbonate coordination extends the lifetime of the Mn(3+) photoproduct by slowing charge recombination. Prior electrochemical measurements show that carbonate complexation thermodynamically stabilizes the Mn(3+) product by 0.9-1 V relative to water ligands. A model for the origin of the water oxidation catalyst is presented that proposes chemically feasible steps in the evolution of oxygenic PSIIs, and is supported by literature results on the photoassembly of contemporary PSIIs.

Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis

An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe.

Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803

Oxygenic photosynthesis supports virtually all life forms on earth. Light energy is converted by two photosystems—photosystem I (PSI) and photosystem II (PSII). Globally, nearly 50% of photosynthesis takes place in the Ocean, where single cell cyanobacteria and algae reside together with their viruses. An operon encoding PSI was identified in cyanobacterial marine viruses. We generated a PSI that mimics the salient features of the viral complex, named PSI^PsaJF. PSI^PsaJF is promiscuous for its electron donors and can accept electrons from respiratory cytochromes. We solved the structure of PSI^PsaJF and a monomeric PSI, with subunit composition similar to the viral PSI, providing for the first time a detailed description of the reaction center and antenna system from mesophilic cyanobacteria, including red chlorophylls and cofactors of the electron transport chain. Our finding extends the understanding of PSI structure, function and evolution and suggests a unique function for the viral PSI.

DOI:http://dx.doi.org/10.7554/eLife.01496.001

Photosynthesis—the process by which plants and other organisms harness the energy in sunlight—is the source of almost all oxygen, food and fuel on earth. Oxygenic photosynthesis in living cells involves a series of reactions catalyzed by large protein complexes, various other soluble chemicals, and the transfer of electrons from so-called donors to acceptors. The energy in the sunlight is captured by two membrane-embedded protein complexes—photosystem I, which is the most powerful electron donor in nature, and photosystem II—and converted into chemical energy.

Almost half of the world’s photosynthesis occurs in the oceans, and is performed by single-celled cyanobacteria and algae. Interestingly, some of the genes that encode photosynthetic enzymes in cyanobacteria are also found in the genomes of viruses that infect these bacteria. It is thought that these viruses can alter photosynthetic pathways in their hosts, but the interactions between these viruses and their hosts are not fully understood.

Now, Mazor et al. have created a photosystem I complex that mimics the viral version of this complex, and have gone on to solve its three-dimensional structure. This mimetic virus-encoded complex was shown to be a ‘promiscuous’ electron acceptor: this means that, unlike most electron acceptors, it can accept electrons from more than one electron donor.

Further, Mazor et al. solved the structure of photosystem I from Synechocystis, a cyanobacterium that lives in fresh water; and found some surprising differences between it and the only other published structure for photosystem I from a cyanobacterium (which was from a species that lives in hot water springs). These included differences in components involved in the electron transfer chain—a series of chemical reactions in which electrons are passed from donor to acceptor molecules—that were thought to be highly conserved. Other differences in the structures allowed Mazor et al. to identify the location of a unique chlorophyll pigment group in the Synechocystis photosystem I.

Since Synechocystis is commonly used as a model to study photosynthesis, an improved understanding of its photosystem I should lead to further improvements in our knowledge of photosynthesis.

DOI:http://dx.doi.org/10.7554/eLife.01496.002

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids

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.

Insight into the evolution of the iron oxidation pathways

Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O(2). This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Arsenics as bioenergetic substrates

Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: redox tuning to survive life in O(2)

The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O(2) environment. When O(2) appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O(2) and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc(1) and b(6)f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of-efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments.

Identification of an oxygenic reaction center psbADC operon in the cyanobacterium Gloeobacter violaceus PCC 7421

Gloeobacter violaceus, the earliest diverging oxyphotobacterium (cyanobacterium) on the 16S ribosomal RNA tree, has five copies of the photosystem II psbA gene encoding the D1 reaction center protein subunit. These copies are widely distributed throughout the 4.6 Mbp genome with only one copy colocalizing with other PSII subunits, in marked contrast to all other psbA genes in all publicly available sequenced genomes. A clustering of two other psb genes around psbA3 (glr2322) is unique to Gloeobacter. We provide experimental proof for the transcription of a psbA3DC operon, encoding three of the five reaction center core subunits (D1, D2, and CP43). This is the first example of a transcribed gene cluster containing the D1/D2 or D1/D2/CP43 subunits of PSII in an oxygenic phototroph (prokaryotic or eukaryotic). Implications for the evolution of oxygenic photosynthesis are discussed.

Fourier transform infrared spectroscopy of special pair bacteriochlorophylls in homodimeric reaction centers of heliobacteria and green sulfur bacteria

Heliobacteria and green sulfur bacteria have type I homodimeric reaction centers analogous to photosystem I. One remaining question regarding these homodimeric reaction centers is whether the structures and electron transfer reactions are truly symmetric or not. This question is relevant to the origin of the heterodimeric reaction centers, such as photosystem I and type II reaction centers. In this mini-review, Fourier transform infrared studies on the special pair bacteriochlorophylls, P798 in heliobacteria and P840 in green sulfur bacteria, are summarized. The data are reinterpreted in the light of the X-ray crystallographic structure of photosystem I and the sequence alignments of type I reaction center proteins, and discussed in terms of hydrogen bonding interactions and the symmetry of charge distribution over the dimer.

Heliobacterial Rieske/cytb complex

Data on structure and function of the Rieske/cytb complex from Heliobacteria are scarce. They indicate that the complex is related to the b (6) f complex in agreement with the phylogenetic position of the organism. It is composed of a diheme cytochrome c, and a Rieske iron-sulfur protein, together with transmembrane cytochrome b (6) and subunit IV. Additional small subunits may be part of the complex. The cofactor content comprises heme c (i), first discovered in the Q(i) binding pocket of b (6) f complexes. The redox midpoint potentials are more negative than in b (6) f complex in agreement with the lower redox midpoint potentials (by about 150 mV) of its reaction partners, menaquinone, and cytochrome c (553). The enzyme is implicated in cyclic electron transfer around the RCI. Functional studies are favored by the absence of antennae and the simple photosynthetic reaction chain but are hampered by the high oxygen sensitivity of the organism, its chlorophyll, and lipids.

The "green" phylogenetic clade of Rieske/cytb complexes

More than a decade ago, Heliobacteria were recognised to contain a Rieske/cytb complex in which the cytochrome b subunit is split into two separate proteins, a peculiar feature characteristic of the cyanobacterial and plastidic b (6) f complex. The common presence of RCI-type reaction centres further emphasise possible evolutionary links between Heliobacteria, Chlorobiaceae and Cyanobacteria. In this contribution, we further explore the evolutionary relationships among these three phototrophic lineages by both molecular phylogeny and consideration of phylogenetic marker traits of the superfamily of Rieske/cytb complexes. The combination of these two methods suggests the existence of a "green" clade involving many non-phototrophs in addition to the mentioned RCI-type photosynthetic organisms. Structural and functional idiosyncrasies are (re-)interpreted in the framework of evolutionary biology and more specifically evolutionary bioenergetics.

Was nitric oxide the first deep electron sink?

Evolutionary histories of enzymes involved in chemiosmotic energy conversion indicate that a strongly oxidizing substrate was available to the last universal common ancestor before the divergence of Bacteria and Archaea. According to palaeogeochemical evidence, O(2) was not present beyond trace amounts on the early Earth. Based on recent phylogenetic, enzymatic and geochemical results, we propose that, in the earliest Archaean, nitric oxide (NO) and its derivatives nitrate and nitrite served as strongly oxidizing substrates driving the evolution of a bioenergetic pathway related to modern dissimilatory denitrification. Aerobic respiration emerged later from within this ancestral pathway via adaptation of the enzyme NO reductase to its new substrate, dioxygen.

Evolutionary ecology during the rise of dioxygen in the Earth's atmosphere

Pre-photosynthetic niches were meagre with a productivity of much less than 10(-4) of modern photosynthesis. Serpentinization, arc volcanism and ridge-axis volcanism reliably provided H(2). Methanogens and acetogens reacted CO(2) with H(2) to obtain energy and make organic matter. These skills pre-adapted a bacterium for anoxygenic photosynthesis, probably starting with H(2) in lieu of an oxygen 'acceptor'. Use of ferrous iron and sulphide followed as abundant oxygen acceptors, allowing productivity to approach modern levels. The 'photobacterium' proliferated rooting much of the bacterial tree. Land photosynthetic microbes faced a dearth of oxygen acceptors and nutrients. A consortium of photosynthetic and soil bacteria aided weathering and access to ferrous iron. Biologically enhanced weathering led to the formation of shales and, ultimately, to granitic rocks. Already oxidized iron-poor sedimentary rocks and low-iron granites provided scant oxygen acceptors, as did freshwater in their drainages. Cyanobacteria evolved dioxygen production that relieved them of these vicissitudes. They did not immediately dominate the planet. Eventually, anoxygenic and oxygenic photosynthesis oxidized much of the Earth's crust and supplied sulphate to the ocean. Anoxygenic photosynthesis remained important until there was enough O(2) in downwelling seawater to quantitatively oxidize massive sulphides at mid-ocean ridge axes.

Genome evolution in cyanobacteria: the stable core and the variable shell

Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis, the evolution of which transformed the biology and geochemistry of Earth. The rapid increase in published genomic sequences of cyanobacteria provides the first opportunity to reconstruct events in the evolution of oxygenic photosynthesis on the scale of entire genomes. Here, we demonstrate the overall phylogenetic incongruence among 682 orthologous protein families from 13 genomes of cyanobacteria. However, using principal coordinates analysis, we discovered a core set of 323 genes with similar evolutionary trajectories. The core set is highly conserved in amino acid sequence and contains genes encoding the major components in the photosynthetic and ribosomal apparatus. Many of the key proteins are encoded by genome-wide conserved small gene clusters, which often are indicative of protein-protein, protein-prosthetic group, and protein-lipid interactions. We propose that the macromolecular interactions in complex protein structures and metabolic pathways retard the tempo of evolution of the core genes and hence exert a selection pressure that restricts piecemeal horizontal gene transfer of components of the core. Identification of the core establishes a foundation for reconstructing robust organismal phylogeny in genome space. Our phylogenetic trees constructed from 16S rRNA gene sequences, concatenated orthologous proteins, and the core gene set all suggest that the ancestral cyanobacterium did not fix nitrogen and probably was a thermophilic organism.

Cyanobacterial emergence at 2.8 gya and greenhouse feedbacks

Apparent cyanobacterial emergence at about 2.8 Gya coincides with the negative excursion in the organic carbon isotope record, which is the first strong evidence for the presence of atmospheric methane. The existence of weathering feedbacks in the carbonate-silicate cycle suggests that atmospheric and oceanic CO2 concentrations would have been high prior to the presence of a methane greenhouse (and thus the ocean would have had high bicarbonate concentrations). With the onset of a methane greenhouse, carbon dioxide concentrations would decrease. Bicarbonate has been proposed as the preferred reductant that preceded water for oxygenic photosynthesis in a bacterial photosynthetic precursor to cyanobacteria; with the drop of carbon dioxide level, Archean cyanobacteria emerged using water as a reductant instead of bicarbonate (Dismukes et al., 2001). Our thermodynamic calculations, with regard to this scenario, give at least a tenfold drop in aqueous CO2 levels with the onset of a methane-dominated greenhouse, assuming surface temperatures of about 60 degrees C and a drop in the level of atmospheric carbon dioxide from about 1 to 0.1 bars. The buildup of atmospheric methane could have been triggered by the boost in oceanic organic productivity that arose from the emergence of pre-cyanobacterial oxygenic phototrophy at about 2.8-3.0 Gya; high temperatures may have precluded an earlier emergence. A greenhouse transition timescale on the order of 50-100 million years is consistent with results from modeling the carbonate-silicate cycle. This is an alternative hypothesis to proposals of a tectonic driver for this apparent greenhouse transition.

Two approaches to the study of the origin of life

This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with--often organic--compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, "life" would not have begun, nor have been maintained; this boundary--and the complex cell membrane that evolved from it--forms the essence of life.

The alkaline solution to the emergence of life: energy, entropy and early evolution

The Earth agglomerates and heats. Convection cells within the planetary interior expedite the cooling process. Volcanoes evolve steam, carbon dioxide, sulfur dioxide and pyrophosphate. An acidulous Hadean ocean condenses from the carbon dioxide atmosphere. Dusts and stratospheric sulfurous smogs absorb a proportion of the Sun's rays. The cooled ocean leaks into the stressed crust and also convects. High temperature acid springs, coupled to magmatic plumes and spreading centers, emit iron, manganese, zinc, cobalt and nickel ions to the ocean. Away from the spreading centers cooler alkaline spring waters emanate from the ocean floor. These bear hydrogen, formate, ammonia, hydrosulfide and minor methane thiol. The thermal potential begins to be dissipated but the chemical potential is dammed. The exhaling alkaline solutions are frustrated in their further attempt to mix thoroughly with their oceanic source by the spontaneous precipitation of biomorphic barriers of colloidal iron compounds and other minerals. It is here we surmise that organic molecules are synthesized, filtered, concentrated and adsorbed, while acetate and methane--separate products of the precursor to the reductive acetyl-coenzyme-A pathway-are exhaled as waste. Reactions in mineral compartments produce acetate, amino acids, and the components of nucleosides. Short peptides, condensed from the simple amino acids, sequester 'ready-made' iron sulfide clusters to form protoferredoxins, and also bind phosphates. Nucleotides are assembled from amino acids, simple phosphates carbon dioxide and ribose phosphate upon nanocrystalline mineral surfaces. The side chains of particular amino acids register to fitting nucleotide triplet clefts. Keyed in, the amino acids are polymerized, through acid-base catalysis, to alpha chains. Peptides, the tenuous outer-most filaments of the nanocrysts, continually peel away from bound RNA. The polymers are concentrated at cooler regions of the mineral compartments through thermophoresis. RNA is reproduced through a convective polymerase chain reaction operating between 40 and 100 degrees C. The coded peptides produce true ferredoxins, the ubiquitous proteins with the longest evolutionary pedigree. They take over the role of catalyst and electron transfer agent from the iron sulfides. Other iron-nickel sulfide clusters, sequestered now by cysteine residues as CO-dehydrogenase and acetyl-coenzyme-A synthase, promote further chemosynthesis and support the hatchery--the electrochemical reactor--from which they sprang. Reactions and interactions fall into step as further pathways are negotiated. This hydrothermal circuitry offers a continuous supply of material and chemical energy, as well as electricity and proticity at a potential appropriate for the onset of life in the dark, a rapidly emerging kinetic structure born to persist, evolve and generate entropy while the sun shines.

Type 1 reaction center of photosynthetic heliobacteria

The reaction center (RC) of heliobacteria contains iron-sulfur centers as terminal electron acceptors, analogous to those of green sulfur bacteria as well as photosystem I in cyanobacteria and higher plants. Therefore, they all belong to the so-called type 1 RCs, in contrast to the type 2 RCs of purple bacteria and photosystem II containing quinone molecules. Although the architecture of the heliobacterial RC as a protein complex is still unknown, it forms a homodimer made up of two identical PshA core proteins, where two symmetrical electron transfer pathways along the C2 axis are assumed to be equally functional. Electrons are considered to be transferred from membrane-bound cytochrome c (PetJ) to a special pair P800, a chlorophyll a-like molecule A0, (a quinone molecule A1) and a [4Fe-4S] center Fx and, finally, to 2[4Fe-4S] centers FA/FB. No definite evidence has been obtained for the presence of functional quinone acceptor A1. An additional interesting point is that the electron transfer reaction from cytochrome c to P800 proceeds in a collisional mode. It is highly dependent on the temperature, ion strength and/or viscosity in a reaction medium, suggesting that a heme-binding moiety fluctuates in an aqueous phase with its amino-terminus anchored to membranes.

Evolution of the Inner Light-Harvesting Antenna Protein Family of Cyanobacteria, Algae, and Plants

Two hypotheses account for the evolution of the inner antenna light-harvesting proteins of oxygenic photosynthesis in cyanobacteria, algae, and plants: one in which the CP43 protein of photosytem II gave rise to the extrinsic CP43-like antennas of cyanobacteria (i.e. IsiA and Pcb proteins), as a late development, and the other in which CP43 and CP43-like proteins derive from an ancestral protein. In order to determine which of these hypotheses is most likely, we analyzed the family of antenna proteins by a variety of phylogenetic techniques, using alignments of the six common membrane-spanning helices, constructed using information on the antenna proteins' three-dimensional structure, and surveyed for evidence of factors that might confound inference of a correct phylogeny. The first hypothesis was strongly supported. As a consequence, we conclude that the ancestral photosynthetic apparatus, with 11 membrane-spanning helices, split at an early stage during evolution to form, on the one hand, the reaction center of photosystem II and, on the other hand, the ancestor of inner antenna proteins, CP43 (PsbC) and CP47 (PsbB). Only much later in evolution did the CP43 lineage give rise to the CP43' proteins (IsiA and Pcb) of cyanobacteria.

The cyanobacterial genome core and the origin of photosynthesis

Comparative analysis of 15 complete cyanobacterial genome sequences, including "near minimal" genomes of five strains of Prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans. The latter group includes 35 families of uncharacterized proteins, which could also be involved in photosynthesis. Only a few components of cyanobacterial photosynthetic machinery are represented in the genomes of the anoxygenic phototrophic bacteria Chlorobium tepidum, Rhodopseudomonas palustris, Chloroflexus aurantiacus, or Heliobacillus mobilis. These observations, coupled with recent geological data on the properties of the ancient phototrophs, suggest that photosynthesis originated in the cyanobacterial lineage under the selective pressures of UV light and depletion of electron donors. We propose that the first phototrophs were anaerobic ancestors of cyanobacteria ("procyanobacteria") that conducted anoxygenic photosynthesis using a photosystem I-like reaction center, somewhat similar to the heterocysts of modern filamentous cyanobacteria. From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer.

Data mining for proteins characteristic of clades

A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and gamma-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools.

Conservation of distantly related membrane proteins: photosynthetic reaction centers share a common structural core

Photosynthesis was established on Earth more than 3 billion years ago. All available evidences suggest that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development. The reaction center complexes that form the heart of the energy storage process are integral membrane pigment proteins that span the membrane in vectorial fashion to carry out electron transfer. The origin and extent of distribution of these proteins has been perplexing from a phylogenetic point of view mostly because of extreme sequence divergence. A series of integral membrane proteins of known structure and varying degrees of sequence identity have been compared using combinatorial extension-Monte Carlo methods. The proteins include photosynthetic reaction centers from proteobacteria and cyanobacterial photosystems I and II, as well as cytochrome oxidase, bacteriorhodopsin, and cytochrome b. The reaction center complexes show a remarkable conservation of the core structure of 5 transmembrane helices, strongly implying common ancestry, even though the residual sequence identity is less than 10%, whereas the other proteins have structures that are unrelated. A relationship of sequence with structure was derived from the reaction center structures; with characteristic decay length of 1.6 A. Phylogenetic trees derived from the structural alignments give insights into the earliest photosynthetic reaction center, strongly suggesting that it was a homodimeric complex that did not evolve oxygen.

The Rieske Protein: A Case Study on the Pitfalls of Multiple Sequence Alignments and Phylogenetic Reconstruction

Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.

The structure of photosystem I and evolution of photosynthesis

Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on earth. The primary step in this process--the conversion of sunlight into chemical energy--is driven by four multi-subunit membrane protein complexes named photosystem I, photosystem II, cytochrome b(6)f complex and F-ATPase. Photosystem I generates the most negative redox potential in nature and thus largely determines the global amount of enthalpy in living systems. The recent structural determination of PSI complexes from cyanobacteria and plants sheds light on the evolutionary forces that shaped oxygenic photosynthesis. The fortuitous formation of our solar system in a space plentiful of elements, our distance from the sun and the long time of uninterrupted evolution enabled the perfection of photosynthesis and the evolution of advanced organisms. The available structural information complements the knowledge gained from genomic and proteomic data to illustrate a more precise scenario for the evolution of life systems on earth.

Effect of low temperatures on photochemical activity of PS1 reaction centers from Synechocystis sp. frozen under illumination

After cooling of Synechocystis sp. photosystem 1 (PS1) reaction centers (RC) to 160 K under illumination most of the photoactive pigment is fixed for a long time in the oxidized state. The same effect is observed in purple bacteria RC. The dark reduction kinetics of PS1 P700 chlorophyll, which still retains its photochemical activity, in these samples was similar to that in samples cooled in the dark. We suggest that the photoinduced charge separation in PS1 RC, as well as in purple bacteria RC, is accompanied by conformational changes that can be fixed in samples cooled under illumination. As a result, the electrons photomobilized in RC cooled under illumination are unable to return backward the process of electron transfer to P700(+) after cessation of actinic illumination. Such irreversible trapping of electrons can take place in different parts of the PS1 RC electron acceptor chain.

Automatic selection of representative proteins for bacterial phylogeny

Background

Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence.

Results

We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria"), and another containing Planctomycetes and Chlamydiales.

Conclusion

Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.

Phylogenetic analyses of the core antenna domain: investigating the origin of photosystem I

Phototrophy, the conversion of light to biochemical energy, occurs throughout the Bacteria and plants, however, debate continues over how different phototrophic mechanisms and the bacteria that contain them are related. There are two types of phototrophic mechanisms in the Bacteria: reaction center type 1 (RC1) has core and core antenna domains that are parts of a single polypeptide, whereas reaction center type 2 (RC2) is composed of short core proteins without antenna domains. In cyanobacteria, RC2 is associated with separate core antenna proteins that are homologous to the core antenna domains of RC1. We reconstructed evolutionary relationships among phototrophic mechanisms based on a phylogeny of core antenna domains/proteins. Core antenna domains of 46 polypeptides were aligned, including the RC1 core proteins of heliobacteria, green sulfur bacteria, and photosystem I (PSI) of cyanobacteria and plastids, plus core antenna proteins of photosystem II (PSII) from cyanobacteria and plastids. Maximum likelihood, parsimony, and neighbor joining methods all supported a single phylogeny in which PSII core antenna proteins (PsbC, PsbB) arose within the cyanobacteria from duplications of the RC1-associated core antenna domains and accessory antenna proteins (IsiA, PcbA, PcbC) arose from duplications of PsbB. The data indicate an evolutionary history of RC1 in which an initially homodimeric reaction center was vertically transmitted to green sulfur bacteria, heliobacteria, and an ancestor of cyanobacteria. A heterodimeric RC1 (=PSI) then arose within the cyanobacterial lineage. In this scenario, the current diversity of core antenna domains/proteins is explained without a need to invoke horizontal transfer.

A redox switch hypothesis for the origin of two light reactions in photosynthesis

Photosynthesis provides energy in the Earth's biosphere and oxygen in its atmosphere. For oxygen to be produced, two different light reactions must operate simultaneously and in series. Known anaerobic, photosynthetic bacteria contain one or other of these photosystems, but never both. Here, I propose that the two photosystems diverged, in structure and function, from a common ancestor, within a single, continuous, anaerobic lineage. In such cells, living examples of which are predicted, the two photosystems are isoenzymes encoded by orthologous genes under co-ordinated, redox regulatory control. A redox switch responds to defined environmental conditions and selects which set of genes is expressed. In these cells, the two photosystems are thus synthesised at different times. It is further proposed that the origin of oxygen-evolving photosynthesis was a simple mutation that disabled the redox switch, permitting simultaneous expression of the two sets of genes. The two, newly co-existing photosystems became connected by shared electron carriers, allowing generation of electrochemical potential high enough to oxidise water; an inexhaustible supply of reductant; and the selective advantages and pressures of an aerobic world.

The complex architecture of oxygenic photosynthesis

Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on earth. The primary step in this process - the conversion of sunlight into chemical energy - is driven by four, multisubunit, membrane-protein complexes that are known as photosystem I, photosystem II, cytochrome b(6)f and F-ATPase. Structural insights into these complexes are now providing a framework for the exploration not only of energy and electron transfer, but also of the evolutionary forces that shaped the photosynthetic apparatus.

Biogenesis of PSI involves a cascade of translational autoregulation in the chloroplast of Chlamydomonas

Photosystem I comprises 13 subunits in Chlamydomonas reinhardtii, four of which-the major reaction center I subunits PsaA and PsaB, PsaC and PsaJ-are chloroplast genome-encoded. We demonstrate that PSI biogenesis involves an assembly-governed regulation of synthesis of the major chloroplast-encoded subunits where the presence of PsaB is required to observe significant rates of PsaA synthesis and the presence of PsaA is required to observe significant rates of PsaC synthesis. Using chimeric genes expressed in the chloroplast, we show that these regulatory processes correspond to autoregulation of translation for PsaA and PsaC. The downregulation of translation occurs at some early stage since it arises from the interaction between unassembled PsaA and PsaC polypeptides and 5' untranslated regions of psaA and psaC mRNAs, respectively. These assembly-dependent autoregulations of translation represent two new instances of a control by epistasy of synthesis process that turns out to be a general feature of protein expression in the chloroplast of C. reinhardtii.

Evolution of photosystem I - from symmetry through pseudo-symmetry to asymmetry

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.