Genes downstream from pucB and pucA are essential for formation of the B800-850 complex of Rhodobacter capsulatus

The phototrophic metabolic behaviour of Candidatus accumulibacter

The phototrophic capability of Candidatus Accumulibacter (Accumulibacter), a common polyphosphate accumulating organism (PAO) in enhanced biological phosphorus removal (EBPR) systems, was investigated in this study. Accumulibacter is phylogenetically related to the purple bacteria Rhodocyclus from the family Rhodocyclaceae, which belongs to the class Betaproteobacteria. Rhodocyclus typically exhibits both chemoheterotrophic and phototrophic growth, however, limited studies have evaluated the phototrophic potential of Accumulibacter. To address this gap, short and extended light cycle tests were conducted using a highly enriched Accumulibacter culture (95%) to evaluate its responses to illumination. Results showed that, after an initial period of adaptation to light conditions (approximately 4-5 h), Accumulibacter exhibited complete phosphorus (P) uptake by utilising polyhydroxyalkanoates (PHA), and additionally by consuming glycogen, which contrasted with its typical aerobic metabolism. Mass, energy, and redox balance analyses demonstrated that Accumulibacter needed to employ phototrophic metabolism to meet its energy requirements. Calculations revealed that the light reactions contributed to the generation of, at least more than 67% of the ATP necessary for P uptake and growth. Extended light tests, spanning 21 days with dark/light cycles, suggested that Accumulibacter generated ATP through light during initial operation, however, it likely reverted to conventional anaerobic/aerobic metabolism under dark/light conditions due to microalgal growth in the mixed culture, contributing to oxygen production. In contrast, extended light tests with an enriched Tetrasphaera culture, lacking phototrophic genes in its genome, clearly demonstrated that phototrophic P uptake did not occur. These findings highlight the adaptive metabolic capabilities of Accumulibacter, enabling it to utilise phototrophic pathways for energy generation during oxygen deprivation, which holds the potential to advance phototrophic-EBPR technology development.

Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics

Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.

Atomic force microscopic analysis of the light-harvesting complex 2 from purple photosynthetic bacterium Thermochromatium tepidum

Structural information on the circular arrangements of repeating pigment-polypeptide subunits in antenna proteins of purple photosynthetic bacteria is a clue to a better understanding of molecular mechanisms for the ring-structure formation and efficient light harvesting of such antennas. Here, we have analyzed the ring structure of light-harvesting complex 2 (LH2) from the thermophilic purple bacterium Thermochromatium tepidum (tepidum-LH2) by atomic force microscopy. The circular arrangement of the tepidum-LH2 subunits was successfully visualized in a lipid bilayer. The average top-to-top distance of the ring structure, which is correlated with the ring size, was 4.8 ± 0.3 nm. This value was close to the top-to-top distance of the octameric LH2 from Phaeospirillum molischianum (molischianum-LH2) by the previous analysis. Gaussian distribution of the angles of the segments consisting of neighboring subunits in the ring structures of tepidum-LH2 yielded a median of 44°, which corresponds to the angle for the octameric circular arrangement (45°). These results indicate that tepidum-LH2 has a ring structure consisting of eight repeating subunits. The coincidence of an octameric ring structure of tepidum-LH2 with that of molischianum-LH2 is consistent with the homology of amino acid sequences of the polypeptides between tepidum-LH2 and molischianum-LH2.

PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides

The mature architecture of the photosynthetic membrane of the purple phototroph Rhodobacter sphaeroides has been characterised to a level where an atomic-level membrane model is available, but the roles of the putative assembly proteins LhaA and PucC in establishing this architecture are unknown. Here we investigate the assembly of light-harvesting LH2 and reaction centre-light-harvesting1-PufX (RC-LH1-PufX) photosystem complexes using spectroscopy, pull-downs, native gel electrophoresis, quantitative mass spectrometry and fluorescence lifetime microscopy to characterise a series of lhaA and pucC mutants. LhaA and PucC are important for specific assembly of LH1 or LH2 complexes, respectively, but they are not essential; the few LH1 subunits found in ΔlhaA mutants assemble to form normal RC-LH1-PufX core complexes showing that, once initiated, LH1 assembly round the RC is cooperative and proceeds to completion. LhaA and PucC form oligomers at sites of initiation of membrane invagination; LhaA associates with RCs, bacteriochlorophyll synthase (BchG), the protein translocase subunit YajC and the YidC membrane protein insertase. These associations within membrane nanodomains likely maximise interactions between pigments newly arriving from BchG and nascent proteins within the SecYEG-SecDF-YajC-YidC assembly machinery, thereby co-ordinating pigment delivery, the co-translational insertion of LH polypeptides and their folding and assembly to form photosynthetic complexes.

The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 alpha and beta proteins on light-harvesting complex 1

Rhodobacter capsulatus contains lhaA and pucC genes that have been implicated in light-harvesting complex 1 and 2 (LH1 and LH2) assembly. The proteins encoded by these genes, and homologues in other photosynthetic organisms, have been classified as the bacteriochlorophyll delivery (BCD) family of the major facilitator superfamily. A new BCD family phylogenetic tree reveals that several PucC, LhaA and Orf428-related sequences each form separate clusters, while plant and cyanobacterial homologues cluster more distantly. The PucC protein is encoded in the pucBACDE superoperon which also codes for LH2 alpha (PucA) and beta (PucB) proteins. PucC was previously shown to be necessary for formation of LH2. This article gives evidence indicating that PucC has a shepherding activity that keeps the homologous alpha and beta proteins of LH1 and LH2 apart, allowing LH1 to assemble properly. This shepherding function was indicated by a 62% reduction in LH1 levels in DeltaLHII strains carrying plasmids encoding pucBA along with a C-terminally truncated pucC gene. More severe reductions in LH1 were seen when the truncated pucC gene was co-expressed in the presence of C-terminal PucC::PhoA fusion proteins. It appears that interaction between truncated PucC::PhoA fusion proteins and the truncated PucC protein disrupts LH1 assembly, pointing towards a PucC dimeric or multimeric functional unit.

Physical mapping of bchG, orf427, and orf177 in the photosynthesis gene cluster of Rhodobacter sphaeroides: functional assignment of the bacteriochlorophyll synthetase gene

The purple photosynthetic bacterium Rhodobacter sphaeroides has within its genome a cluster of photosynthesis-related genes approximately 41 kb in length. In an attempt to identify genes involved in the terminal esterification stage of bacteriochlorophyll biosynthesis, a previously uncharacterized 5-kb region of this cluster was sequenced. Four open reading frames (ORFs) were identified, and each was analyzed by transposon mutagenesis. The product of one of these ORFs, bchG, shows close homologies with (bacterio)chlorophyll synthetases, and mutants in this gene were found to accumulate bacteriopheophorbide, the metal-free derivative of the bacteriochlorophyll precursor bacteriochlorophyllide, suggesting that bchG is responsible for the esterification of bacteriochlorophyllide with an alcohol moiety. This assignment of function to bchG was verified by the performance of assays demonstrating the ability of BchG protein, heterologously synthesized in Escherichia coli, to esterify bacteriochlorophyllide with geranylgeranyl pyrophosphate in vitro, thereby generating bacteriochlorophyll. This step is pivotal to the assembly of a functional photosystem in R. sphaeroides, a model organism for the study of structure-function relationships in photosynthesis. A second gene, orf177, is a member of a large family of isopentenyl diphosphate isomerases, while sequence homologies suggest that a third gene, orf427, may encode an assembly factor for photosynthetic complexes. The function of the remaining ORF, bchP, is the subject of a separate paper (H. Addlesee and C. N. Hunter, J. Bacteriol. 181:7248-7255, 1999). An operonal arrangement of the genes is proposed.

Cloning, sequencing and analysis of the pucC genes from Rubrivivax gelatinosus strain 151 and Rhodopseudomonas acidophila strain 10050

The pucC genes of Rubrivivax gelatinosus strain 151 and Rhodopseudomonas acidophila strain 10050 have been identified, cloned and sequenced. In Rubrivivax gelatinosus the arrangement of the pucC gene with regard to the pucBA genes was shown to differ from that found in other species of photosynthetic bacteria. The Rhodopseudomonas acidophila pucC was found downstream of four new pucBA gene pairs, bringing the sequenced pucBA pairs to a total of eight in this strain. The predicted PucC protein sequences were compared to those of PucC from other species and showed high similarity. Similarity was also seen to more distantly related proteins LhaA and orf428 of Rhodobacter capsulatus, orf G115 of Rhodospirillum rubrum and 'orf428' from Synechocystis sp. PCC6803. An analysis of the predicted secondary structure of these proteins is given, and their structural similarity to proteins in the Major Facilitator Superfamily is discussed with regard to their possible function.

Transcript cleavage, attenuation, and an internal promoter in the Rhodobacter capsulatus puc operon

The stoichiometry of the structural proteins of the photosynthetic apparatus in purple photosynthetic bacteria is achieved primarily by complex regulation of the levels of mRNA encoding the different proteins, which has been studied in the greatest detail in the puf operon. Here we investigated the transcriptional and posttranscriptional regulation of the puc operon, which encodes the peripheral light harvesting complex LHII. We show that, analogous to the puf operon, a primary transcript encoding five puc genes is rapidly processed to generate more stable RNA subspecies. Contrary to previous hypotheses, translational coupling and regulation of puc transcription by puc gene products were found not to occur. A putative RNA stem-loop structure appears to attenuate transcription initiated at the puc operon major promoter. We also found that a minor pucD-internal promoter contributes to the levels of a message that encodes the LHII 14-kDa gamma (PucE) protein.

Heterologous expression of genes encoding bacterial light-harvesting complex II in Rhodobacter capsulatus and Rhodovulum sulfidophilum

In the present work we report the high-level expression of foreign genes encoding the light-harvesting (LHII) membrane-spanning polypeptides in photosynthetic bacteria. To do this we first constructed three deletion strains of Rhodovulum (Rhv.) sulfidophilum in which all or part of the puc operon, encoding the peripheral light-harvesting proteins, is missing. To investigate the heterologous expression of the light-harvesting polypeptides from Rb. capsulatus in Rhv. sulfidophilum and vice versa we have reintroduced functional foreign LH genes into these and equivalent strains of Rhodobacter (Rb.) capsulatus. In some cases very high levels of expression were obtained (85%) of those observed in the wild type), while in other cases much lower expression was observed; possible reasons for these differences are discussed. The heterologously expressed proteins were shown to contain normal pigment-binding sites and to be normally and functionally integrated within the host photosynthetic apparatus. The results indicate that heterologous proteins are able to assemble properly and enter into the same protein-protein interactions as their analogs originally present in the host strain.

Analysis of the puc operon promoter from Rhodobacter capsulatus

Expression of the Rhodobacter capsulatus puc operon, which codes for structural polypeptides of the light-harvesting-II peripheral antenna complex, is highly regulated in response to alterations in oxygen tension and light intensity. To obtain an understanding of the puc promoter region we report the high-resolution 5' mapping of the puc mRNA transcriptional start site and DNA sequence analysis of the puc upstream regulatory sequence (pucURS). A sigma70-type promoter sequence was identified (pucP1) which has a high degree of sequence similarity with carotenoid and bacteriochlorophyll biosynthesis promoters. Inspection of the DNA sequence also indicated the presence of two CrtJ and four integration host factor (IHF) binding sites. Transcriptional fusions of the pucURS fused to lacZ also confirmed that puc promoter activity is regulated by the transcriptional regulators IHF, CrtJ, and RegA. Gel retardation analysis using cell extracts indicates that mutations in IHF and RegA disrupt protein binding to DNA fragments containing the pucURS.

Gene cloning and regulation of gene expression of the puc operon from Rhodovulum sulfidophilum

Rhodovulum (Rhv.) sulfidophilum, unlike other nonsulfur purple bacteria, is able to synthesize the peripheral antenna complex even under fully aerobic conditions in the dark. We have obtained strong evidence that Rhv. sulfidophilum encodes only one copy of the puc operon, comprising pucB, pucA and pucC. pucB and pucA encode the beta- and alpha-polypeptides. The third ORF (pucC), downstream of pucA, has a strong homology to pucC of Rhodobacter (Rb.) capsulatus. Deletion mutation analysis indicated that the requirement for the pucC gene product for LH II expression was less strict than in Rb. capsulatus. Comparison of the deduced alpha and beta polypeptide sequences with the directly determined primary structure revealed a C-terminal processing of the alpha-subunit. Primer extension analysis showed that the pucBAC is transcribed from a sigma70-type promoter 130 bases upstream of the translational start of pucB. Transcriptional expression of the pucBAC operon in Rhv. sulfidophilum is higher, the lower the light intensity is, and is not reduced to a ground-level by the presence of oxygen. Based on lacZ fusions the relative promoter activities were, for dark aerobic:dark semiaerobic:low light anaerobic:medium light anaerobic:high light anaerobic, 5.5:7.0:2.0:1.0:0.78. Still unidentified cis-regulatory elements or binding sites of trans-regulatory elements are apparently localized in two distinct upstream regions. Furthermore, comparison of the promoter region of the Rhv. sulfidophilum pucBAC with the promoter regions of puc operons in related species showed distinct differences in the regulatory elements. The significance of these results with respect to the regulation of transcription and the oxygen-independent synthesis of LH II from Rhv. sulfidophilum is discussed.

Differences between porin isolated from Rhodobacter capsulatus B10 and 37b4

Porin was isolated from Rhodobacter (Rb.) capsulatus wild type B10, as well as from Rb. capsulatus 37b4 as a control. The porin from Rb. capsulatus B10 shows significant differences to that of Rb. capsulatus 37b4 in N-terminal sequence, amino acid composition and molecular mass. The apparent molecular mass of the purified porin from Rb. capsulatus B10 is about 28 kDa by SDS-PAGE, whereas the native porin trimer migrates at 75 kDa. For Rb. capsulatus 37b4 the molecular mass of the momomer is about 30 kDa and for the trimer about 76 kDa. These differences may be related to the morphological differences between the two wild type strains. Rb. capsulatus B10 has an extracellular capsule whereas Rb. capsulatus 37b4 is capsuleless. The native proteins from both wild types showed similar single channel conductance measurements in black lipid membranes. The B10 porin has been crystallised using the detergent beta-d-octyl-gluco-pyranoside. The crystals diffracted to 3 A and belong to the orthorhombic space-group P212121. The crystal packing could be elucidated by molecular replacement.

Topological analysis of the Rhodobacter capsulatus PucC protein and effects of C-terminal deletions on light-harvesting complex II

A theoretical model for the cytoplasmic membrane topology of the Rhodobacter capsulatus PucC protein was derived and tested experimentally with pucC'::pho'A gene fusions. The alkaline phosphatase (AP) activities of selected fusions were assayed, and the resultant pattern of high and low activity was compared with that of the theoretical model. High AP activity correlated well with fusion joints located in regions predicted to be periplasmic, and most fusions in predicted cytoplasmic loops yield approximately 1/20th as much activity. Replacement of pho'A with lac'Z in nine of the fusions confirmed the topology, as beta-galactosidase activities were generally reciprocal to the corresponding AP activity. On the basis of the theoretical analysis and the information provided by the activities of fusions, a model for PucC topology in which there are 12 membrane-spanning segments and both the N and C termini are located in the cytoplasm is proposed. Translationally out-of-frame pucC::phoA fusions were expressed in an R. capsulatus delta pucC strain. None of the fusions missing only one or two of the proposed C-terminal transmembrane segments restored the wild-type phenotype, suggesting that the C terminus of PucC is important for function.

Forty-five years of developmental biology of photosynthetic bacteria

Developmental biology and cell differentiation of photosynthetic prokaryotes are less noticed fields than the showpieces of eukaryotes, e.g. Drosophila melanogaster. The large metabolic versatility of the facultative purple bacteria and their great capability to adapt to different ecological conditions, however, aroused the inquisitiveness to investigate the process of cell differentiation and to use these bacteria as model system to study structure, function and biosynthesis of the photosynthetic apparatus. The great progress in research in this field paved the way to study principal mechanisms of cellular organization and differentiation in these bacteria. In this article, the history of the research on membrane structure and development of anoxygenic photosynthetic prokaryotes during the last 45 years is described. A personal account of how I entered the field through research on the phototaxis of cyanobacteria is given. Intracytoplasmic membranes (ICM) were detected by electron microscopy in cyanobacteria and in purple non-sulfur bacteria. The formation of ICM by invagination of the cytoplasmic membrane in purple bacteria was observed for the first time. Investigations on the effect of changes in oxygen tension and light intensity on the formation of pigments and intracytoplasmic membranes followed. The isolation, purification, and analysis of light-harvesting complexes and of pigment-binding proteins was the next step of our research. Lipopolysaccharides and peptidoglycans were detected and analyzed in the outer membrane of photosynthetic bacteria. Functional membrane differentiation includes variations in the rates of photophosphorylation and electron transport. Molecular genetic approaches have initiated the investigation of transcriptional regulation and the analysis of correlation between pigment and protein synthesis. Molecular analysis of assembly of light-harvesting complexes and membrane differentiation are the present aspects of our research. Cell differentiation has been considered under evolutionary view.

Heterologous expression of genes encoding bacterial light-harvesting complexes in Rhodobacter sphaeroides

One of the major problems in structural work on membrane-spanning proteins is the identification of an expression system which will allow the production of enough pure protein for structural studies; an inadequate expression system can lead, for example, to the formation of unwanted protein inclusion bodies. In the present work we report the expression of genes encoding the light-harvesting 2 (LH2) membrane-spanning proteins from a number of species of purple bacteria in mutants of Rhodobacter sphaeroides that lack the native LH2 antenna. The LH2 structural genes (pucBA) from the photosynthetic bacteria Rhodopseudomonas acidophila and Rubrivivax gelatinosus were amplified and tailed by polymerase chain reaction, and cloned into an LH2 expression vector, which was then introduced into three LH2-minus Rb. sphaeroides mutants; DBC omega/G5 and DD13 (DD13/G1); the resulting transconjugant strains synthesized LH2 complexes that were examined using absorption and fluorescence spectroscopy, and Western blotting. Thus, we have created a heterologous expression system which supports the assembly of a functional "foreign" light-harvesting complex. This work opens up the possibility of creating site-directed LH2 mutants from bacteria for which no genetic system is available; this is particularly significant in the case of Rps. acidophila, since this bacterium has been the source of the LH2 complex that has recently been structurally resolved to atomic resolution.

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.

Identification of a gene required for the oxygen-regulated formation of the photosynthetic apparatus of Rhodobacter capsulatus

The pigment-binding proteins of Rhodobacter capsulatus are encoded by the polycistronic puf and puc operons. Both operons show higher expression under low oxygen tension than under high oxygen tension in the wild-type strain. The Tn5 mutant strain AH2 shows only low levels of puf and puc mRNA under high and low oxygen tension, indicating that it lacks a gene product required for stimulation of puf and puc gene expression under low oxygen tension. The formation of wild-type levels of photosynthetic complexes and normal oxygen regulation could be restored by the expression in trans of a 1.7 kb fragment of the R. capsulatus wild-type chromosome or by addition of 10 micrograms l-1 vitamin B12 to the growth medium. An open reading frame of 798 nucleotides containing the Tn5 insertion was identified on the 1.7 kb fragment. This open reading frame shows no homology to known genes and has a remarkably high GC content of 76%.

Cloning of a new antenna gene cluster and expression analysis of the antenna gene family of Rhodopseudomonas palustris

The genome of Rhodopseudomonas palustris contains five antenna gene clusters, alpha beta a, alpha beta b, alpha beta c, alpha beta d and alpha beta e, which encode the light-harvesting peripheral antenna complex II polypeptides. The isolation and characterisation of the gene which encodes the alpha e and beta e polypeptides are reported. The primary structure of the beta e polypeptide is identical to that of beta b whilst the structure of alpha e is different from the other alpha subunits so far characterised. All five of the gene clusters were transcribed under high-light conditions while under low-light conditions only three were transcribed (alpha beta b, alpha beta d and alpha beta e). Furthermore, Northern-blot analysis showed that the gene clusters encode RNA transcripts of either 500 or 650 nucleotides. Individual members of the gene family showed a differential response in terms of the regulation of abundance of mRNA upon growth under either high-light or low-light intensities. Possible promoter sequences and operator sites upstream of the alpha beta b, alpha beta d and alpha beta e genes were located. Furthermore using puc-lacZ fusions in trans in R. palustris, we were able to examine the positions of the promoter of the gene clusters. The significance of these observations with respect to the regulation, organization and role of the peripheral antenna is discussed.

The role of mRNA degradation in the regulated expression of bacterial photosynthesis genes

Regulation of gene expression in bacteria, as in eukaryotic cells, is often achieved by variation of mRNA levels. Since the steady state levels of mRNA depend on both the rate of synthesis and the rate of decay, both mechanisms are important for gene regulation. After considerable effort undertaken over many years to understand the regulation of transcription, mRNA degradation has recently gained increasing attention as an important step in the regulation of some bacterial genes, and many investigations have addressed the mechanisms involved in mRNA decay. The puf mRNA of Rhodobacter capsulatus encoding pigment binding proteins has become a model system to study decay of a polycistronic mRNA and the role of mRNA degradation in gene expression. Individual segments of the polycistronic puf mRNA display extremely different half-lives. These differences in stability of mRNA segments are involved in the differential expression of puf encoded genes and consequently contribute to the stoichiometry of light-harvesting I and reaction centre complexes that results in optimal growth. In addition, control of mRNA stability is involved in the oxygen-dependent regulation of photosynthesis genes. High oxygen tension results in decreased stability of the reaction-centre specific puf mRNA segment, most likely by affecting the rate of endonucleolytic cleavage within the reaction centre coding region. The results obtained from studying puf mRNA degradation in R. capsulatus and Escherichia coli suggest that a specific distribution of decay promoting and decay impeding mRNA elements along the polycistronic mRNA is responsible for the different half-lives of individual puf segments.

A putative anaerobic coproporphyrinogen III oxidase in Rhodobacter sphaeroides. II. Analysis of a region of the genome encoding hemF and the puc operon

The puc operon of Rhodobacter sphaeroides encoding polypeptides of the major light-harvesting complex, LH2, has been found to be linked to hemF, a gene encoding a putative anaerobic coproporphyrinogen III oxidase. The puc-hemF region of the R. sphaeroides genome has been investigated by insertional mutagenesis, complementation analysis of these insertional mutants and DNA sequencing. A third gene, designated pucC, has been found immediately downstream of pucA and has been shown to be essential for LH2 expression. pucC is cotranscribed with pucB and pucA; however, hemF and the pucBAC operon were found not to be transcriptionally linked. Ultrastructural studies indicated that the morphology of the intracytoplasmic membrane may depend upon expression of pucC as well as pucBA.

NosR, a membrane-bound regulatory component necessary for expression of nitrous oxide reductase in denitrifying Pseudomonas stutzeri

The regulatory element NosR was identified within the nos region of the denitrification gene cluster of Pseudomonas stutzeri ZoBell (ATCC 14405) and characterized. It is essential for expression of the N2O reductase encoded by nosZ immediately downstream of nosR. The nosR region was initially identified by Tn5 mutagenesis (W. G. Zumft, K. Döhler, and H. Körner, J. Bacteriol. 163:918-924, 1985). It consists of a single open reading frame of 2,172 nucleotides and has the coding capacity for an 81.9-kDa protein. The codon usage for nosR, with its high G + C content of 62.4 mol% and a preference for G or C at the third position, is characteristic for a Pseudomonas gene. Hydropathy analysis classified NosR as an integral membrane protein with at least seven membrane-spanning segments. No similarity to known bacterial regulator proteins was found in a data bank search. However, the C terminus of NosR shows sequence similarity to the cysteine clusters of several 2[4Fe-4S] bacterial ferrodoxins. A monocistronic mRNA for nosZ which allowed us to monitor NosR function was identified. Complementation of Nos- mutant MK418 (nosR::Tn5) with the nosR gene supplied in trans restored nosZ transcription and expression of a catalytically active N2O reductase. In addition to evidence of the requirement for NosR, indirect evidence for involvement of the transcriptional regulator Fnr is presented.

Mutants of Rhodobacter sphaeroides lacking one or more pigment-protein complexes and complementation with reaction-centre, LH1, and LH2 genes

The photosynthetic apparatus of Rhodobacter sphaeroides is comprised of three types of pigment-protein complex: the photochemical reaction centre and its attendant LH1 and LH2 light-harvesting complexes. To augment existing deletion/insertion mutants in the genes coding for these complexes we have constructed two further mutants, one of which is a novel double mutant which is devoid of all three types of complex. We have also constructed vectors for the expression of either LH1, LH2 or reaction-centre genes. The resulting system allows each pigment-protein complex to be studied either as part of an intact photosystem or as the sole complex in the cell. In this way we have demonstrated that reaction centres can assemble independently of either light-harvesting complex in R. sphaeroides. In addition, the isolation of derivatives of the deletion/insertion mutants exhibiting spontaneous mutations in carotenoid biosynthesis provides an avenue for examining the role of carotenoids in the assembly of the photosynthetic apparatus. We show that the LH1 complex is assembled regardless of the carotenoid background, and that the type of carotenoid present modifies the absorbance of the LH1 bacteriochlorophylls.

cis-acting regulatory elements involved in oxygen and light control of puc operon transcription in Rhodobacter sphaeroides

Transcriptional expression of the puc operon in Rhodobacter sphaeroides is highly regulated by both oxygen and light. The approximately 600 bp of DNA upstream of the 5' ends of the two puc-specific transcripts encompasses two functionally separable cis-acting domains. The upstream regulatory region (URS) (-629 to -150) is responsible for enhanced transcriptional regulation of puc operon expression by oxygen and light. The more proximal upstream region (downstream regulatory region [DRS]), containing putative promoter(s), operator(s), and factor binding sites (-150 to -1), is involved in unenhanced transcriptional expression of the puc operon under aerobic and anaerobic conditions. Thus, the DRS shows normal derepression of puc operon expression when cells are shifted from aerobic to photosynthetic growth conditions in terms of percent change but does not show the potential range of expression that is only observed when elements of the URS are present. Because of these observations, we have made a distinction between anaerobic control (describing the shift) and oxygen control (describing the magnitude of derepression). Promoter(s) and/or activator function(s) of the puc operon is associated with a 35-bp DNA region between -92 and -57. Homologous sequences at -10 to -27 and -35 to -52 appear to involve additional regulatory elements: mutations at -12 (A to C) and -26 (G to A) result in partial derepression of puc operon expression under conditions of high aeration. Both point mutations require the upstream regulatory region (-629 to -150) to be present in cis for partial derepression of puc operon transcription under aerobic conditions. Immediately upstream of the promoter and/or activator region are overlapping consensus sequences for IHF (integratin host factor) and FNR (fumarate nitrate reductase) (-105 to -129). This region appears to be essential for enhanced expression of the puc operon. Thus, these two regulatory domains (URS and DRS) appear to involve approximately seven unique regulatory elements. In addition, the data reveal a direct interaction between the URS (-629 to -150) and the DRS (-150 to -1).

Isolation and characterization of trans-acting mutations involved in oxygen regulation of puc operon transcription in Rhodobacter sphaeroides

Transcriptional expression of the puc operon in Rhodobacter sphaeroides 2.4.1 is dependent on the partial pressure of oxygen. By using transcriptional fusions in trans of a promoterless fragment derived from the aminoglycoside-3'-phosphotransferase gene of Tn903 to puc operon-specific DNA containing a 629-bp 5' cis-acting regulatory region involved in the expression of puc-specific mRNA, we selected Kmr colonies under aerobic conditions. Two broad classes of mutations, trans and cis, which are involved in O2 control of puc operon transcription, fall into several distinct phenotypic classes. The cis-acting regulatory mutations are characterized in detail elsewhere (J.K. Lee and S. Kaplan, J. Bacteriol. 174:1146-1157, 1992). Two trans-acting regulatory mutants, CL1a and T1a, which are B800-850- Car- and apparently B875-, respectively, were shown to derepress puc operon transcription in the presence of oxygen. The mutation giving rise to CL1a has been shown to act at the puc operon-specific cis-acting upstream regulatory region (-629 to -92). On the other hand, the mutation giving rise to T1a, identifying a second trans-acting regulatory factor(s), appears to act at both the upstream (-629 to -92) and the downstream (-92 to -1) regulatory regions of the puc operon as well as at the level(s) of bacteriochlorophyll and carotenoid biosyntheses, as revealed by the presence of the B800-850 complex under chemoheterotrophic growth conditions. Both the B800-850- Car- phenotype and the trans-acting effect on puc operon expression in mutant CL1a were complemented with a 2.2-kb DNA fragment located within the carotenoid gene cluster. Mutant T1a was complemented with a 7.0-kb EcoRI restriction fragment containing the puhA gene and its flanking DNA (6.3 kb) to restore expression of the B875 complex and to suppress the trans-acting effect resulting in the loss of 02 control. Under chemoheterotrophic conditions, mutant T1a was highly unstable, segregating into a PS- mutant designated T4.

A base pair transition in a DNA sequence with dyad symmetry upstream of the puf promoter affects transcription of the puc operon in Rhodobacter capsulatus

A DNA sequence with dyad symmetry upstream of the transcriptional start of the Rhodobacter capsulatus puf operon, which encodes pigment-binding proteins of the light-harvesting I complex and of the reaction center, has previously been shown to be a protein-binding site (G. Klug, Mol. Gen. Genet. 226:167-176, 1991). When a low-copy-number plasmid with a base pair transition at position -43 within this dyad symmetry in front of the puf structural genes was transferred into a Rhodobacter strain with the puf operon deleted, different phenotypes occurred during cultivation of the transconjugants and the kinetics of the loss of the wild-type phenotype was dependent on the oxygen tension in the culture. After growth for 150 generations, the different phenotypes were stably inherited. The strains having the wild-type phenotype carried the wild-type puf DNA sequence. The original mutation was still present in the strains that showed lighter color. These strains had less light-harvesting II complex in the membrane and showed lower rates of transcription of the puc operon, which encodes the proteins of this complex. This deregulation of puc expression was due to one or more chromosomally located, secondary mutations, not directly to the mutation present on the plasmid. Thus, a single-base-pair transition in the puf upstream region can result in a deregulation of puc expression, suggesting a direct or indirect transcriptional coregulation of both these operons by a common factor.

The superoperonal organization of genes for pigment biosynthesis and reaction center proteins is a conserved feature in Rhodobacter capsulatus: analysis of overlapping bchB and puhA transcripts

Most of the essential biosynthetic and structural genes involved in bacterial photosynthesis are clustered in a 46 kb region of the Rhodobacter capsulatus genome. Previous analyses have demonstrated that the puf operon, which encodes light harvesting and reaction center structural genes as well as a regulatory gene for bacteriochlorophyll biosynthesis, is expressed from a complex set of overlapping transcripts. Differential initiation and processing of these transcripts is thought to be involved in regulating expression of puf-encoded genes. In this study we demonstrate that the puh operon, which is located 39 kb away from the puf operon, also contains overlapping transcripts. One large 11 kb puhA transcript is shown to be a product of read-through from an upstream operon (bchB) which encodes numerous bacteriochlorophyll biosynthesis genes. A second 1.1 kb mRNA is shown to be derived from the 11 kb bchB transcript by processing and a third, highly expressed, 0.95 kb transcript is shown to be initiated from a promoter located within the distal gene of the bchB operon. The occurrence of overlapping transcripts for the puf and puh operons was further shown to influence development of the photochemical apparatus during conditions of environmental shifts in oxygen tension. Evidence for the occurrence of a "superoperonal" organization of overlapping operons in several different species of purple photosynthetic bacteria is discussed.

Photosynthetic reaction centers: interfacing molecular genetics and optical spectroscopy

In the elucidation of the mechanism by which certain photosynthetic bacteria convert light into chemical energy, genetics has become intertwined with biophysical techniques. While X-ray crystallography has yielded an atomic resolution structure of the photosynthetic reaction center (RC), optical spectroscopy remains the most important technique for screening mutants. Newly developed imaging devices and genetic techniques should enable biophysicists to characterize rapidly the spectra of extremely large numbers of RC and light harvesting (LH) antennae mutants. The intrinsic pigments of the RC and LH antennae act as spectroscopic reporters for assembly and function of these integral membrane proteins. To optimize this genetics/spectroscopy interface, new algorithms that relate the structure of the genetic code to the physico-chemical properties of the amino acids are being developed to design libraries of mutants.

A DNA sequence upstream of the puf operon of Rhodobacter capsulatus is involved in its oxygen-dependent regulation and functions as a protein binding site

The transcription of the polycistronic puf operon which encodes pigment binding proteins of the reaction center and light-harvesting complex I of Rhodobacter capsulatus is regulated by the oxygen tension in the culture. A DNA sequence upstream of the puf transcriptional start was identified as a protein binding site. A DNA fragment carrying this DNA sequence participated in the formation of two DNA-protein complexes. The relative amounts of the two complexes were dependent on the oxygen tension in cultures from which the cytosolic fraction used for the in vitro binding studies was isolated. A single base pair transition within the protein binding site affected the oxygen-dependent expression of puf in vivo and the formation of DNA-protein complexes in vitro. The data suggest that the formation of specific DNA-protein complexes is involved in the oxygen-dependent regulation of the puf promoter. A DNA fragment containing the promoter region of the puc operon that encodes proteins of the light-harvesting complex II acted as a competitor for the formation of the DNA-protein complexes with the puf-specific fragment, indicating coregulation of the two operons.

Endonucleolytic degradation of puf mRNA in Rhodobacter capsulatus is influenced by oxygen

The formation of pigment-protein complexes in facultatively photosynthetic bacteria is regulated by the oxygen tension in the culture. It is shown that the degradation of some mRNA species encoding components of the photosynthetic apparatus is affected by oxygen. The puf mRNA segment, encoding the pigment-binding proteins of the reaction center, and the 0.5-kb puc mRNA species, encoding pigment-binding proteins of the light-harvesting LHII antenna complex of Rhodobacter capsulatus were degraded more rapidly under high oxygen tension than under low oxygen tension. Studies on strains having deletions or insertions in the puf operon indicate that rate-limiting endonucleolytic cleavage in the reaction center coding region of the polycistronic puf mRNA was influenced by growth conditions. However, other mRNA segments, for which exonucleolytic degradation was postulated to be rate-limiting, decayed with the same rate under either high or low oxygen tension. Likewise, the degradation of the puhA mRNA, the cycA mRNA, and the cytfbc mRNA was found to be independent of the oxygen tension in the culture. The data strongly suggest that specific mRNA sequences or structures are responsible for the observed oxygen effect on mRNA stability.

Overlapping mRNA transcripts of photosynthesis gene operons in Rhodobacter capsulatus

The crtEF, bchCA, and puf operons of the facultative phototrophic bacterium Rhodobacter capsulatus encode gene products that are necessary for the formation of various components of the photosynthetic apparatus. The crtEF operon encodes two enzymes involved in the biosynthesis of carotenoids, the bchCA operon codes for two enzymes of the bacteriochlorophyll biosynthetic pathway, and the puf operon encodes four pigment-binding polypeptides as well as two polypeptides with less well understood functions. These three operons are adjacent to one another on the chromosome and are transcribed in the same direction. We present the results of RNA blotting and S1 nuclease protection end-mapping experiments which provide direct evidence that the mRNA transcripts of these three operons overlap. Therefore, it is likely that the crtEF, bchCA, and puf operons can be expressed as a single transcriptional unit, although RNA polymerase may initiate transcription at any of several promoters.

A negatively charged N terminus in the alpha polypeptide inhibits formation of light-harvesting complex I in Rhodobacter capsulatus

Light-harvesting complex I (LHI) of Rhodobacter capsulatus contains bacteriochlorophyll and carotenoids which are noncovalently bound to two different apoproteins (alpha and beta polypeptides) carrying oppositely charged N-terminal ends. The contribution of these charged segments to the assembly of LHI was studied with mutants having oppositely charged amino acids in the alpha or beta polypeptide. The influence of these mutations on the insertion and assembly process of the LHI complex was investigated by means of spectroscopic analysis of isolated intracytoplasmic membranes and pulse-chase experiments. Exchange of four positively charged amino acids to negatively charged amino acids on the N-terminal domain of the alpha subunit inhibited completely the assembly of the LHI complex. Although this mutant has no antenna, the reaction center is active and the cells were able to grow anaerobically in the light. Conversely, mutation of the four negatively charged amino acids of the N-terminal segment of the beta polypeptide did not prevent the assembly of the LHI complex, although the stability of the complex and the size of the photosynthetic unit were affected. The presence of the mutated beta polypeptide was confirmed by protein sequencing.

Effects on the formation of antenna complex B870 of Rhodobacter capsulatus by exchange of charged amino acids in the N-terminal domain of the alpha and beta pigment-binding proteins

The N-terminal domains of the alpha and beta polypeptides of the B870 antenna complex of Rhodobacter capsulatus are oppositely charged. In both polypeptides two charged amino acids are located close to the N-terminus, and two of them are close to the hydrophobic central domain. To test the hypothesis that charged amino acids in the N-terminus have a function for insertion and assembly of pigment-binding polypeptides, charged amino acids were replaced by amino acids of opposite charge. The results show that an exchange of amino acid positions 3 and 6 in alpha (Lys----Glu) or 2 and 5 in beta (Asp----Lys, Arg) has little effect under semiaerobic conditions on the formation of B870 but the additional exchange of positions 14 and 15 in alpha (Arg----Glu, Asp) and/or 13 and 14 in beta (Asp, Glu----Arg) inhibits strongly under semiaerobic dark and anaerobic light conditions the stable incorporation of the polypeptides into the membrane and the formation of the B870 complex. The mutant U43(pTXAB5) is able to grow without any antenna.

Development of a cell-free system to study the membrane assembly of photosynthetic proteins of Rhodobacter capsulatus

A cell-free translation system from the facultatively photoheterotrophic bacterium Rhodobacter capsulatus is described. Synthesis of two proteins of the bacterium's photosynthetic apparatus (light-harvesting complex B870 alpha and beta) was performed by SP6 polymerase transcription of the subcloned genes, isolation of the mRNA and translation in vitro using a cell-free extract of R. capsulatus cells. The integration of these proteins in vitro into added intracytoplasmic membrane vesicles (ICM) is demonstrated. Without addition of ICM approximately 70% of the synthesized B870 proteins were soluble. If, however, ICM were present during synthesis, the majority of the soluble protein was found to associate with the membranes. The membrane-associated polypeptides could be solubilized only by detergent treatment but could not be extracted by treatment at alkaline pH (Na2CO3), suggesting that the proteins had been firmly inserted into the lipid bilayer. Moreover, the B870 alpha and beta proteins that integrated in vitro into ICM were also found to associate with pigment ligands and to assemble into a native reaction center/B870 complex. The native conformation of this complex isolated from ICM by Triton fractionation was demonstrated by microspectral analysis of the bound pigments.

Cloning and sequencing of the hemA gene of Rhodobacter capsulatus and isolation of a delta-aminolevulinic acid-dependent mutant strain

The Rhodobacter capsulatus hemA gene, coding for the enzyme delta-aminolevulinic acid synthase (ALAS), was isolated from a genome bank by hybridization with a hemT probe from Rhodobacter sphaeroides. Subcloning of the initial 3.9 kb HindIII fragment allowed the isolation of a 2.5 kb HindIII-BglII fragment which was able to complement the delta-aminolevulinic acid-requiring (ALA-requiring) Escherichia coli mutant SHSP19. DNA sequencing revealed an open reading frame coding for a protein with 401 amino acids which displayed similarity to the amino acid sequences of other known ALASs. However, no resemblance was seen to the HemA protein of E. coli K12. Based on the sequence data, an ALA-requiring mutant strain of R. capsulatus was constructed by site-directed insertion mutagenesis. Introduction of a plasmid, containing the hemA gene of R. capsulatus on the 3.9 kb HindIII fragment, restored ALA-independent growth of the mutant indicating that there is only one gene for ALA biosynthesis in R. capsulatus. Transfer of the R' factor pRPS404 and hybridization analysis revealed that the ALAS gene is not located within the major photosynthetic gene cluster.