In vitro models for photosynthetic energy conversion

A summary is presented of recent work on the photochemistry of chlorophyll in solution. It is shown that reactions occur which are close counterparts ofin vivo photoprocesses. These are (a) photoproduction of chlorophyll cation radical (analog of photosystem I reaction centre primary photoprocess), (b) one-electron phototransfer from bacterio-chlorophyll to quinone (analog of bacterial reaction centre primary photoprocess), (c) chlorophyll photosensitized one-electron transfer from hydroxylic compounds to quinone (analog of photosystem II reaction centre photoprocess). The mechanisms of these reactions and their implications for photosynthetic energy conversion are discussed.     

Potential enhancement of photosynthetic energy conversion in algal mass culture

Actual laboratory data obtained from steady-state Dunaliella tertiolecta cultures grown under a wide range of photon flux densities were used in a simple model to calculate daily production in a conventional algal mass culture system. In spite of large physiological and biochemical variations between low-light- (LL) and high light- (HL) adapted cultures, the overall calculated daily productivity is almost identical for both strains grown at optimal conditions. When production of fine biochemicals is considered, however, a hypothetical HL strain, which cannot shade adapt, is advantageous. Based on biochemical and biophysical analysis of D. tertiolecta responses to growth irradiance levels, specific targets are defined for genetic manipulation to enhance productivity in algal mass culture systems. The targets identified are (1) amplification of the carboxylation enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase relative to the electron transport complexes, which should increase photosynthetic capacity at light saturation, and (2) enlargement of the light-harvesting complexes by varying their pigment composition in order to increase light harvesting at low photon flux densities.     

Gene conversion and concerted evolution in bacterial genomes

Gene conversion is defined as the non-reciprocal transfer of information between homologous sequences. Despite methodological problems to establish non-reciprocity, gene conversion has been demonstrated in a wide variety of bacteria. Besides examples of high-frequency reversion of mutations in repeated genes, gene conversion in bacterial genomes has been implicated in concerted evolution of multigene families. Gene conversion also has a prime importance in the generation of antigenic variation, an interesting mechanism whereby some bacterial pathogens are able to avoid the host immune system. In this review, we analyze examples of bacterial gene conversion (some of them spawned from the current genomic revolution), as well as the molecular models that explain gene conversion and its association with crossovers.     

Modulation of photosynthetic energy conversion efficiency in nature: from seconds to seasons

Modulation of the efficiency with which leaves convert absorbed light to photochemical energy [intrinsic efficiency of open photosystem II (PSII) centers, as the ratio of variable to maximal chlorophyll fluorescence] as well as leaf xanthophyll composition (interconversions of the xanthophyll cycle pigments violaxanthin and zeaxanthin) were characterized throughout single days and nights to entire seasons in plants growing naturally in contrasting light and temperature environments. All pronounced decreases of intrinsic PSII efficiency took place in the presence of zeaxanthin. The reversibility of these PSII efficiency changes varied widely, ranging from reversible-within-seconds (in a vine experiencing multiple sunflecks under a eucalypt canopy) to apparently permanently locked-in for entire seasons (throughout the whole winter in a subalpine conifer forest at 3,000?m). While close association between low intrinsic PSII efficiency and zeaxanthin accumulation was ubiquitous, accompanying features (such as trans-thylakoid pH gradient, thylakoid protein composition, and phosphorylation) differed among contrasting conditions. The strongest and longest-lasting depressions in intrinsic PSII efficiency were seen in the most stress-tolerant species. Evergreens, in particular, showed the most pronounced modulation of PSII efficiency and thermal dissipation, and are therefore suggested as model species for the study of photoprotection. Implications of the responses of field-grown plants in nature for mechanistic models are discussed.     

Helicobacter pylori: molecular evolution of a bacterial quasi-species

Helicobacter pylori persists chronically within individuals and as they spread the mutating bacteria migrate with them. The continuous selection and microevolution generates a population of closely related but different bacteria that behave like a quasi-species. Within this heterogeneity, H. pylori strains fall into distinct types, into the virulent (type I) and less virulent (type II) strains, based on the presence of a pathogenicity island (cag) that encodes a specialized secretion machinery. We propose that during chronic infection a dynamic equilibrium between bacteria expressing a disparate degree of virulence is established, and that diverse forms prevail at different times.     

Engineering photosynthetic light capture: impacts on improved solar energy to biomass conversion

The main function of the photosynthetic process is to capture solar energy and to store it in the form of chemical 'fuels'. Increasingly, the photosynthetic machinery is being used for the production of biofuels such as bio-ethanol, biodiesel and bio-H₂. Fuel production efficiency is directly dependent on the solar photon capture and conversion efficiency of the system. Green algae (e.g. Chlamydomonas reinhardtii ) have evolved genetic strategies to assemble large light-harvesting antenna complexes (LHC) to maximize light capture under low-light conditions, with the downside that under high solar irradiance, most of the absorbed photons are wasted as fluorescence and heat to protect against photodamage. This limits the production process efficiency of mass culture. We applied RNAi technology to down-regulate the entire LHC gene family simultaneously to reduce energy losses by fluorescence and heat. The mutant Stm3LR3 had significantly reduced levels of LHCI and LHCII mRNAs and proteins while chlorophyll and pigment synthesis was functional. The grana were markedly less tightly stacked, consistent with the role of LHCII. Stm3LR3 also exhibited reduced levels of fluorescence, a higher photosynthetic quantum yield and a reduced sensitivity to photoinhibition, resulting in an increased efficiency of cell cultivation under elevated light conditions. Collectively, these properties offer three advantages in terms of algal bioreactor efficiency under natural high-light levels: (i) reduced fluorescence and LHC-dependent heat losses and thus increased photosynthetic efficiencies under high-light conditions; (ii) improved light penetration properties; and (iii) potentially reduced risk of oxidative photodamage of PSII.     

Protein modifications affecting triplet energy transfer in bacterial photosynthetic reaction centers.

The efficiency of triplet energy transfer from the special pair (P) to the carotenoid (C) in photosynthetic reaction centers (RCs) from a large family of mutant strains has been investigated. The mutants carry substitutions at positions L181 and/or M208 near chlorophyll-based cofactors on the inactive and active sides of the complex, respectively. Light-modulated electron paramagnetic resonance at 10 K, where triplet energy transfer is thermally prohibited, reveals that the mutations do not perturb the electronic distribution of P. At temperatures > or = 70 K, we observe reduced signals from the carotenoid in most of the RCs with L181 substitutions. In particular, triplet transfer efficiency is reduced in all RCs in which a lysine at L181 donates a sixth ligand to the monomeric bacteriochlorophyll B(B). Replacement of the native Tyr at M208 on the active side of the complex with several polar residues increased transfer efficiency. The difference in the efficiencies of transfer in the RCs demonstrates the ability of the protein environment to influence the electronic overlap of the chromophores and thus the thermal barrier for triplet energy transfer.     

Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers.

The reorganization energy (lambda) for electron transfer from the primary electron donor (P*) to the adjacent bacteriochlorophyll (B) in photosynthetic bacterial reaction centers is explored by molecular-dynamics simulations. Relatively long (40 ps) molecular-dynamics trajectories are used, rather than free energy perturbation techniques. When the surroundings of the reaction center are modeled as a membrane, lambda for P* B --> P+ B- is found to be approximately 1.6 kcal/mol. The results are not sensitive to the treatment of the protein's ionizable groups, but surrounding the reaction center with water gives higher values of lambda (approximately 6.5 kcal/mol). In light of the evidence that P+ B- lies slightly below P* in energy, the small lambda obtained with the membrane model is consistent with the speed and temperature independence of photochemical charge separation. The calculated reorganization energy is smaller than would be expected if the molecular dynamics trajectories had sampled the full conformational space of the system. Because the system does not relax completely on the time scale of electron transfer, the lambda obtained here probably is more pertinent than the larger value that would be obtained for a fully equilibrated system.     

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution

We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the alpha-Proteobacteria, the gamma-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for approximately 70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.     

Stepwise conversion of a mesophilic to a thermophilic ribozyme

A fundamental question in RNA folding is the mechanism of thermodynamic stability. We investigated the equilibrium folding of a series of sequence variants in which one to three motifs of a 255-nucleotide mesophilic ribozyme were substituted with the corresponding motifs from its thermophilic homologue. Substitution of three crucial motifs individually or in groups results in a continual increase in the stability and folding cooperativity in a stepwise fashion. We find an unexpected relationship between stability and folding cooperativity. Without changing the folding cooperativity, RNAs having a similar native structure can only achieve moderate change in stability and likewise, without changing stability, RNAs having a similar native structure can only achieve moderate change in folding cooperativity. This intricate relationship must be included in the predictions of tertiary RNA stability.     

The purple bacterial photosynthetic unit

Now is a very exciting time for researchers in the area of the primary reactions of purple bacterial photosynthesis. Detailed structural information is now available for not only the reaction center (Lancaster et al. 1995, in: Blankenship RE et al. (eds) Anoxygenic Photosynthetic Bacteria, pp 503–526), but also LH2 from Rhodopseudomonas acidophila (McDermott et al. 1995, Nature 374: 517–521) and LH1 from Rhodospirillum rubrum (Karrasch et al. 1995. EMBO J 14: 631–638). These structures can now be integrated to produce models of the complete photosynthetic unit (PSU) (Papiz et al., 1996, Trends Plant Sci, in press), which opens the door to a much more detailed understanding of the energy transfer events occurring within the PSU.Abbreviations Bchl bacteriochlorophyll - LH light-harvesting - PSU photosynthetic unit Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences     

Stepwise evolution of the Sec machinery in Proteobacteria

The Sec machinery facilitates the translocation of proteins across and into biological membranes. In several of the Proteobacteria, this machinery contains accessory features that are not present in any other bacterial division. The genomic distribution of these features in the context of bacterial phylogeny suggests that the Sec machinery has evolved in discrete steps. The canonical Sec machinery was initially supplemented with SecB; subsequently, SecE was extended with two transmembrane segments and, finally, SecM was introduced. The Sec machinery of Escherichia coli and other Enterobacteriales represents the end product of this stepwise evolution.     

State transitions--the molecular remodeling of photosynthetic supercomplexes that controls energy flow in the chloroplast

In oxygen-evolving photosynthesis, the two photosystems-photosystem I and photosystem II-function in parallel, and their excitation levels must be balanced to maintain an optimal photosynthetic rate under natural light conditions. State transitions in photosynthetic organisms balance the absorbed light energy between the two photosystems in a short time by relocating light-harvesting complex II proteins. For over a decade, the understanding of the physiological consequences, the molecular mechanism, and its regulation has increased considerably. After providing an overview of the general understanding of state transitions, this review focuses on the recent advances of the molecular aspects of state transitions with a particular emphasis on the studies using the green alga Chlamydomonas reinhardtii. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.     

Tracking the molecular evolution of photosynthesis through characterization of atomic contents of the photosynthetic units

Oxygen molecules have a great impact on protein evolution. We have performed a comparative study of key photosynthetic proteins in order to seek the answer to the question; did the evolutionary substitution of oxygen- and nitrogen-containing residues in the photosynthetic proteins correspond to nutrient constraints and metabolic optimization? The D1 peptide in RC II complexes has higher oxygen-containing amino acid residues and PufL/PufM have lower oxygen content in their peptides. In this article, we also discuss the possible influences of micro-environment and the available nutrients on the protein structure and their atomic distribution.     

Development of the bacterial photosynthetic apparatus

Anoxygenic photosynthetic bacteria have provided us with crucial insights into the process of solar energy capture, pathways of metabolic and societal importance, specialized differentiation of membrane domains, function or assembly of bioenergetic enzymes, and into the genetic control of these and other activities. Recent insights into the organization of this bioenergetic membrane system, the genetic control of this specialized domain of the inner membrane and the process by which potentially photosynthetic and non-photosynthetic cells protect themselves from an important class of reactive oxygen species will provide an unparalleled understanding of solar energy capture and facilitate the design of solar-powered microbial biorefineries.