Microaerophilic growth and induction of the photosynthetic reaction center in Rhodopseudomonas viridis

Effects of vegetation on bacterial communities, carbon and nitrogen in dryland soil surfaces: implications for shrub encroachment in the southwest Kalahari

Shrub encroachment is occurring in many of the world's drylands, but its impacts on ecosystem structure and function are still poorly understood. In particular, it remains unclear how shrub encroachment affects dryland soil surfaces, including biological soil crust (biocrust) communities. In this study, soil surfaces (0-1 cm depth) were sampled from areas of Grewia flava shrubs and Eragrostis lehmanniana and Schmidtia kalahariensis grasses in the southwest Kalahari during two different seasons (March and November). Our hypothesis is that the presence of different vegetation cover types (shrubs versus grasses) alters the microbial composition of soil surfaces owing to their contrasting microenvironments. The results showed that more significant differences in microclimate (light, soil surface temperatures) and soil surface microbial communities were observed between shrubs and grasses than between sampling seasons. Based on high-throughput 16S rRNA gene sequencing, our findings showed that approximately one third (33.5%) of the operational taxonomic units (OTUs) occurred exclusively in soil surfaces beneath shrubs. Soil surfaces with biocrusts in grass areas were dominated by the cyanobacteria Microcoleus steenstrupii, whereas the soil surfaces beneath shrubs were dominated by the proteobacteria Microvirga flocculans. Soil surfaces beneath shrubs are associated with reduced cyanobacterial abundance but have higher total carbon and total nitrogen contents compared to biocrusts in grass areas. These findings infer changes in the relative contributions from different sources of carbon and nitrogen (e.g. cyanobacterial and non-cyanobacterial fixation, plant litter, animal activity). The distinctive microbial composition and higher carbon and nitrogen contents in soil surfaces beneath shrubs may provide a positive feedback mechanism promoting shrub encroachment, which helps to explain why the phenomenon is commonly observed to be irreversible.

A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria

All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.

Microbiomes and chemical components of feed water and membrane-attached biofilm in reverse osmosis system to treat membrane bioreactor effluents

Reverse osmosis (RO) system at a stage after membrane bioreactor (MBR) is used for the wastewater treatment and reclamation. One of the most serious problems in this system is membrane fouling caused by biofilm formation. Here, microbiomes and chemical components of the feed water and membrane-attached biofilm of RO system to treat MBR effluents were investigated by non-destructive confocal reflection microscopy, excitation-emission fluorescence spectroscopy and high-throughput sequencing of 16S rRNA genes. The microscopic visualization indicated that the biofilm contained large amounts of microbial cells (0.5 ± 0.3~3.9 ± 2.3 µm³/µm²) and the extracellular polysaccharides (3.3 ± 1.7~9.4 ± 5.1 µm³/µm²) and proteins (1.0 ± 0.2~1.3 ± 0.1 µm³/µm²). The spectroscopic analysis identified the humic and/or fulvic acid-like substances and protein-like substances as the main membrane foulants. High-throughput sequencing showed that Pseudomonas spp. and other heterotrophic bacteria dominated the feed water microbiomes. Meanwhile, the biofilm microbiomes were composed of diverse bacteria, among which operational taxonomic units related to the autotrophic Hydrogenophaga pseudoflava and Blastochloris viridis were abundant, accounting for up to 22.9 ± 4.1% and 3.1 ± 0.4% of the total, respectively. These results demonstrated that the minor autotrophic bacteria in the feed water played pivotal roles in the formation of polysaccharide- and protein-rich biofilm on RO membrane, thereby causing membrane fouling of RO system.

Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community

In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis showed the presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales (59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria were primarily responsible for photosynthesis with the presence of multiple copies of genes for both photosystems I and II, with a smaller but significant fraction of proteobacterial anoxic photosystem II genes. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.

Engineered biosynthesis of bacteriochlorophyll b in Rhodobacter sphaeroides

Bacteriochlorophyll b has the most red-shifted absorbance maximum of all naturally occurring photopigments. It has a characteristic ethylidene group at the C8 position in place of the more common ethyl group, the product of a C8-vinyl reductase, which is carried by the majority of chlorophylls and bacteriochlorophylls used in photosynthesis. The subsequent and first step exclusive to bacteriochlorophyll biosynthesis, the reduction of the C7 = C8 bond, is catalyzed by chlorophyllide oxidoreductase. It has been demonstrated that the enzyme from bacteriochlorophyll a-utilizing bacteria can catalyze the formation of compounds carrying an ethyl group at C8 from both ethyl- and vinyl-carrying substrates, indicating a surprising additional C8-vinyl reductase function, while the enzyme from organisms producing BChl b could only catalyze C7 = C8 reduction with a vinyl substrate, but this product carried an ethylidene group at the C8 position. We have replaced the native chlorophyllide oxidoreductase-encoding genes of Rhodobacter sphaeroides with those from Blastochloris viridis, but the switch from bacteriochlorophyll a to b biosynthesis is only detected when the native conventional C8-vinyl reductase is absent. We propose a non-enzymatic mechanism for ethylidene group formation based on the absence of cellular C8-vinyl reductase activity.

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We engineer the production of a foreign photopigment in Rhodobacter sphaeroides.

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Native COR-encoding genes are replaced with those from Blastochloris viridis.

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Bacteriochlorophyll b is produced upon additional deletion of conventional 8VR.

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We propose that loss of 8VR activity by COR leads to ethylidene bond formation.

Putative hydrogen bond to tyrosine M208 in photosynthetic reaction centers from Rhodobacter capsulatus significantly slows primary charge separation

Slow, ∼50 ps, P* → P⁺H_A^– electron transfer is observed in Rhodobacter capsulatus reaction centers (RCs) bearing the native Tyr residue at M208 and the single amino acid change of isoleucine at M204 to glutamic acid. The P* decay kinetics are unusually homogeneous (single exponential) at room temperature. Comparative solid-state NMR of [4′-¹³C]Tyr labeled wild-type and M204E RCs show that the chemical shift of Tyr M208 is significantly altered in the M204E mutant and in a manner consistent with formation of a hydrogen bond to the Tyr M208 hydroxyl group. Models based on RC crystal structure coordinates indicate that if such a hydrogen bond is formed between the Glu at M204 and the M208 Tyr hydroxyl group, the −OH would be oriented in a fashion expected (based on the calculations by Alden et al., J. Phys. Chem.1996, 100, 16761–16770) to destabilize P⁺B_A^– in free energy. Alteration of the environment of Tyr M208 and B_A by Glu M204 via this putative hydrogen bond has a powerful influence on primary charge separation.

Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center

Heterodimer mutant reaction centers (RCs) of Blastochloris viridis were crystallized using microfluidic technology. In this mutant, a leucine residue replaced the histidine residue which had acted as a fifth ligand to the bacteriochlorophyll (BChl) of the primary electron donor dimer M site (HisM200). With the loss of the histidine-coordinated Mg, one bacteriochlorophyll of the special pair was converted into a bacteriopheophytin (BPhe), and the primary donor became a heterodimer supermolecule. The crystals had dimensions 400 x 100 x 100 microm, belonged to space group P4(3)2(1)2, and were isomorphous to the ones reported earlier for the wild type (WT) strain. The structure was solved to a 2.5 A resolution limit. Electron-density maps confirmed the replacement of the histidine residue and the absence of Mg. Structural changes in the heterodimer mutant RC relative to the WT included the absence of the water molecule that is typically positioned between the M side of the primary donor and the accessory BChl, a slight shift in the position of amino acids surrounding the site of the mutation, and the rotation of the M194 phenylalanine. The cytochrome subunit was anchored similarly as in the WT and had no detectable changes in its overall position. The highly conserved tyrosine L162, located between the primary donor and the highest potential heme C(380), revealed only a minor deviation of its hydroxyl group. Concomitantly to modification of the BChl molecule, the redox potential of the heterodimer primary donor increased relative to that of the WT organism (772 mV vs. 517 mV). The availability of this heterodimer mutant and its crystal structure provides opportunities for investigating changes in light-induced electron transfer that reflect differences in redox cascades.

Photosynthetic system in Blastochloris viridis revisited

The bacterium Blastochloris viridis carries one of the simplest photosynthetic systems, which includes a single light-harvesting complex that surrounds the reaction center, membrane soluble quinones, and a soluble periplasmic protein cytochrome c(2) that shuttle between the reaction center and the bc(1) complex and act as electron carriers, as well as the ATP synthase. The close arrangement of the photosynthetic membranes in Bl. viridis, along with the extremely tight arrangement of the photosystems within these membranes, raises a fundamental question about the diffusion of the electron carriers. To address this issue, we analyzed the structure and response of the Bl. viridis photosynthetic system to various light conditions, by using a combination of electron microscopy, whole-cell cryotomography, and spectroscopic methods. We demonstrate that in response to high light intensities, the ratio of both cytochrome c(2) and bc(1) complexes to the reaction centers is increased. The shorter membrane stacks, along with the notion that the bc(1) complex is located at the highly curved edges of these stacks, result in a smaller average distance between the reaction centers and the bc(1) complexes, leading to shorter pathways of cytochrome c(2) between the two complexes. Under anaerobic conditions, the slow diffusion rate is further mitigated by keeping most of the quinone pool reduced, resulting in a concentration gradient of quinols that allows for a constant supply of theses electron carriers to the bc(1) complex.

Microaerophilic cooperation of reductive and oxidative pathways allows maximal photosynthetic membrane biosynthesis in Rhodospirillum rubrum

The purple nonsulfur bacterium Rhodospirillum rubrum has been employed to study physiological adaptation to limiting oxygen tensions (microaerophilic conditions). R. rubrum produces maximal levels of photosynthetic membranes when grown with both succinate and fructose as carbon sources under microaerophilic conditions in comparison to the level (only about 20% of the maximum) seen in the absence of fructose. Employing a unique partial O(2) pressure (pO(2)) control strategy to reliably adjust the oxygen tension to values below 0.5%, we have used bioreactor cultures to investigate the metabolic rationale for this effect. A metabolic profile of the central carbon metabolism of these cultures was obtained by determination of key enzyme activities under microaerophilic as well as aerobic and anaerobic phototrophic conditions. Under aerobic conditions succinate and fructose were consumed simultaneously, whereas oxygen-limiting conditions provoked the preferential breakdown of fructose. Fructose was utilized via the Embden-Meyerhof-Parnas pathway. High levels of pyrophosphate-dependent phosphofructokinase activity were found to be specific for oxygen-limited cultures. No glucose-6-phosphate dehydrogenase activity was detected under any conditions. We demonstrate that NADPH is supplied mainly by the pyridine-nucleotide transhydrogenase under oxygen-limiting conditions. The tricarboxylic acid cycle enzymes are present at significant levels during microaerophilic growth, albeit at lower levels than those seen under fully aerobic growth conditions. Levels of the reductive tricarboxylic acid cycle marker enzyme fumarate reductase were also high under microaerophilic conditions. We propose a model by which the primary "switching" of oxidative and reductive metabolism is performed at the level of the tricarboxylic acid cycle and suggest how this might affect redox signaling and gene expression in R. rubrum.

Cloning, sequencing, and characterization of the recA gene from Rhodopseudomonas viridis and construction of a recA strain

A recombination-deficient strain of the phototrophic bacterium Rhodopseudomonas viridis was constructed for the homologous expression of modified photosynthetic reaction center genes. The R. viridis recA gene was cloned and subsequently deleted from the R. viridis genome. The cloned R. viridis recA gene shows high identity to known recA genes and was able to complement the Rec- phenotype of a Rhizobium meliloti recA strain. The constructed R. viridis recA strain showed the general Rec- phenotype, i.e., increased sensitivity to DNA damage and severely impaired recombination ability. The latter property of this strain will be of advantage in particular for expression of modified, nonfunctional photosynthetic reaction centers which are not as yet available.

Membrane lipids of Rhodopseudomonas viridis

In search of the precyanobacterial origin of the typical thylakoid lipids found in cyanobacteria and chloroplasts, we analyzed the polar lipids of the anaerobic phototrophic bacterium Rhodopseudomonas viridis. Glycolipids (monogalactosyl-, digalactosyl- and glucuronosyl diacylglycerol), phospholipids (phosphatidyl choline, -ethanolamine, -glycerol and cardiolipin) and an ornithine lipid were isolated and identified by NMR (1H, 13C, 31P) and mass spectrometry. Positional distribution and pairing of fatty acids in molecular species show small, but significant differences between glyco- and phospholipids. In this context, a new enzymatic method is described for assigning the enantiomeric structure of the diacylglycerol moiety in glyco- and phospholipids. 14C-Labelling studies suggest that monogalactosyl diacylglycerol is formed by galactosylation of diacylglycerol as in chloroplasts and not by glucosylation followed by epimerization as in cyanobacteria. The two 1,6-linked galactopyranose residues of digalactosyl diacylglycerol are both in beta-linkage and thus differ from the corresponding chloroplast lipid with its alpha-beta-sequence. R. viridis does not contain the sulfolipid, and even phosphate starvation does not induce the synthesis of this most characteristic thylakoid lipid, which on the other hand is present in other anaerobic phototrophic bacteria.

Electron and proton transfer to the quinones in bacterial photosynthetic reaction centers: insight from combined approaches of molecular genetics and biophysics

We present here new results together with an overview of the current knowledge on the coupled processes of electron and proton transfer in bacterial reaction centers. The importance of a multidisciplinary approach associating molecular genetics, structural biology, biochemistry and spectroscopy is underlined. We emphasize the electrostatic role of the protein to maintain a negative electrostatic potential near the second quinone electron acceptor in order to: i) accelerate the overall rate of proton transfer from the cytoplasm to this acceptor by increasing the pKs of some groups involved in this process; ii) increase the local proton concentration near this acceptor. We also point out the possibility of long distance propagation of the electrostatic effects through the protein associated with relaxation processes triggered by the formation of the semiquinone anions on the first flash.

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.

Sequence analysis and transcriptional organization of the Rhodopseudomonas viridis cytochrome c2 gene

The cytochrome c2 gene (cycA) of the purple nonsulfur bacterium Rhodopseudomonas viridis was isolated from a genomic library by using two degenerate oligonucleotides containing all possible DNA sequences predicted from the published amino acid sequence of this protein (Ambler et al., Proc. Natl. Acad. Sci. USA 73:472-475, 1976). Cloning and sequence analysis of the cytochrome c2 gene indicated the presence of a typical procaryotic 20-residue signal peptide, suggesting that this periplasmic protein in synthesized in vivo as a precursor. In addition, four amino acids were found to be different by comparing the published sequence of the mature protein with that deduced from the isolated cycA gene (Lys-14----Leu, Ser-46----Ala, Ile-84----Val, Leu-97----Ile). Northern (RNA) blot analysis and fine mapping of the 5' and 3' ends of the cycA gene transcript from photoheterotrophically grown R. viridis cells revealed one abundant transcript of 523 to 530 nucleotides in length, with the transcription start site at position -39 relative to the coding region of cytochrome c2. A low-abundance transcript with an extended 3' end (about 600 bases in length) is thought to be processed by exonucleases, resulting in the slightly shorter main transcript.

Structure and transcription of the genes encoding the B1015 light-harvesting complex beta and alpha subunits and the photosynthetic reaction center L, M, and cytochrome c subunits from Rhodopseudomonas viridis

The genes encoding the beta and alpha subunits of the B1015 light-harvesting complex (LHC) and the L, M, and cytochrome c subunits of the photosynthetic reaction center from Rhodopseudomonas viridis are organized in an operon, in analogy to other nonsulfur purple bacteria, named the puf operon. In photoheterotrophically grown cells, two abundant puf operon mRNA species of 3,581 and 621 bases were present. The large transcript encoded the LHC beta, LHC alpha, and reaction center L, M, and cytochrome c polypeptides, whereas the small transcript only coded for the LHC beta and alpha polypeptides. Both transcripts share a common 5' end which is located 115 bases upstream from the initiation codon of the LHC beta gene. Two additional low-level transcripts of 3,718 and 758 bases with 5' ends 254 +/- 3 bases upstream from the LHC beta gene were detected. Analysis of the DNA sequence preceding the different 5' ends revealed DNA elements of striking homology. The 3' ends of the small transcripts were mapped within the alpha-L intercistronic DNA region downstream from a sequence capable of forming a very stable stem-loop when transcribed into RNA. The 3' termini of the large transcripts are located immediately downstream from the region coding the cytochrome c subunit in two areas resembling rho-independent transcription terminators. No open reading frames corresponding to pufQ and pufX from Rhodobacter capsulatus and Rhodobacter sphaeroides were present in the flanking DNA regions of the puf operon. In contrast, an open reading frame ending 191 base pairs upstream from the LHC beta gene showed 50% homology at the amino acid level to the available sequence of the bchA gene from R. capsulatus. The genes coding for the B1015 LHC subunits had C-terminal extensions of 13 (beta) and 10 (alpha) amino acids which were not present in the proteins isolated from intracytoplasmic membranes.

Gene transfer system for Rhodopseudomonas viridis

A gene transfer system for Rhodopseudomonas viridis was established which uses conjugation with Escherichia coli S17-I as the donor and mobilizable plasmids as vectors. Initially, plasmids of the incompatibility group P1 (pRK290 and pRK404) were used. The more effective shuttle vectors between E. coli and R. viridis, pKV1 and pKVS1, were derived from plasmid pBR322 and showed the highest conjugation frequency (10(-2] thus far demonstrated in purple bacteria. It was also demonstrated that Rhizobium meliloti can be used as a donor for conjugation with R. viridis. From a genomic cosmid library of R. viridis constructed in the vector pHC79, clones that coded for subunits H (puh operon), L, M and cytochrome c (puf operon) of the photosynthetic reaction center were isolated and characterized. For linkage of the two operons on the genome, cosmids that overlapped with the operon-carrying clones were identified. The relative positions of the two operons could not be determined, but the operons must be more than 100 kilobase pairs apart. Thus, the genomic organization of the reaction center in R. viridis is different from that of Rhodobacter capsulatus, for which a distance of about 39 kilobase pairs was determined. From a spontaneous mutant of R. viridis that is resistant to the herbicide terbutryn, the puf operon was cloned in pKVS1 and transferred by conjugation into R. viridis wild-type cells. The resulting exconjugants were resistant to the herbicide, which demonstrated that the puf operon on pKVS1 constructions was functionally expressed in R. viridis.