Primary structure of the M subunit of the reaction center from Rhodopseudomonas sphaeroides

Photosynthetic reaction center-functionalized electrodes for photo-bioelectrochemical cells

During the last few years, intensive research efforts have been directed toward the application of several highly efficient light-harvesting photosynthetic proteins, including reaction centers (RCs), photosystem I (PSI), and photosystem II (PSII), as key components in the light-triggered generation of fuels or electrical power. This review highlights recent advances for the nano-engineering of photo-bioelectrochemical cells through the assembly of the photosynthetic proteins on electrode surfaces. Various strategies to immobilize the photosynthetic complexes on conductive surfaces and different methodologies to electrically wire them with the electrode supports are presented. The different photoelectrochemical systems exhibit a wide range of photocurrent intensities and power outputs that sharply depend on the nano-engineering strategy and the electroactive components. Such cells are promising candidates for a future production of biologically-driven solar power.

The three-dimensional structures of bacterial reaction centers

This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.

George Feher: a pioneer in reaction center research

Our understanding of photosynthesis has been greatly advanced by the elucidation of the structure and function of the reaction center (RC), the membrane protein responsible for the initial light-induced charge separation in photosynthetic bacteria and green plants. Although today we know a great deal about the details of the primary processes in photosynthesis, little was known in the early days. George Feher made pioneering contributions to photosynthesis research in characterizing RCs from photosynthetic bacteria following the ground-breaking work of Lou Duysens and Rod Clayton (see articles in this issue by van Gorkom and Wraight). The work in his laboratory at the University of California, San Diego, started in the late 1960s and continued for over 30 years. He isolated a pure RC protein and used magnetic resonance spectroscopy to study the primary reactants. Following this pioneering work, Feher studied the detailed structure of the RC and the basic electron and proton transfer functions that it performs using a wide variety of biophysical and biochemical techniques. These studies, together with work from many other researchers, have led to our present detailed understanding of these proteins and their function in photosynthesis. The present article is a brief historical account of his pioneering contributions to photosynthesis research. A more detailed description of his work can be found in an earlier biographical paper (Feher in Photosynth Res 55:1-40, 1998a).

Light-harvesting II (B800-B850 complex) structural genes from Rhodopseudomonas capsulata

The light-harvesting II (LHII) structural genes coding for the (B800-B850 complex) beta- and alpha-polypeptides have been cloned and the nucleotide and deduced polypeptide sequences have been determined. This completes the sequencing of all seven structural genes coding for the structural polypeptides of the photosynthetic apparatus that bind the pigments and cofactors participating in the primary light reactions of photosynthesis. Unlike the structural genes coding for the reaction center L, M, and H subunits and the light-harvesting I (LHI) (B870 complex) structural polypeptides, the LHII structural genes are not within the 46-kilobase photosynthetic gene cluster carried by the R-prime plasmid pRPS404. Identical organization of the beta and alpha structural genes for both LHI and LHII and sequence homologies between the two beta-polypeptides and between the two alpha-polypeptides suggests that both complexes arose by gene duplication from a single ancestral light-harvesting complex and that the putative bacteriochlorophyll binding sequence Ala-X-X-X-His has been absolutely conserved.

Isotope effect on electron transfer in reaction centers from Rhodopseudomonas sphaeroides

Previous ENDOR studies on reaction centers from Rhodopseudomonas sphaeroides have shown the presence of two hydrogen-bonded protons associated with the primary, ubiquinone, acceptor Q(A). These protons exchange with deuterons from solvent (2)H(2)O. The effect of this deuterium substitution on the charge-recombination kinetics (BChl)(2) (+)Q(A) (-) --> (BChl)(2)Q(A) has been studied with a sensitive kinetic difference technique. The electron-transfer rate was found to increase with deuterium exchange up to a maximum Deltak/k of 5.7 +/- 0.3%. The change in rate was found to have an exchange time of 2 hr, which matched the disappearance of the ENDOR lines due to the exchangeable protons. These results indicate that these protons play a role in the vibronic coupling associated with electron transfer. A simple model for the isotope effect on electron transfer predicts a maximum rate increase of 20%, which is consistent with the experimental results.

Labeling quinone-binding sites in photosynthetic reaction centers: A 38-kilodalton protein associated with the acceptor side of photosystem II

2-Acetoxymethyl-1,4-naphthoquinone (2-AcOMeNQ) binds with rapid kinetics and high affinity to the primary quinone Q(A) site of reaction centers from Rhodopseudomonas capsulata. Binding of 2-AcOMeNQ fully restores electron-transfer activity with kinetics that is similar, but not identical, to that seen with ubiquinone-50. When bound at the Q(A) site, 2-AcOMeNQ preferentially labels the L subunit. This preference suggests that 2-AcOMeNQ labels primarily the region of a quinone-binding site that is close to the first isoprenoid unit of the side chain, which is expected from the location and structure of the reaction region of the molecule. In photosystem II particles from Synechococcus sp., 2-AcOMeNQ primarily labels two polypeptides with apparent molecular masses of 38 and 19 kDa. Labeling of only the 38-kDa polypeptide is sufficiently sensitive to 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) to conclude that it is involved in binding quinones on the acceptor side of photosystem II. Although we have not yet identified the 38-kDa protein, its properties suggest that it is the D2 protein. From the DCMU-sensitive labeling and from homologies to functionally important regions of the bacterial reaction-center subunits, we propose that the 38-kDa protein is intimately involved in binding the cofactors that mediate primary photochemistry.

Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa Q(B) protein of chloroplast membranes.

Elastic interactions of photosynthetic reaction center proteins affecting phase transitions and protein distributions

Reaction-center proteins of Rhodopseudomonas Sphaeroides reconstituted into phosphatidylcholine vesicles shift and broaden the fluid-gel transition of the lipid bilayer. The amount of broadening and temperature shift of the transition depend both on protein concentration and on lipid chain length. In particular, the direction of the transition temperature shift is very sensitive to lipid chain length. Electron micrographs show homogeneous protein distribution on the fluid surface whereas the solid phase contains protein aggregates the type depending on chain length. The results can qualitatively be understood in the framework of a mattress model of lipid/protein interactions in membranes.

The Photosynthetic Reaction Centre from the Purple Bacterium Rhodopseudomonasviridis

We first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. The structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure.

My daily constitutional in martinsried

The three-dimensional structures of bacterial reaction centers have served as the framework for much of our understanding of anoxygenic photosynthesis. A key step in the determination of the structure of the reaction center from Rhodobacter sphaeroides was the use the molecular replacement technique. For this technique, we made use of two sets of data. First, X-ray diffraction data had been measured from crystals of the reaction center from R. sphaeroides by our research group in California, led by George Feher and Douglas Rees. The second data set consisted of the coordinates of the three-dimensional structure of the reaction center from Rhodopseudomonas (now Blastochloris) viridis, which had been solved in the pioneering efforts of a group in Martinsried, led by Johann Deisenhofer, Robert Huber and Hartmut Michel. The collaborative efforts of these two groups to determine the structure of the reaction center from R. sphaeroides is described.

Time line of discoveries: anoxygenic bacterial photosynthesis

A time line of important research relating to anoxygenic photosynthetic organisms is presented. The time line includes discoveries of organisms, metabolic capabilities, molecular complexes and genetic systems. It also pinpoints important milestones in our understanding of the structure, function, organization, assembly and regulation of photosynthetic complexes.

Photoinhibition - a historical perspective

Photoinhibition is a state of physiological stress that occurs in all oxygen evolving photosynthetic organisms exposed to light. The primary damage occurs within the reaction center of Photosystem II (PS II). While irreversible photoinduced damage to PS II occurs at all light intensities, the efficiency of photosynthetic electron transfer decreases markedly only when the rate of damage exceeds the rate of its repair, which requires de novo PS II protein synthesis. Photoinhibition has been studied for over a century using a large variety of biochemical, biophysical and genetic methodologies. The discovery of the light induced turnover of a protein, encoded by the plastid psbA gene (the D1 protein), later identified as one of the photochemical reaction center II proteins, has led to the elucidation of the underlying mechanism of photoinhibition and to a deeper understanding of the PS II 'life cycle.'

Photosynthesis research: advances through molecular biology - the beginnings, 1975-1980s and on

Restriction endonuclease recognition sites and genes for rRNAs were first mapped on chloroplast chromosomes in 1975-1976. This marked the beginning of the application of molecular biology tools to photosynthesis research. In the first phase, knowledge about proteins involved in photosynthesis was used to identify plastid and nuclear genes encoding these proteins on cloned segments of DNA. Soon afterwards the DNA sequences of the cloned genes revealed the full primary sequences of the proteins. Knowledge of the primary amino acid sequences provided deeper understanding of the functioning of the protein and interactions among proteins of the photosynthetic apparatus. Later, as chloroplast DNA sequencing proceeded, genes were discovered that encoded proteins that had not been known to be part of the photosynthetic apparatus. This more complete knowledge of the composition of reaction centers and of the primary amino acid sequences of individual proteins comprising the reaction centers opened the way to determining the three-dimensional structures of reaction centers. At present, the availability of cloned genes, knowledge of the gene sequences and systems developed to genetically manipulate photosynthetic organisms is permitting experimental inquiries to be made into crucial details of the photosynthetic process.

Apparatus and mechanism of photosynthetic oxygen evolution: a personal perspective

This historical minireview describes basic lines of progress in our understanding of the functional pattern of photosynthetic water oxidation and the structure of the Photosystem II core complex. After a short introduction into the state of the art about 35 years ago, results are reviewed that led to identification of the essential cofactors of this process and the kinetics of their reactions. Special emphasis is paid on the flash induced oxygen measurements performed by Pierre Joliot (in Paris, France) and Bessel Kok (Baltimore, MD) and their coworkers that led to the scheme, known as the Kok-cycle. These findings not only unraveled the reaction pattern of oxidation steps leading from water to molecular oxygen but also provided the essential fingerprint as prerequisite for studying individual redox reactions. Starting with the S. Singer and G. Nicolson model of membrane organization, attempts were made to gain information on the structure of the Photsystem II complex that eventually led to the current stage of knowledge based on the recently published X-ray crystal structure of 3.8 A resolution in Berlin (Germany).With respect to the mechanism of water oxidation, the impact of Gerald T. Babcock's hydrogen abstractor model and all the considerations of electron/proton transfer coupling are outlined. According to my own model cosiderations, the protein matrix is not only a 'cofactor holder' but actively participates by fine tuning via hydrogen bond networks, playing most likely an essential role in water substrate coordination and in oxygen-oxygen bond formation as the key step of the overall process.

Photosynthesis genes and their expression in Rhodobacter sphaeroides 2.4.1: a tribute to my students and associates

This minireview traces the photosynthesis genes, their structure, function and expression in Rhodobacter sphaeroides 2.4.1, as applied to our understanding of the inducible photosynthetic intracytoplasmic membrane system or ICM. This focus has represented the research interests of this laboratory from the late 1960s to the present. This opportunity has been used to highlight the contributions of students and postdoctorals to this research effort. The work described here took place in a much greater and much broader context than what can be conveyed here. The 'timeline' begins with a clear acknowledgment of the work of June Lascelles and William Sistrom, whose foresight intuitively recognized the necessity of a 'genetic' approach to the study of photosynthesis in R. sphaeroides. The 'timeline' concludes with the completed genome sequence of R. sphaeroides 2.4.1. However, it is hoped the reader will recognize this event as not just a new beginning, but also as another hallmark describing this continuum.

Role of the H protein in assembly of the photochemical reaction center and intracytoplasmic membrane in Rhodospirillum rubrum

Rhodospirillum rubrum is a model for the study of membrane formation. Under conditions of oxygen limitation, this facultatively phototrophic bacterium forms an intracytoplasmic membrane that houses the photochemical apparatus. This apparatus consists of two pigment-protein complexes, the light-harvesting antenna (LH) and photochemical reaction center (RC). The proteins of the photochemical components are encoded by the puf operon (LHalpha, LHbeta, RC-L, and RC-M) and by puhA (RC-H). R. rubrum puf interposon mutants do not form intracytoplasmic membranes and are phototrophically incompetent. The puh region was cloned, and DNA sequence determination identified open reading frames bchL and bchM and part of bchH; bchHLM encode enzymes of bacteriochlorophyll biosynthesis. A puhA/G115 interposon mutant was constructed and found to be incapable of phototrophic growth and impaired in intracytoplasmic membrane formation. Comparison of properties of the wild-type and the mutated and complemented strains suggests a model for membrane protein assembly. This model proposes that RC-H is required as a foundation protein for assembly of the RC and highly developed intracytoplasmic membrane. In complemented strains, expression of puh occurred under semiaerobic conditions, thus providing the basis for the development of an expression vector. The puhA gene alone was sufficient to restore phototrophic growth provided that recombination occurred.

The LH1-RC core complex of Rhodobacter sphaeroides: interaction between components, time-dependent assembly, and topology of the PufX protein

Mutant strains of the photosynthetic bacterium Rhodobacter sphaeroides, lacking either LH1, the RC or PufX, were analysed by mild detergent fractionation of the cores. This reveals a hierarchy of binding of PufX in the order RC:LH1 > LH1 > RC. The assembly of photosynthetic membranes was studied by switching highly aerated cells to conditions of low aeration in the dark. The RC-H subunit appears before other components, followed by the pufBALMX then pufBA transcripts. Synthesis of the PufX polypeptide precedes that of LH1alpha and beta, which suggests that PufX associates with a limited amount of LH1alpha, beta and the RC, and prior to the encirclement of the RC by the rest of the LH1 complex. The topology of PufX within the intracytoplasmic membrane was determined by proteolytic treatment of membrane vesicles followed by protein sequencing; PufX is N-terminally exposed on the cytoplasmic surface of the photosynthetic membrane.

Low-temperature electron transfer from cytochrome to the special pair in Rhodopseudomonas viridis: role of the L162 residue

Electron transfer from the tetraheme cytochrome c to the special pair of bacteriochlorophylls (P) has been studied by flash absorption spectroscopy in reaction centers isolated from seven strains of the photosynthetic purple bacterium Rhodopseudomonas viridis, where the residue L162, located between the proximal heme c-559 and P, is Y (wild type), F, W, G, M, T, or L. Measurements were performed between 294 K and 8 K, under redox conditions in which the two high-potential hemes of the cytochrome were chemically reduced. At room temperature, the kinetics of P+ reduction include two phases in all of the strains: a dominant very fast phase (VF), and a minor fast phase (F). The VF phase has the following t(1/2): 90 ns (M), 130 ns (W), 135 ns (F), 189 ns (Y; wild type), 200 ns (G), 390 ns (L), and 430 ns (T). These data show that electron transfer is fast whatever the nature of the amino acid at position L162. The amplitudes of both phases decrease suddenly around 200 K in Y, F, and W. The effect of temperature on the extent of fast phases is different in mutants G, M, L, and T, in which electron transfer from c-559 to P+ takes place at cryogenic temperatures in a substantial fraction of the reaction centers (T, 48%; G, 38%; L, 23%, at 40 K; and M, 28%, at 60 K), producing a stable charge separated state. In these nonaromatic mutants the rate of VF electron transfer from cytochrome to P+ is nearly temperature-independent between 294 K and 8 K, remaining very fast at very low temperatures (123 ns at 60 K for M; 251 ns at 40 K for L; 190 ns at 8 K for G, and 458 ns at 8 K for T). In all cases, a decrease in amplitudes of the fast phases is paralleled by an increase in very slow reduction of P+, presumably by back-reaction with Q(A)-. The significance of these results is discussed in relation to electron transfer theories and to freezing at low temperatures of cytochrome structural reorganization.

A single mutation in the M-subunit of Rhodospirillum rubrum confers herbicide resistance

Cells of the photosynthetic bacterium Rhodospirillum rubrum were rendered resistant against the inhibitor 2-(1-phenyl)ethylamino-3-propionylamino-4-cyano-thiazole (PPCTH). Electron transport in reaction centers prepared from one of the mutants (M6) was neither inhibited by PPCTH and other NH-thiazoles nor terbutryn. These inhibitors are known to bind at the Q(B) site of the L-subunit. Compared to the wild type, chromatophores from M6 exhibited strongly altered Q(B)- Fe2+ and Q(A)- Fe2+ EPR signals. Inhibitor resistance is due to a mutation in the bacterial reaction center M-subunit, where Glu234 is exchanged against Lys. This is the first example of an inhibitor resistance in the Q(B) site caused by a mutation in the M-subunit.

Comparative study of reaction centers from purple photosynthetic bacteria: Isolation and optical spectroscopy

Reaction centers from two species of purple bacteria, Rhodospirillum rubrum and Rhodospirillum centenum, have been characterized and compared to reaction centers from Rhodobacter sphaeroides and Rhodobacter capsulatus. The reaction centers purified from these four species can be divided into two classes according to the spectral characteristics of the primary donor. Reaction centers from one class have a donor optical band at a longer wavelength, 865 nm compared to 850 nm, and an optical absorption band associated with the oxidized donor at 1250 nm that has a larger oscillator strength than reaction centers from the second class. Under normal buffering conditions, reaction centers isolated from Rb. sphaeroides and Rs. rubrum exhibit characteristics of the first class while those from Rb. capsulatus and Rs. centenum exhibit characteristics of the second class. However, the reaction centers can be converted between the two groups by the addition of charged detergents. Thus, the observed spectral differences are not due to intrinsic differences between reaction centers but represent changes in the electronic structure of the donor due to interactions with the detergents as has been confirmed by recent ENDOR measurements (Rautter J, Lendzian F, Lubitz W, Wang S and Allen JP (1994) Biochemistry 33: 12077-12084). The oxidation midpoint potential for the donor has values of 445 mV, 475 mV, 480 mV and 495 mV for Rs. rubrum, Rs. centenum, Rb. capsulatus, and Rb. sphaeroides, respectively. Despite this range of values for the midpoint potential, the decay rates of the stimulated emission are all fast with values of 4.1 ps, 4.5 ps. 5.5 ps and 6.1 ps for quinone-reduced RCs from Rs. rubrum, Rb. capsulatus, Rs. centenum, and Rb. sphaeroides, respectively. The general spectral features of the initial charge separated state are essentially the same for the four species, except for differences in the wavelengths of the absorption changes due to the different donor band positions. The pH dependence of the charge recombination rates from the primary and secondary quinones differ for reaction centers from the four species indicating different interactions between the quinones and ionizable residues. A different mechanism for charge recombination from the secondary quinone, that probably is direct recombination, is proposed for RCs from Rs. centenum.

Reconstitution of a functional photosynthetic receptor complex with isolated subunits of core light-harvesting complex and reaction centers

The B820 subunit form of the core light-harvesting complex LHI, isolated from the photosynthetic bacterium Rhodospirillum rubrum, was combined in a reassociation assay with the reaction center (RC) isolated from the same or related bacteria. This reassociation produced a photoreceptor complex (PRC) which appeared, by absorption spectroscopy, circular dichroism measurements, and kinetic absorption spectroscopy measuring transient photochanges, as analogous to the PRC in the intact bacteria. Energy transfer between the LHI and reaction center progressed with almost 100% efficiency and indicated a cooperative pattern of transfer. Treatment of the RC with proteinase K resulted in peptide cleavages of all three polypeptides of the RC but did not alter the light-induced charge separation in the RC or prevent the reassociation of the LHI and modified RC. Energy transfer efficiency from LHI to RC still approached 100% but the cooperative behavior seen in reconstitutions with the intact RC was not observed. Initial experiments using interspecies reassociations (LHI from Rhodobacter sphaeroides and RC from Rs. rubrum) showed a low efficiency of energy transfer from LHI to RC. Possible association domains for the LHI-RC interaction based on considerations of the comparative amino acid sequences of the RC of each bacteria and the most feasible remaining residues in the proteinase K treated RC are considered.

The Rhodobacter sphaeroides PufX protein is not required for photosynthetic competence in the absence of a light harvesting system

The effects of deletion of the gene encoding the PufX protein from Rhodobacter sphaeroides have been examined using bacterial strains with simplified photosystems. We find that the PufX protein is required for photosynthetic growth in strains which have the LH1 antenna complex, but is not required in a reaction centre-only strain, suggesting that the PufX protein does not directly facilitate cyclic electron transfer between the reaction centre and the cytochrome bc1 complex. The influence of PufX and carotenoid type on the size of the reaction center/LH1 core complex has also been examined in these strains.

Influence of M subunit Thr222 and Trp252 on quinone binding and electron transfer in Rhodobacter sphaeroides reaction centres

M subunit Trp252 is the only amino acid residue which is located between the bacteriopheophytin HA and the quinone QA in the photosynthetic reaction centre of Rhodobacter sphaeroides. Oligodeoxynucleotide-directed mutagenesis was employed to elucidate the influence of this aromatic amino acid on the electron transfer between these two chromophores. For this, M subunit Trp252 was changed to tyrosine or phenylalanine, and Thr222, which presumably forms a hydrogen bridge to the indole ring of M subunit Trp252, to valine. In all three mutated reaction centres, the electron-accepting ubiquinone QA is less firmly bound to its binding site than in the wild-type protein. The electron transfer from the reduced bacteriopheophytin HA- to QA proceeds in the wild-type and in the mutant ThrM222Val within 220 ps. However, in the mutants TrpM252Tyr and TrpM252Phe the time constants are 600 ps and 900 ps, respectively. This indicates that M subunit Trp252 participates in the binding of QA and reduction of this quinone.

The Q gene of Rhodobacter sphaeroides: its role in puf operon expression and spectral complex assembly

The Q gene of the facultative photoheterotroph Rhodobacter sphaeroides, localized immediately upstream of the oxygen- and light-regulated puf operon, encodes a 77-amino-acid polypeptide. The 5' and 3' ends of the 561-bp Q transcript were determined. To gain insight into the role of the Q gene product, a number of Q mutations were constructed by oligonucleotide-directed mutagenesis and subsequent substitution of the mutated form of the gene in single copy for the chromosomal copy via homologous recombination. The resulting mutants can grow photosynthetically, with the exception of QSTART, in which the initiation codon for the Q protein was altered. Spectral analysis of the intracytoplasmic membranes showed that one of the missense mutants (QdA) was deficient in the formation of detectable B875 light-harvesting complex (LHC), whereas deletion of the stem-loop structure (Qloop) failed to form B800-850 LHC when grown anaerobically either in the dark or under light intensity of 100 W/m2. Other missense mutants (QuA and QuB) contained either more B800-850 LHC or more B875 LHC, respectively, than the wild type. Although the levels of puf and puc transcripts isolated from QSTART grown anaerobically on succinate-dimethyl sulfoxide in the dark were comparable to wild-type levels, no B875 spectral complex was detected and there was a greater than 90% reduction in the level of the B800-850 pigment-protein complex. It has also been confirmed that the ultimate cellular levels of either the B875 or B800-850 spectral complexes can vary over wide limits without any change in the level(s) of complex specific transcripts. When the wild-type Q gene was reintroduced in trans into the Q mutations, QSTART was able to grow photosynthetically and both B800-850 and B875 spectral complexes were formed in either QdA or Qloop. Finally, we demonstrated that the level of each puf-specific mRNA behaves independently of one another as well as independently of the level(s) of Q gene-specific mRNA. These results are compatible with the existence of regulatory sequences affecting the puf mRNA level(s) being localized within the Q structural gene. These results suggest that Q-specific expression is uncoupled from puf-specific transcription and that the Q protein is not involved in the regulation of transcription of the puf operon but is directly involved in the assembly of both the B875 and B800-850 pigment-protein complexes.

The relationship between carotenoid biosynthesis and the assembly of the light-harvesting LH2 complex in Rhodobacter sphaeroides

Coloured carotenoids play some undefined role in the assembly of a functional light-harvesting 2 (LH2) complex in photosynthetic bacteria. We have used a series of transposon Tn5 insertion mutants disrupted at various stages of the carotenoid-biosynthetic pathway, together with an LH2 deletion/insertion mutant, to investigate this effect in Rhodobacter sphaeroides. Mutants were initially characterized by low-temperature absorbance spectroscopy and ultrastructural analysis: Northern-blot analysis demonstrated normal pucBA transcripts for LH2 polypeptides in all the carotenoid mutants. Analysis of translation of the puc transcript and investigation of the fate of any resulting LH2 polypeptides by SDS/PAGE, Western-blot and pulse-chase experiments clearly demonstrated that, in the absence of coloured carotenoids, the LH2 alpha- and beta-polypeptides are synthesized but are rapidly turned over and do not become stably integrated into the membrane. Complementation of mutants with lesions in the crtB and crtI genes, encoding phytoene synthase and phytoene desaturase respectively, with the cloned R. sphaeroides crtI gene, resulted in restoration of carotenoid biosynthesis and stable assembly of the LH2 complex in the crtI mutant but not in the crtB mutant, despite the presence of the CrtI protein.

Structure and function of the photosynthetic reaction center from Rhodobacter sphaeroides

The three-dimensional structure of the photosynthetic reaction center from Rhodobacter sphaeroides is described. The reaction center is a transmembrane protein that converts light into chemical energy. The protein has three subunits: L, M, and H. The mostly helical L and M subunits provide the scaffolding and the finely tuned environment in which the chromophores carry out electron transfer. The details of the protein-chromophore interactions are from studies of a trigonal crystal form that diffracted to 2.65-A resolution. Functional studies of the multi-subunit complex by site-specific replacement of key amino acid residues are summarized in the context of the molecular structure.

Site-specific and compensatory mutations imply unexpected pathways for proton delivery to the QB binding site of the photosynthetic reaction center

In photosynthetic reaction centers, a quinone molecule, QB, is the terminal acceptor in light-induced electron transfer. The protonatable residues Glu-L212 and Asp-L213 have been implicated in the binding of QB and in proton transfer to QB anions generated by electron transfer from the primary quinone QA. Here we report the details of the construction of the Ala-L212/Ala-L213 double mutant strain by site-specific mutagenesis and show that its photosynthetic incompetence is due to an inability to deliver protons to the QB anions. We also report the isolation and biophysical characterization of a collection of revertant and suppressor strains that have regained the photosynthetic phenotype. The compensatory mutations that restore function are diverse and show that neither Glu-L212 nor Asp-L213 is essential for efficient light-induced electron or proton transfer in Rhodobacter capsulatus. Second-site mutations, located within the QB binding pocket or at more distant sites, can compensate for mutations at L212 and L213 to restore photocompetence. Acquisition of a single negatively charged residue (at position L213, across the binding pocket at position L225, or outside the pocket at M43) or loss of a positively charged residue (at position M231) is sufficient to restore proton transfer activity to the complex. The proton transport pathways in the suppressor strains cannot, in principle, be identical to that of the wild type. The apparent mutability of this pathway suggests that the reaction center can serve as a model system to study the structural basis of protein-mediated proton transport.

Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: Possibility of horizontal gene transfer in purple bacteria

Nucleotide sequences of the genes coding for the M and cytochrome subunits of the photosynthetic reaction center of Rhodocyclus gelatinosus, a purple bacterium in the β subdivision, were determined. The deduced amino acid sequences of these proteins were compared with those of other photosynthetic bacteria. Based on the homology of these two photosynthetic proteins, Rc. gelatinosus was placed in the α subdivision of purple bacteria, which disagrees with the phylogenetic trees based on 16S rRNA and soluble cytochrome c 2. Horizontal transfer of the genes which code for the photosynthetic apparatus in purple bacteria can be postulated if the phylogenetic trees based on 16S rRNA and soluble cytochrome c 2 reflect the real history of purple bacteria.

Photosynthetic reaction center mutagenesis via chimeric rescue of a non-functional Rhodobacter capsulatus puf operon with sequences from Rhodobacter sphaeroides

Photosynthetically active chimeric reaction centers which utilize genetic information from both Rhodobacter capsulatus and Rb. sphaeroides puf operons were isolated using a novel method termed chimeric rescue. This method involves in vivo recombination repair of a Rb. capsulatus host operon harboring a deletion in pufM with a non-expressed Rb. sphaeroides donor puf operon. Following photosynthetic selection, three revertant classes were recovered: 1) those which used Rb. sphaeroides donor sequence to repair the Rb. capsulatus host operon without modification of Rb. sphaeroides puf operon sequences (conversions), 2) those which exchanged sequence between the two operons (inversions), and 3) those which modified plasmid or genomic sequences allowing expression of the Rb. sphaeroides donor operon. The distribution of recombination events across the Rb. capsulatus puf operon was decidedly non-random and could be the result of the intrinsic recombination systems or could be a reflection of some species-specific, functionally distinct characteristic(s). The minimum region required for chimeric rescue is the D-helix and half of the D/E-interhelix of M. When puf operon sequences 3' of nucleotide M882 are exchanged, significant impairment of excitation trapping is observed. This region includes both the 3' end of pufM and sequences past the end of pufM.

Pathway of proton transfer in bacterial reaction centers: second-site mutation Asn-M44-->Asp restores electron and proton transfer in reaction centers from the photosynthetically deficient Asp-L213-->Asn mutant of Rhodobacter sphaeroides

Site-directed mutagenesis of the photosynthetic reaction center (RC) from Rhodobacter sphaeroides has shown Asp-213 of the L subunit (Asp-L213) to be important for photosynthetic viability. Replacement of Asp-L213 with Asn resulted in a photosynthetically deficient mutant, due to the 10(4)-fold slower rate for the proton-coupled electron transfer reaction QA-QB- + 2H+-->QAQBH2 (k(2)AB). The detrimental effect of Asn-L213 is surprising since RCs from Rhodopseudomonas viridis, Rhodospirillum rubrum, and Chloroflexus aurantiacus have Asn at the homologous position. However, RCs from these bacteria have an Asp located near QB (the secondary quinone acceptor) at the position homologous to Asn-M44 in Rb. sphaeroides which might function in place of Asp-L213. To test this conjecture a "viridis-like" structure was introduced into Rb. sphaeroides by replacing Asp-L213 with Asn and Asn-M44 with Asp. The RCs from this double mutant displayed near-native rates for the electron transfer reaction k(2)AB and restored photosynthetic competence. The rates for the first electron transfer reaction QA-QB-->QAQB- (k(1)AB) and charge recombination D+QAQB--->DQAQB (kBD) were also restored to near-native values. These results indicate that Asp at either the L213 or the M44 site near QB can provide a pathway for rapid proton transfer and explain why Asp-L213 need not be conserved in different photosynthetic bacteria. To test further the effect of Asp at M44 on electron and proton transfer to QB a mutant containing Asp at both L213 and M44 was constructed. The RCs from this mutant (Asn-M44-->Asp) exhibited faster proton-coupled electron transfer to QB-. The increased rate of proton-coupled electron transfer (k(2)AB) in the presence of negatively charged Asp residues near QB suggests the role of an Asp near QB as (i) a proton donor group in the proton transfer chain and/or (ii) a negatively charged residue stabilizing proton transfer to reduced QB.

The significant conservative and variable regions of the homologous protein sequences

A method of identification of significant conservative and variable regions in homologous protein sequences is presented. A set of aligned homologous sequences is divided into two groups consisting of m and n most related sequences. Each pair of sequences from different group is compared using unitary similarity matrix. The superposition of pairwise comparisons scanned by a window of 10 amino acid residues gives intergroup local variability profile (VP). Area S of the figure between the VP and its mean value line is compared with averaged area S(r) of 1000 VPs of artificial homologous protein families. The difference (S-S(r)) given in standard deviation units sigma r is believed to be the amino acid substitution overall irregularity along the homologous protein sequences OI = (S-S(r))/sigma r. If OI greater than 2, the real VP extrema containing the surplus of area S-(S(r) + 2 sigma r) are cut off. The cut off stretches are likely to be significant conservative and variable regions. The significant conservative and variable regions of six homologous sequence families (phospholipases A2, cytochromes b, alpha-subunits of Na, K-ATPase, L- and M-subunits of photosynthetic bacteria photoreaction centre and human rhodopsins) were identified. It was shown that for artificial homologous protein sequences derived by k-fold lengthening of natural proteins the OI value rises as square root of k. To compare the degree of substitution irregularity in homologous protein sequence families of different length L the value of standard substitution overall irregularity for L = 250 is proposed.

Second-site mutation at M43 (Asn→Asp) compensates for the loss of two acidic residues in the QB site of the reaction center

Two acidic residues, L212Glu and L213Asp, in the QB binding sites of the photosynthetic reaction centers of Rhodobacter capsulatus and Rhodobacter sphaeroides are thought to play central roles in the transfer of protons to the quinone anion(s) generated by photoinduced electron transfer. We constructed the site-specific double mutant L212Ala-L213Ala in R. capsulatus, that is incapable of growth under photosynthetic conditions. A photocompetent derivative of that strain has been isolated that carries the original L212Ala-L213Ala double mutation and a second-site suppressor mutation at residue M43 (Asn→Asp), outside of the QB binding site, that is solely responsible for restoring the photosynthetic phenotype. The Asp,Asn combination of residues at the L213 and M43 positions is conserved in the five species of photosynthetic bacteria whose reaction center sequences are known. In R. capsulatus and R. sphaeroides, the pair is L213Asp-M43Asn. But, the reaction centers of Rhodopseudomonas viridis, Rhodospirillum rubrum and Chloroflexus aurantiacus reverse the combination to L213Asn-M43Asp. In this respect, the QB site of the suppressor strain resembles that of the latter three species in that it couples an uncharged residue at L213 with an acidic residue at M43. These reaction centers, in which L213 is an amide, must employ an alternative proton transfer pathway. The observation that the M43Asn→Asp mutation in R. capsulatus compensates for the loss of both acidic residues at L212 and L213 suggests that M43Asp is involved in a new proton transfer route in this species that resembles the one normally used in reaction centers of Rps. virddis, Rsp. rubrum and C. aurantiacus.

Origin and early evolution of photosynthesis

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

DNA sequencing and complementation/deletion analysis of the bchA-puf operon region of Rhodobacter sphaeroides: in vivo mapping of the oxygen-regulated puf promoter

Within the photosynthetic gene cluster of Rhodobacter sphaeroides the genes encoding light-harvesting LHI and reaction-centre complexes are transcriptionally linked in the order pufBALMX. The region stretching 1.6 kb upstream of pufB has been examined by DNA sequencing and by complementation/deletion analysis. These studies demonstrate that three open reading frames are located upstream of pufB. One open reading frame, designated bchA, terminates just inside pufQ, which is located proximal to pufB. BchA contains a 37 bp region that functions as the oxygen-regulated promoter for pufQ, and probably for the puf operon as a whole. We also demonstrate that the protein encoded by pufQ appears to play a role in bacteriochlorophyll biosynthesis.