In vivo analysis of puf operon expression in Rhodobacter sphaeroides after deletion of a putative intercistronic transcription terminator

PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase

Facultative phototrophs such as Rhodobacter sphaeroides can switch between heterotrophic and photosynthetic growth. This transition is governed by oxygen tension and involves the large-scale production of bacteriochlorophyll, which shares a biosynthetic pathway with haem up to protoporphyrin IX. Here, the pathways diverge with the insertion of Fe2+ or Mg2+ into protoporphyrin by ferrochelatase or magnesium chelatase, respectively. Tight regulation of this branchpoint is essential, but the mechanisms for switching between respiratory and photosynthetic growth are poorly understood. We show that PufQ governs the haem/bacteriochlorophyll switch; pufQ is found within the oxygen-regulated pufQBALMX operon encoding the reaction centre-light-harvesting photosystem complex. A pufQ deletion strain synthesises low levels of bacteriochlorophyll and accumulates the biosynthetic precursor coproporphyrinogen III; a suppressor mutant of this strain harbours a mutation in the hemH gene encoding ferrochelatase, substantially reducing ferrochelatase activity and increasing cellular bacteriochlorophyll levels. FLAG-immunoprecipitation experiments retrieve a ferrochelatase-PufQ-carotenoid complex, proposed to regulate the haem/bacteriochlorophyll branchpoint by directing porphyrin flux toward bacteriochlorophyll production under oxygen-limiting conditions. The co-location of pufQ and the photosystem genes in the same operon ensures that switching of tetrapyrrole metabolism toward bacteriochlorophyll is coordinated with the production of reaction centre and light-harvesting polypeptides.

Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: transcriptome flexibility at diverse growth modes

A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes--aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis--were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirrored known functional changes, suggesting that massive changes in gene expression are the major means used by R. sphaeroides in adaptation to diverse conditions. Differential expression was observed for genes encoding putative new participants in these pathways (additional photosystem genes, duplicate NADH dehydrogenase, ATP synthases), whose functionality has yet to be investigated. The DNA microarray data correlated well with data derived from quantitative reverse transcription-PCR, as well as with data from the literature, thus validating the R. sphaeroides genechip as a powerful and reliable tool for studying unprecedented metabolic versatility of this bacterium.

Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple photosynthetic bacteria

To understand the evolutionary relationship between triheme and tetraheme cytochrome subunits in the reaction center complex, genes located downstream of that coding for the M subunit of the reaction center complex (pufM) were amplified by PCR and analyzed in six established and two unidentified species of the genus Rhodovulum and five species of the genus Rhodobacter. All the Rhodovulum species tested had the pufC gene coding for the reaction-center-bound cytochrome subunit, while all the Rhodobacter species were found to have the pufX gene at the corresponding position. Analyses of the amino acid sequences of the pufC gene products showed that the cytochrome subunits of all the Rhodovulum species have three heme-binding-motifs and lack a methionine residue probably working as the sixth axial-ligand to one of the three hemes. Phylogenetic relationships among Rhodovulum species based on the pufC gene products were basically consistent with those based on 16S rRNA sequences, suggesting that the basic characteristics of the triheme cytochrome subunit have been conserved during the evolutionary process of the Rhodovulum species.

The protein complex composed of nickel-binding SrnQ and DNA binding motif-bearing SrnR of Streptomyces griseus represses sodF transcription in the presence of nickel

Nickel-responsive transcriptional repression of sodF, which codes for iron- and zinc-containing superoxide dismutase of Streptomyces griseus, was mediated through an operator (-2 to +15) spanning over the 5' end (+1) of the transcript. Two open reading frames, SrnR (12,343 Da) and SrnQ (12,486 Da), with overlapping stop-start codons were identified downstream from sodF and found responsible for the repression of sodF. The deduced amino acid sequence of SrnR revealed a DNA binding motif and showed homology to the transcriptional regulators of ArsR family, whereas SrnQ did not show any similarity to any known proteins. When srnRQ DNA was maintained in trans in S. griseus on a multicopy plasmid, sodF transcription was highly repressed by nickel, but neither srnR nor srnQ alone showed the effect. Consistently, the sodF transcription of srnR-interrupted mutant was no longer repressed by nickel, which was complemented only with srnRQ DNA. Nickel-dependent binding of SrnR and SrnQ to the sodF operator DNA was observed only when the two proteins were provided together. The maximum protein-DNA interaction was shown when SrnR and SrnQ were present in one-to-one stoichiometric ratio. The two proteins appear to constitute an octamer composed of four subunits of each protein. SrnR directly interacted with SrnQ, and the protein interaction did not require nickel. The conformation of SrnQ was changed upon nickel binding, which was in the ratio of one Ni(2+) ion per protein molecule. A model is proposed in which SrnQ of the protein complex senses nickel and subsequently enhances the DNA binding activity of SrnR through the protein-protein interaction.

Sequence analysis reveals new membrane anchor of reaction centre-bound cytochromes possibly related to PufX

Most of the bacterial photosynthetic reaction centres known to date contain a cytochrome subunit with four covalently bound haem groups. In the case of Blastochloris viridis, this reaction centre subunit is anchored in the membrane by a lipid molecule covalently attached to the cysteine which forms the N-terminus of the mature protein after processing by a signal peptidase. We show that posttranslational N-terminal cleavage of the cytochrome subunit does not occur in the aerobic photosynthetic bacterium Roseobacter denitrificans. From sequence analysis of the resulting elongated N-terminus it follows that a transmembrane helix is anchoring the reaction centre-bound cytochrome in the membrane. Comparative sequence analysis strongly suggests that all cytochrome subunits lacking the lipid coupling cysteine share this structural feature. Comparison of the N-terminal segment of the cytochrome subunit of Roseobacter denitrificans with the sequences of the PufX proteins from Rhodobacter sphaeroides and Rhodobacter capsulatus suggests a phylogenetic relation.

Transcription of three sets of genes coding for the core light-harvesting proteins in the purple sulfur bacterium, Allochromatium vinosum

The nucleotide sequence of the puf operon coding for the subunits of the photosynthetic reaction center and the core light-harvesting complex (LH1) of the purple sulfur bacterium, Allochromatium (A.) vinosum (formally Chromatium vinosum), was completely determined. Unlike other known puf operons, which contain only one set of genes coding for the LH1 apoproteins, pufB and pufA, the A. vinosum puf operon included three sets of pufB and pufA genes with a gene order of pufB (1) A (1) LMCB (2) A (2) B (3) A (3). Northern hybridization analysis suggested that all of the nine puf genes are co-transcribed as a 4.43 kb mRNA. Three small mRNAs corresponding to pufB (2) A (2) B (3) A (3), pufB (2) A (2) B (3), and pufB (2) A (2) were detected, as well as two small mRNAs covering pufB (1) A (1). Analysis of the nucleotide sequence of the puf operon, including the flanking regions and 5'-ends of the six mRNAs, suggested that the transcription of the A. vinosum puf operon is initiated at 74 bp downstream from the bchZstop codon (295 bp upstream from the pufB (1) start codon), and regulated by a promoter located at its direct upstream. The possible promoter is overlapped with a binding motif of a repressor protein for pigment-biosynthesis genes, PpsR or CrtJ, known in other purple bacteria. No other possible promoters were found within the puf genes. These findings indicate that three sets of pufA and pufB genes of A. vinosum are co-transcribed as a long mRNA containing all the puf genes, and, from this long mRNA, the five short mRNAs are possibly derived by post-transcriptional modifications.

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

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

Transcriptional control of expression of genes for photosynthetic reaction center and light-harvesting proteins in the purple bacterium Rhodovulum sulfidophilum

The purple photosynthetic bacterium Rhodovulum sulfidophilum synthesizes photosynthetic apparatus even under highly aerated conditions in the dark. To understand the oxygen-independent expression of photosynthetic genes, the expression of the puf operon coding for the light-harvesting 1 and reaction center proteins was analyzed. Northern blot hybridization analysis showed that puf mRNA synthesis was not significantly repressed by oxygen in this bacterium. High-resolution 5' mapping of the puf mRNA transcriptional initiation sites and DNA sequence analysis of the puf upstream regulatory region indicated that there are three possible promoters for the puf operon expression, two of which have a high degree of sequence similarity with those of Rhodobacter capsulatus, which shows a high level of oxygen repression of photosystem synthesis. Deletion analysis showed that the third promoter is oxygen independent, but the activity of this promoter was not enough to explain the aerobic level of mRNA. The posttranscriptional puf mRNA degradation is not significantly influenced by oxygen in R. sulfidophilum. From these results, we conclude that puf operon expression in R. sulfidophilum is weakly repressed by oxygen, perhaps as a result of the following: (i) there are three promoters for puf operon transcription, at least one of which is oxygen independent; (ii) readthrough transcripts which may not be affected by oxygen may be significant in maintaining the puf mRNA levels; and (iii) the puf mRNA is fairly stable even under aerobic conditions.

Expression of the Pseudomonas aeruginosa gentamicin resistance gene aacC3 in Escherichia coli

The Pseudomonas aeruginosa aacC3 gene was expressed in Escherichia coli after cloning of the single gene behind the strong tac promoter. In the original Pseudomonas strain, aacC3 is preceded by cysC; together they form a single transcription unit. The ribosome-binding site and start codon of aacC3 are involved in a putative intercistronic hairpin, the stability of which interfered with the aminoglycoside resistance level. In Northern blots, full-length transcripts comprising both cysC and aacC3 could not be detected either in the original Pseudomonas strain or in E. coli harboring a plasmid with the cloned operon. In contrast, cysC transcripts were abundant. Cloning of the operon between the tac promoter and a transcription termination signal resulted in higher mRNA levels and phenotypic expression in E. coli. The absence of a transcription termination signal in the wild-type cysC-aacC3 sequence is associated with transcripts of heterogeneous size that were undetected in Northern blots. Our results shed more light on the expression of this gentamicin resistance determinant, although the discrepancies between its expression in E. coli and Pseudomonas are not fully solved.

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

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

Regulation of CO2 assimilation in Ralstonia eutropha: premature transcription termination within the cbb operon

In the facultatively chemoautotrophic bacterium Ralstonia eutropha (formerly Alcaligenes eutrophus), most genes required for CO2 assimilation via the Calvin cycle are organized within two highly homologous cbb operons located on the chromosome and on megaplasmid pHG1, respectively, of strain H16. These operons are subject to tight control exerted by a promoter upstream of the 5'-terminal cbbL gene that is regulated by the activator CbbR. The existence of subpromoters within the operons was now excluded, as determined with lacZ operon fusions to suitable cbb gene fragments in the promoter-probe vector pBK. Nevertheless, marked differential expression of the promoter-proximal ribulose-1,5-bisphosphate carboxylase-oxygenase genes cbbLS and the remaining distal genes occurs within the operons. Computer analysis revealed a potential stem-loop structure immediately downstream of cbbS that was suspected to be involved in the differential gene expression. Nuclease S1 mapping identified a major 3' end and a minor 3' end of the relatively stable cbbLS partial transcript just downstream of this structure. Moreover, operon fusions containing progressively deleted stem-loop structures showed that the structure primarily caused transcriptional termination downstream of cbbS rather than increased the segmental stability of the cbbLS transcript. Premature transcription termination thus represents an important mechanism leading to differential gene expression within the cbb operons.

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

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

Identification of cis-acting regulatory regions upstream of the rRNA operons of Rhodobacter sphaeroides

The promoter region(s) for the rRNA operons of Rhodobacter sphaeroides was identified. By utilizing both in vivo and in vitro techniques, the transcriptional start sites of all three operons were identified. Upstream of the transcriptional start, -10 and -35 promoter regions that bear little similarity to typical Escherichia coli promoter sequences were identified. In addition to the promoter sequences, probable Fis protein-binding sites were identified upstream of all three rRNA operons. Transcriptional fusions of the promoter regions from rrnA and rrnB were constructed by utilizing the reporter molecule encoded by xylE and analyzed under various growth conditions, in both a wild-type background and an rrnBC mutant background. Production of the xylE gene product (catechol 2,3-dioxygenase) was always greatest under photosynthetic growth conditions. However, the upstream region of rrnB, when fused with xylE, produced significantly more catechol 2,3-dioxygenase than did analogous regions of rrnA, suggesting that the promoters of the rrn operons differ in strength. These results were further confirmed by the study of mutant strains altered for the rrn operons either singly or in combination. Little or no expression of the xylE gene was manifest in E. coli when directed by rDNA sequences derived from R. sphaeroides.

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.

Mutational analysis of segmental stabilization of transcripts from the Zymomonas mobilis gap-pgk operon

In Zymomonas mobilis, the genes encoding glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase are transcribed together from the gap-pgk operon. However, higher levels of the former enzyme are present in the cytoplasm because of increased stability of a 5' segment containing the gap coding region. This segment is bounded by an upstream untranslated region which can be folded into many stem-loop structures and a prominent intercistronic stem-loop. Mutations eliminating a proposed stem-loop in the untranslated region or the intercistronic stem-loop resulted in a decrease in the stability and pool size of the 5' gap segment. Site-specific mutations in the unpaired regions of both of these stems also altered the message pools. Elimination of the intercistronic stem appeared to reduce the endonucleolytic cleavage within the pgk coding region, increasing the stability and abundance of the full-length message. DNA encoding the prominent stem-loop at the 3' end of the message was shown to be a transcriptional terminator both in Z. mobilis and in Escherichia coli. This third stem-loop region (part of the transcriptional terminator) was required to stabilize the full-length gap-pgk message.

5-Aminolevulinic acid availability and control of spectral complex formation in hemA and hemT mutants of Rhodobacter sphaeroides

In the photosynthetic bacterium Rhodobacter sphaeroides, two genes, hemA and hemT, each encode a distinct 5-aminolevulinic acid (ALA) synthase isozyme (E. L. Neidle and S. Kaplan, J. Bacteriol. 175:2292-2303, 1993). This enzyme catalyzes the first and rate-limiting step in a branched pathway for tetrapyrrole formation, leading to the biosynthesis of hemes, bacteriochlorophylls, and corrinoids. In an attempt to determine the functions of hemA and hemT, mutant strains were constructed with specific chromosomal disruptions. These chromosomal disruption allowed hemA and hemT to be precisely localized on the larger and smaller of two R. sphaeroides chromosomes, respectively. Mutants carrying a single hemA or hemT disruption grew well without the addition of ALA, whereas a mutant, HemAT1, in which hemA and hemT had both been inactivated required exogenous ALA for growth. The growth rates, ALA synthase enzyme levels, and the amounts of bacteriochlorophyll-containing intracytoplasmic membrane spectral complexes of all strains were compared. Under photosynthetic growth conditions, the levels of bacteriochlorophyll, carotenoids, and B800-850 and B875 light-harvesting complexes were significantly lower in the Hem mutants than in the wild type. In the mutant strains, available bacteriochlorophyll appeared to be preferentially targeted to the B875 light-harvesting complex relative to the B800-850 complex. In strain HemAT1, the amount of B800-850 complex varied with the concentration of ALA added to the growth medium, and under conditions of ALA limitation, no B800-850 complexes could be detected. In the Hem mutants, there were aberrant transcript levels corresponding to the puc and puf operons encoding structural polypeptides of the B800-850 and B875 complexes. These results suggest that hemA and hemT expression is coupled to the genetic control of the R. sphaeroides photosynthetic apparatus.

Control of photosystem genes in Rhodobacter capsulatus

Two environmental factors, oxygen and high light intensity, are known to repress synthesis of the Rhodobacter capsulatus photosystem. One level of regulation is the control of light harvesting and reaction centre gene expression at the point of transcription initiation. This has recently been shown to involve transcriptional activators which exhibit sequence similarity to members of the 'two-component' class of prokaryotic regulators. An additional level of regulation involves the formation of 'superoperons' that transcriptionally link pigment biosynthesis operons with operons that code for the light harvesting and reaction centre structural genes. A final level of regulation involves the selective degradation of reaction centre mRNA transcripts which influence the stoichiometric synthesis of the light harvesting and reaction centre complexes.

Construction and characterization of a mutant of Rhodobacter sphaeroides with the reaction center as the sole pigment-protein complex

A strain of Rhodobacter sphaeroides has been constructed in which the photosynthetic reaction center is the sole pigment-protein complex. The strain, named RCO1, is capable of photoheterotrophic growth and possesses assembled and functional reaction centers which can undergo photochemical charge separation and are reduced by electrons derived from the cytochrome b/c1 complex. The circular dichroism and linear dichroism of reaction centers in membranes from strain RCO1 are similar to those described previously for reaction centers isolated in detergent solution. A second strain, named RCLH11, which is devoid of the peripheral LH2 antenna complex has also been constructed. A description of the properties of these strains is presented.

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.

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

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

Construction, characterization, and complementation of Rhodospirillum rubrum puf region mutants

Rhodospirillum rubrum is a facultatively phototrophic bacterium that, under certain growth conditions, forms an intracytoplasmic chromatophore membrane (ICM) housing the photochemical apparatus. The puf operon of R. rubrum encodes protein subunits of the photochemical reaction center and the B880 light-harvesting antenna complex. Mutant strains of R. rubrum were constructed by interposon mutagenesis through which a kanamycin resistance gene cartridge was inserted into restriction sites and in place of restriction fragments of the puf region. Southern blot analysis demonstrated that the defective copies of puf sequences had replaced their normal chromosomal counterparts through homologous recombination. The phenotypes of the mutant strains were evaluated on the basis of puf gene expression, spectral analysis, pigment content of membranes, and electron-microscopic examination of thin sections of cells grown under semi-aerobic and dark anaerobic conditions. Alterations of the puf region affect phototrophic competence and the formation of the ICM. The latter result implies an obligatory role for puf gene products in ICM formation in R. rubrum. One mutant with a deletion in puf structural genes was complemented in trans to the wild-type phenotype. Other mutants could be restored to the wild-type phenotype only by recombination.

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.

Segmental message stabilization as a mechanism for differential expression from the Zymomonas mobilis gap operon

In Zymomonas mobilis, three- to fourfold more glyceraldehyde-3-phosphate dehydrogenase protein than phosphoglycerate kinase is needed for glycolysis because of differences in catalytic efficiency. Consistent with this requirement, higher levels of glyceraldehyde-3-phosphate dehydrogenase were observed with two-dimensional polyacrylamide gel electrophoresis. The genes encoding these enzymes (gap and pgk, respectively) form a bicistronic operon, and some form of regulation is required to provide this differential expression. Two transcripts were observed in Northern RNA analyses with segments of gap as a probe: a more abundant 1.2-kb transcript that contained gap alone and a 2.7-kb transcript that contained both genes. Based on the relative amounts of these transcripts, the coding regions for glyceraldehyde-3-phosphate dehydrogenase were calculated to be fivefold more abundant than those for phosphoglycerate kinase. Assuming equal translational efficiency, this is sufficient to provide the observed differences in expression. Operon fusions with lacZ provided no evidence for intercistronic terminators or attenuation mechanisms. Both gap operon messages were very stable, with half-lives of approximately 16 min (1.2-kb transcript) and 7 min (2.7-kb transcript). Transcript mapping and turnover studies indicated that the shorter gap message was a stable degradation product of the full-length message. Thus differential expression of gap and pgk results primarily from increased translation of the more stable 5' segment of the transcript containing gap. The slow turnover of the messages encoding glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase is proposed as a major feature contributing to the high level of expression of these essential enzymes.

Differential stability of mRNA species of Alcaligenes eutrophus soluble and particulate hydrogenases

The functional half-lives of Alcaligenes eutrophus hydrogenase mRNAs were determined by physiological studies. Evidence was obtained for a functional half-life of about 1 h for the soluble NAD-linked hydrogenase (HoxS) mRNA and 14 min for the particulate hydrogenase (HoxP) mRNA. The synthesis of active HoxS continued for about 4 h, albeit at a decreasing rate after inhibition of transcription, e.g., by rifampin. In this strain, the mRNA of HoxS appeared to be stable, while the mRNA of HoxP did not. Different species of hoxS mRNA were detected by the Northern (RNA) hybridization technique using as a probe plasmid pCH139 carrying hoxS structural genes. The sizes of the major hoxS mRNA species were 7.6, 6.2, 5.0, and 0.9 kb. The chemical half-lives of these species ranged from 1 h (5.0-kb mRNA) to 7 h (0.9-kb mRNA). Evidence for a specific cleavage of the 6.2-kb transcript yielding the 0.9-kb species was obtained from RNA-DNA hybridizations with subcloned hoxS DNA. The chemical half-life of total hoxP mRNA was 8 min.

Gene encoding the 5.7-kilodalton chlorosome protein of Chloroflexus aurantiacus: regulated message levels and a predicted carboxy-terminal protein extension

The major light-harvesting pigment of the green filamentous bacterium Chloroflexus aurantiacus is bacteriochlorophyll (Bchl) c, localized in chlorosomes attached to the inner surface of the cytoplasmic membrane. Chlorosomes consist of four polypeptides and associated pigments and lipids. Previous studies of the inducible assembly of the photosynthetic apparatus had indicated that the major chlorosomal polypeptides are present as high-molecular-weight aggregates before the appearance of mature chlorosomes, and a mechanism for posttranslational processing of a polyprotein had been proposed. We have isolated the gene (csmA) encoding the 5.7-kilodalton chlorosomal polypeptide from C. aurantiacus in order to determine whether this protein is synthesized as part of a polyprotein. Analysis of the nucleotide sequence of csmA indicates that the gene is not large enough to encode more than one known chlorosome polypeptide. Transcriptional analysis indicates that csmA is transcribed as a small message whose abundance is regulated in response to oxygen, so that no csmA message is detectable in cells grown aerobically in the dark. Comparison of the sequence predicted by csmA with the peptide sequence of the Bchl c binding protein purified from chlorosomes indicates that this protein is synthesized with a carboxy-terminal extension of 27 amino acids. We discuss possible roles for this carboxy-terminal extension in the assembly of chlorosomes.

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.

Localized transposon Tn5 mutagenesis of the photosynthetic gene cluster of Rhodobacter sphaeroides

Four genes essential for bacteriochlorophyll biosynthesis were known to be encoded within a 45 kb region of the Rhodobacter sphaeroides genome, the boundaries of which are defined by puh and puf genes for reaction-centre and light-harvesting LH1 complexes. The cluster is represented by eight overlapping inserts cloned in the mobilizable vector pSUP202. We have used localized transposon Tn5 mutagenesis to characterize this cluster further; a total of 87 independent insertions were generated which identify nine genes for bacteriochlorophyll biosynthesis, six for carotenoid biosynthesis, and puhA encoding the reaction-centre H subunit. This work provides an essential framework for a detailed study of the structure and expression of genes for photosynthesis in this bacterium.

Phosphoribulokinase activity and regulation of CO2 fixation critical for photosynthetic growth of Rhodobacter sphaeroides

The Rhodobacter sphaeroides genome contains two unlinked genetic regions each encoding numerous proteins involved in CO2 fixation which include phosphoribulokinases (prkA and prkB), ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcLS and rbcR) (P. L. Hallenbeck and S. Kaplan, Photosynth. Res. 19:63-71, 1988; F. R. Tabita, Microbiol. Rev. 52:155-189, 1988), and two open reading frames linked to rbcLS and rbcR, namely, cfxA and cfxB, respectively (P. L. Hallenbeck, R. Lerchen, P. Hessler, and S. Kaplan, J. Bacteriol. 172:1736-1748). In this study, we examined the unique role(s) of each phosphoribulokinase activity in the regulation of CO2 fixation. Strains were constructed which contain null mutations in prkA and/or prkB. Studies utilizing these strains suggested that CO2 fixation plays an essential role in attaining the cellular redox balance necessary for photoheterotrophic growth. The presence of an external electron acceptor can negate the requirement for CO2 for photoheterotrophic growth. Each form of phosphoribulokinase and ribulose 1,5-bisphosphate carboxylase/oxygenase was shown to have distinct roles in CO2 metabolism when cells were exposed to extremes in CO2 levels. Evidence is also presented which unequivocally demonstrated that regulation of the expression of the enzymes involved in CO2 metabolism is effective at the transcriptional level. Although the two regions of the DNA involved in CO2 fixation are physically unlinked, each region of the DNA can have a profound effect on the expression of the other region of the DNA.

Roles of CfxA, CfxB, and external electron acceptors in regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase expression in Rhodobacter sphaeroides

The Rhodobacter sphaeroides genome contains two unlinked genetic regions each encoding a series of proteins involved in CO2 fixation which include phosphoribulokinase (prkA and prkB) and ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcLS and rbcR) (P. L. Hallenbeck and S. Kaplan, Photosynth. Res. 19:63-71, 1988; F. R. Tabita, Microbiol. Rev. 52:155-189, 1988). We examined the effect of CO2 in the presence and absence of an alternate electron acceptor, dimethyl sulfoxide, on the expression of rbcR and rbcLS in photoheterotrophically grown R. sphaeroides. The expression of both rbcR and rbcLS was shown to depend on the CO2 concentration when succinate was used as the carbon source. It was also demonstrated that CO2 fixation is critical for photoheterotrophic growth but could be replaced by the alternative reduction of dimethyl sulfoxide to dimethyl sulfide. Dimethyl sulfoxide severely depressed both rbcR and rbcLS expression in cells grown photoheterotrophically at CO2 concentrations of 0.05% or greater. However, cells grown photoheterotrophically in the absence of exogenous CO2 but in the presence of dimethyl sulfoxide had intermediate levels of expression of rbcL and rbcR, suggesting partially independent control by limiting CO2 tension. We also present evidence for the existence of two gene products, namely, CfxA and CfxB, which are encoded by genes immediately upstream of rbcLS and rbcR, respectively. Strains were constructed which contained null mutations in cfxA and/or cfxB. Each mutation eliminated expression of the linked downstream rbc operon. Further, studies utilizing these strains demonstrated that each form of ribulose 1,5-bisphosphate carboxylase/oxygenase plays an essential role in maintaining the cellular redox balance during photoheterotrophic growth at differing CO2 concentrations.

Complementation of a reaction center-deficient Rhodobacter sphaeroides pufLMX deletion strain in trans with pufBALM does not restore the photosynthesis-positive phenotype

The puf operon in Rhodobacter sphaeroides is composed of the genes for the photosynthetic reaction center L and M subunits, light-harvesting antenna complex I, and one other open reading frame termed pufX. Complementation of a reaction center-deficient, photosynthetically incompetent pufLMX deletion strain in trans with a fragment containing the entire puf operon, including pufX and an additional 1,100 base pairs of DNA downstream of pufX, restored the reaction center and the photosynthesis-positive phenotype. Complementation of the same strain with pufBALM restores the reaction center to the level seen with the entire puf operon but not the photosynthesis-positive phenotype. Northern (RNA) blot analysis revealed that oxygen regulated transcription was not blocked in the absence of pufX and the downstream region. Spectroscopic and protein analyses indicated that the pigment-binding protein complexes, including the reaction center, were expressed and showed normal absorption characteristics. A 20% reduction in the amount of light-harvesting antenna complex II and a corresponding increase in the amount of light-harvesting antenna complex I were observed in the deletion strain harboring the plasmid with the puf insert lacking the pufX gene and the downstream region compared with those complemented with the entire puf operon and an additional downstream 1,100 base pairs.

Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences

RsrI DNA methyltransferase (M-RsrI) from Rhodobacter sphaeroides has been purified to homogeneity, and its gene cloned and sequenced. This enzyme catalyzes methylation of the same central adenine residue in the duplex recognition sequence d(GAATTC) as does M-EcoRI. The reduced and denatured molecular weight of the RsrI methyltransferase (MTase) is 33,600 Da. A fragment of R. sphaeroides chromosomal DNA exhibited M.RsrI activity in E. coli and was used to sequence the rsrIM gene. The deduced amino acid sequence of M.RsrI shows partial homology to those of the type II adenine MTases HinfI and DpnA and N4-cytosine MTases BamHI and PvuII, and to the type III adenine MTases EcoP1 and EcoP15. In contrast to their corresponding isoschizomeric endonucleases, the deduced amino acid sequences of the RsrI and EcoRI MTases show very little homology. Either the EcoRI and RsrI restriction-modification systems assembled independently from closely related endonuclease and more distantly related MTase genes, or the MTase genes diverged more than their partner endonuclease genes. The rsrIM gene sequence has also been determined by Stephenson and Greene (Nucl. Acids Res. (1989) 17, this issue).

Posttranscriptional control of puc operon expression of B800-850 light-harvesting complex formation in Rhodobacter sphaeroides

The puc operon of Rhodobacter sphaeroides comprises the pucBA structural genes which encode B800-850 light-harvesting beta and alpha polypeptides, respectively. Northern (RNA) blot hybridization analysis of puc operon expression has identified two pucBA-specific transcripts. The small (0.5-kilobase [kb]) transcript encodes the beta and alpha polypeptides and, under photoheterotrophic growth conditions, was approximately 200-fold more abundant than the large (2.3-kb) transcript. The 5' end of the 0.5-kb transcript was mapped at 117 nucleotides upstream from the start of pucB. The 3' ends of the 0.5-kb transcript were mapped to two adjacent nucleotides, which follow a stem-loop structure immediately 3' to the pucA stop codon. Two mutant strains, PUC705-BA and PUC-Pv, were constructed by replacement of the pucBA genes and adjacent DNA in the former case or by insertional interruption of the DNA downstream of the pucBA genes in the latter case. The two mutant strains were devoid of B800-850 complexes during photosynthetic growth but were otherwise apparently normal. The B800-850 phenotype of both PUC705-BA and PUC-Pv was not complemented in trans with a 2.5-kb PstI restriction endonuclease fragment extending from 0.75 kb upstream of pucBA to 1.3 kb downstream of pucBA, despite the presence of the 0.5-kb pucBA-specific transcript. Both of the mutant strains, however, showed restoration of B800-850 expression with a 10.5-kb EcoRI restriction endonuclease fragment in trans encompassing the 2.5-kb PstI fragment. Western immunoblot analysis revealed no B800-850-beta polypeptide as well as no polypeptide designated 15A in either mutant. Nonetheless, under photoheterotrophic growth conditions, the 0.5-kb pucBA-specific transcript was present in PUC-Pv, although no 2.3-kb transcript was detectable. We suggest that the DNA region immediately downstream of pucBA encodes a gene product(s) essential for translational or posttranslational expression of the B800-850 beta and alpha polypeptides.

Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences

A reaction center H- strain (RCH-) of Rhodobacter sphaeroides, PUHA1, was made by in vitro deletion of an XhoI restriction endonuclease fragment from the puhA gene coupled with insertion of a kanamycin resistance gene cartridge. The resulting construct was delivered to R. sphaeroides wild-type 2.4.1, with the defective puhA gene replacing the wild-type copy by recombination, followed by selection for kanamycin resistance. When grown under conditions known to induce intracytoplasmic membrane development, PUHA1 synthesized a pigmented intracytoplasmic membrane. Spectral analysis of this membrane showed that it was deficient in B875 spectral complexes as well as functional reaction centers and that the level of B800-850 spectral complexes was greater than in the wild type. The RCH- strain was photosythetically incompetent, but photosynthetic growth was restored by complementation with a 1.45-kilobase (kb) BamHI restriction endonuclease fragment containing the puhA gene carried in trans on plasmid pRK404. B875 spectral complexes were not restored by complementation with the 1.45-kb BamHI restriction endonuclease fragment containing the puhA gene but were restored along with photosynthetic competence by complementation with DNA from a cosmid carrying the puhA gene, as well as a flanking DNA sequence. Interestingly, B875 spectral complexes, but not photosynthetic competence, were restored to PUHA1 by introduction in trans of a 13-kb BamHI restriction endonuclease fragment carrying genes encoding the puf operon region of the DNA. The effect of the puhA deletion was further investigated by an examination of the levels of specific mRNA species derived from the puf and puc operons, as well as by determinations of the relative abundances of polypeptides associated with various spectral complexes by immunological methods. The roles of puhA and other genetic components in photosynthetic gene expression and membrane assembly are discussed.