Skip to main content
Log in

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

  • Published:
Molecular and General Genetics MGG Aims and scope Submit manuscript

Summary

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Armengod M, Lambíes E (1986) Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences. Gene 43:183–196

    Google Scholar 

  • Armstrong GA, Alberti M, Leach F, Hearst JE (1989) Nucleotide sequence, organization, and nature of the protein products of the carotenoid biosynthesis gene cluster of Rhodobacter capsulatus. Mol Gen Genet 216:254–268

    Google Scholar 

  • Barany F (1985) Single-stranded hexameric linkers: a system for in-phase insertion mutagenesis and protein engineering. Gene 37:111–123

    Google Scholar 

  • Bauer CE, Marrs BL (1988) Rhodobacter capsulatus puf operon encodes a regulatory protein (PufQ) for bacteriochlorophyll biosynthesis. Proc Natl Acad Sci USA 85:7074–7078

    Google Scholar 

  • Bauer CE, Young DA, Marrs BL (1988) Analysis of the Rhodobacter capsulatus puf operon. Location of the oxygen-regulated promoter region and the identification of an additional puf-encoded gene. J Biol Chem 263:4820–4827

    Google Scholar 

  • Belanger G, Gingras G (1988) Structure and expression of the puf operon messenger RNA in Rhodospirillum rubrum. J Biol Chem 263:7639–7645

    Google Scholar 

  • Belasco JG, Beatty JT, Adams CW, von Gabain A, Cohen SN (1985) Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxc transcript. Cell 40:171–181

    Google Scholar 

  • Berard J, Belanger G, Gingras G (1989) Mapping of the puh messenger RNAs from Rhodospirillum rubrum. J Biol Chem 264:10897–10903

    Google Scholar 

  • Biel AJ, Marrs BL (1983) Transcriptional regulation of several genes for bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata in response to oxygen. J Bacteriol 156:686–694

    Google Scholar 

  • Chen CA, Beatty TJ, Cohen SN, Belasco JG (1988) An intercistronic stem-loop structure functions as an mRNA decay terminator necessary but insufficient for puf mRNA stability. Cell 52:609–619

    Google Scholar 

  • Clayton RK (1966) Spectroscopic analysis of bacteriochlorophylls in vitro and in vivo. Photochem Photobiol 5:669–677

    Google Scholar 

  • Coomber SA, Chaudhri M, Connor A, Britton G, Hunter CN (1990) Localized transposon Tn5 mutagenesis of the photosynthetic gene cluster of Rhodobacter sphaeroides. Mol Microbiol 4:977–989

    Google Scholar 

  • DeHoff BS, Lee JK, Donahue TJ, Gumport RI, Kaplan S (1988) In vivo analysis of puf operon expression in Rhodobacter sphaeroides after deletion of a putative intercistronic transcription terminator. J Bacteriol 170:4681–4692

    Google Scholar 

  • DeMartini M, Inouye M (1978) Interaction between two major outer membrane proteins of E. coli: the matrix protein and lipoprotein. J Bacteriol 133:329–335

    Google Scholar 

  • Donahue TJ, Hoger JH, Kaplan S (1986) Cloning and expression of the Rhodobacter sphaeroides reaction center H gene. J Bacteriol 168:953–961

    Google Scholar 

  • Farchaus JW, Gruenberg H, Oesterhelt D (1990) Complementation of a reaction center-deficient Rhodobacter sphaeroides pufLMX deletion strain in trans with pufBALM does not restore photosynthesis-positive phenotype. J Bacteriol 172:977–985

    Google Scholar 

  • Gough JA, Murray NE (1983) Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol 166:1–19

    Google Scholar 

  • Hurlbert RE, Golecki JR, Drews G (1974) Isolation and characterization of Chromatium vinosum membranes. Arch Microbiol 101:169–185

    Google Scholar 

  • Jackson WJ, Prince RC, Stewart GJ, Marrs BL (1986) Energetic and topographic properties of a Rhodopseudomonas capsulata mutant deficient in the B870 complex. Biochemistry 25:8440–8446

    Google Scholar 

  • Jones R, Haselkorn R (1989) The DNA sequence of the Rhodobacter capsulatus ntrA, ntrB and ntrC gene analogues required for nitrogen fixation. Mol Gen Genet 215:507–516

    Google Scholar 

  • Klug G, Cohen SN (1988) Pleiotropic effects of localized Rhodobacter capsulatus puf operon deletions on pigment production of light-absorbing pigment-protein complexes. J Bacteriol 170:5814–5821

    Google Scholar 

  • Klug G, Adams CW, Belasco J, Doerge B, Cohen SN (1987) Biological consequences of segmental alterations in mRNA stability: effects of deletion of the intercistronic hairpin loop region of the R. capsulatus puf operon. EMBO J 6:3315–3520

    Google Scholar 

  • Lee JK, Kiley PJ, Kaplan S (1989a) Posttranscriptional control of puc operon expression of B800–850 light-harvesting complex formation in Rhodobacter sphaeroides. J Bacteriol 171:3391–3405

    Google Scholar 

  • Lee JK, DeHoff BS, Donohue TJ, Gumport RI, Kaplan S (1989b) Transcriptional analysis of puf operon expression of Rhodobacter sphaeroides 2.4.1 and an intercistronic transcription terminator mutant. J Biol Chem 262:19354–19365

    Google Scholar 

  • Marrs B (1981) Mobilization of the genes for photosynthesis from Rhodopseudomonas capsulata by a promiscuous plasmid. J Bacteriol 146:1003–1012

    Google Scholar 

  • Maxam AM, Gilbert W (1980) Sequencing end labeled DNA with base-specific chemical cleavages. Methods Enzymol 65:499–560

    Google Scholar 

  • Mead DA, Szczesna SE, Kemper B (1986) Single stranded DNA Blue T7 promoter plasmids a versatile tandem promoter system for cloning and protein engineering. Protein Engineering 1:67–74

    Google Scholar 

  • Minton NP (1984) Improved plasmid vectors for the isolation of translated lac gene fusions. Gene 31:269–273

    Google Scholar 

  • Narro ML, Adams CW, Cohen SN (1990) Isolation and characterization of Rhodobacter capsulatus mutants defective in oxygen regulation of the puf operon. J Bacteriol 172:4549–4554

    Google Scholar 

  • Normark S, Bergström S, Edlund T, Grundström T, Jaurin B, Lindberg FP, Olsson O (1983) Overlapping genes. Annu Rev Genet 17:499–525

    Google Scholar 

  • Prentki P, Krisch HM (1984) In vitro insertional mutagenesis with a selectable DNA fragment. Gene 29:303–313

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

    Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    CAS  PubMed  Google Scholar 

  • Scolnik PA, Haselkorn R (1984) Activation of extra copies of genes coding for nitrogenase in Rhodopseudomonas capsulata. Nature 307:289–292

    Google Scholar 

  • Shen V, Imamoto F, Schlessinger D (1982) RNase III cleavage of Escherichia coli β-galactosidase and tryptophan operon mRNA. J Bacteriol 150:1489–1494

    Google Scholar 

  • Socket RE, Donahue TJ, Varga AR, Kaplan S (1989) Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences. J Bacteriol 171:436–446

    Google Scholar 

  • Taylor DP, Cohen SN, Clark WG, Marrs BL (1983) Alignment of the genetic and restriction maps of the photosynthetic region of the Rhodopseudomonas capsulata chromosome by a conjugation-mediated marker rescue technique. J Bacteriol 154:580–590

    Google Scholar 

  • Tichy HV, Oberle B, Stiehle H, Schiltz E, Drews G (1989) Genes downstream from pucB and pucA are essential for formation of the B800–850 complex of Rhodobacter capsulatus. J Bacteriol 171:4914–4922

    Google Scholar 

  • Vieira J, Messing J (1982) The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259–268

    Google Scholar 

  • Weaver PF, Wall JD, Gest H (1975) Characterization of Rhodoseudomonas capsulatus. Arch Microbiol 105:207–216

    CAS  PubMed  Google Scholar 

  • Wellington CL, Beatty T (1991) Overlapping mRNA transcripts of photosynthesis gene operons in Rhodobacter capsulatus. J Bacteriol 173:1432–1443

    Google Scholar 

  • Wiessner C, Dunger I, Michel H (1990) Sturcture and transcription of the genes encoding the B1015 light harvesting complex β and α subunits and the photosynthetic reaction center L, M, and cytochrome C subunits from Rhodopseudomonas viridis. J Bacteriol 172:2877–2887

    Google Scholar 

  • Yang Z, Bauer CE (1990) Rhodobacter capsulatus genes involved in early steps of the bacteriochlorophyll biosynthetic pathway. J Bacteriol 172:5001–5010

    Google Scholar 

  • Yen HC, Marrs BL (1976a) Map of genes for carotenoid and bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata. J Bacteriol 126:619–629

    Google Scholar 

  • Yen HC, Marrs BL (1976b) Growth of Rhodopseudomonas capsulata under anaerobic dark conditions with dimethyl sulfoxide. Arch Biochem Biophys 181:411–418

    Google Scholar 

  • Young DA, Bauer CE, Williams JC, Marrs BL (1989) genetic evidence for superoperonal organization of genes for photosynthetic pigments and pigment binding proteins in Rhodobacter capsulatus. Mol Gen Genet 218:1–12

    Google Scholar 

  • Youvan DC, Ismail S (1985) Light harvesting II (B800–B850 complex) structural genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 82:58–62

    Google Scholar 

  • Youvan DC, Bylina EJ, Alberti M, Begusch H, Hearst JE (1984) Nucleotide and deduced polypeptide sequences of the photosynthetic reaction center, B870 antenna, and flanking polypeptides from R. capsulata. Cell 37:949–957

    Google Scholar 

  • Youvan DC, Ismail S, Bylina EJ (1985) Chromosomal deletion and plasmid complementation of the photosynthetic reaction center and light-harvesting genes from Rhodopseudomonas capsulata. Gene 38:19–30

    Google Scholar 

  • Zhu YS, Hearst JE (1986) Regulation of expression of genes for light-harvesting antenna proteins LH-I and LH-II; reaction center polypeptides RC-L, RC-M and RC-H; and enzymes of bcteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus by light and oxygen. Proc Natl Acad Sci USA 83:7613–7617

    Google Scholar 

  • Zsebo KM, Hearst JE (1984) Genetic-physical mapping of a photosynthetic gene cluster from R. capsulata. Cell 37:937–947

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Additional information

Communicated by J. Lengeler

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bauer, C.E., Buggy, J.J., Yang, Z. et al. 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. Molec. Gen. Genet. 228, 433–444 (1991). https://doi.org/10.1007/BF00260637

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00260637

Key words

Navigation