1887

Abstract

Summary: Analysis of the nucleotide sequence of the form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes ( and ) of the non-sulfur purple bacterium indicated that the deduced amino acid sequence of the large subunit was not closely homologous to the large subunit from related organisms. Indeed, phylogenetic analysis suggested that the large subunit protein (CbbL) more closely resembled the enzyme from αlβlγ purple bacteria and cyanobacteria and is within a ‘green-like’ radiation of the RubisCO phylogenetic tree, well separated from CbbL of the related organism A gene was discovered downstream of in , a gene arrangement which also appears to be limited to certain organisms containing a ‘green-like’ RubisCO. Upstream, and divergently transcribed from , is a gene ( ) that encodes a LysR-type transcriptional activator. Phylogenetic analysis of the deduced amino acid sequence of CbbR also suggests that this protein is quite distinct from the CbbR protein, and is even distinct from the previously described CbbR protein, the gene of which is upstream and divergently transcribed from the operon of Interestingly, CbbR is more closely related to CbbR from bacteria whose RubisCO falls within the ‘greenlike’ radiation of the CbbL tree. These studies suggest that the - genes were acquired by via horizontal gene transfer from a bacterial species containing a ‘green-like’ RubisCO.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-144-1-219
1998-01-01
2021-10-27
Loading full text...

Full text loading...

/deliver/fulltext/micro/144/1/mic-144-1-219.html?itemId=/content/journal/micro/10.1099/00221287-144-1-219&mimeType=html&fmt=ahah

References

  1. Arai H., Igarashi Y., Kodama T. 1994; Structure and ANR-dependent transcription of the nir genes for denitrification from Pseudomonas aeruginosa. . Biosci Biotechnol Biochem 58:1286–1291
    [Google Scholar]
  2. van den Bergh E. R. E., Dijkhuizen L., Meijer W. G. 1993; CbbR, a LysR-type transcriptional activator, is required for expression of the autotrophic CO2 fixation enzymes of Xantho-bacter flavus. . J Bacteriol 175:6097–6104
    [Google Scholar]
  3. Blankenship R. B. 1992; Origin and early evolution of photosynthesis. Photosynth Res 33:91–111
    [Google Scholar]
  4. Boulygina E. S., Chumakov K. M., Netrusov A. L. 1993; Systematics of Gram-negative methylotrophic bacteria based on 5S rRNA sequences. In Microbial Growth on C1 Compounds pp 275–284 Edited by Murrell J. C., Kelly D. P. Andover: Intercept;
    [Google Scholar]
  5. Delwiche C. F., Palmer J. D. 1996; Rampant horizontal transfer and duplication of RubisCO genes in eubacteria and plastids. Mol Biol Evol 13:873–882
    [Google Scholar]
  6. Dickerson R. E. 1980; Evolution and gene transfer in purple photosynthetic bacteria. Nature 283:210–212
    [Google Scholar]
  7. Felsenstein J. 1989; PHYLIP – phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  8. Fonstein M., Koshy E. G., Nikolskaya T., Mourachov P., Haselkorn R. 1993; Refinement of the high resolution physical and genetic map of Rhodobacter capsulatus and genome surveys using blots of the cosmid encyclopedia. EMBO J 14:1827–1841
    [Google Scholar]
  9. Gibson J. L. 1995; Genetic analysis of CO2 fixation genes. In Anoxygenic Photosynthetic Bacteria pp 1107–1124 Edited by Blankenship R. E., Madigan M. T., Bauer C. E. Dordrecht: Kluwer;
    [Google Scholar]
  10. Gibson J. L., Tabita F. R. 1977a; Different molecular forms of D-ribulose-l,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides. . J Biol Chem 252:943–949
    [Google Scholar]
  11. Gibson J. L., Tabita F. R. 1977b; Isolation and preliminary characterization of two forms of ribulose 1,5-bisphosphate carboxylase from Rhodopseudomonas capsulata. . J Bacteriol 132:818–823
    [Google Scholar]
  12. Gibson J. L., Tabita F. R. 1993; Nucleotide sequence and functional analysis of CbbR, a positive regulator of the Calvin cycle operons of Rhodobacter sphaeroides. . J Bacteriol 175:5778–5784
    [Google Scholar]
  13. Gibson J. L., Tabita F. R. 1996; The molecular regulation of the reductive pentose phosphate pathway in proteobacteria and cyanobacteria. Arch Microbiol 166:141–150
    [Google Scholar]
  14. Goethals K., van Montagu M., Holsters M. 1992; Conserved motifs in a divergent nod box of Azorhizobium caulinodans ORS571 reveal a common structure in promoters regulated by LysR-type proteins. Proc Natl Acad Sci USA 89:1646–1650
    [Google Scholar]
  15. Igarashi Y., Kodama T. 1996; Genes related to carbon dioxide fixation in Hydrogenovibrio marinus and Pseudomonas hydrogenothermophila. . In Microbial Growth on C1 Compounds pp 88–93 Edited by Lidstrom M. E., Tabita F. R. Dordrecht: Kluwer;
    [Google Scholar]
  16. Imhoff J. F., Truper H. G., Pfennig N. 1984; Rearrangement of the species and genera of the phototrophic ‘purple nonsulfur bacteria’. Int J Syst Bacteriol 34:340–343
    [Google Scholar]
  17. Jungst A., Zumft W. G. 1992; Interdependence of respiratory NO reduction and nitrite reduction revealed by mutagenesis of nirQ, a novel gene in the denitrification gene cluster of Pseudomonas stutzeri. . FEBS Lett 314:308–314
    [Google Scholar]
  18. Kusano T., Sugawara K. 1993; Specific binding of Thiobacillus ferrooxidans RbcR to the intergenic sequence between the rbc operon and the rbcR gene. ] Bacteriol 175:1019–1025
    [Google Scholar]
  19. Kutsche M., Leimkuhler S., Angermuller S., Klipp W. 1996; Promoters controlling expression of the alternative nitrogenase and the molybdenum uptake system in Rhodobacter capsulatus are activated by NtrC, independent of σ54, and repressed by molybdenum. J Bacteriol 178:2010–2017
    [Google Scholar]
  20. Larimer F. W., Lu T. S. -Y., Buley D. M. 1995; Sequence and expression of the form II ribulose bisphosphate carboxylase/oxygenase (RUBISCO) gene from Rhodobacter capsulatus. . FASEB J 9:A1275
    [Google Scholar]
  21. Lorbach S. C., Shively J. M. 1995; Identification, isolation, and sequencing of the ribulose bisphosphate carboxylase/oxygenase regulatory genes (cbbRI and cbbRII) in Thiobacillus denitrificans. . In Abstracts of the 95th General Meeting of the American Society for Microbiology p 528 Washington, DC: American Society for Microbiology;
    [Google Scholar]
  22. Ludwig W., Rosello-Mora R., Aznar R. 14 other authors 1995; Comparative sequence analysis of 23S rRNA from proteobacteria. Syst Appl Microbiol 18:164–188
    [Google Scholar]
  23. Meijer W. G., van den Bergh E. R. E., Smith L. M. 1996; Induction of the gap–pgk operon encoding glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase of Xanthobacter flavus requires the LysR-type transcriptional activator CbbR. J Bacteriol 178:881–887
    [Google Scholar]
  24. Paoli G. C., Strom-Morgan N., Shively J. M., Tabita F. R. 1995; Expression of the cbbLcbbS and cbbM genes and distinct organization of the ebb Calvin cycle structural genes of Rhodobacter capsulatus. . Arch Microbiol 164:396–405
    [Google Scholar]
  25. Pridmore R. D. 1987; New and versatile cloning vectors with kanamycin-resistance marker. Gene 56:309–312
    [Google Scholar]
  26. Schell M. A. 1993; Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597–626
    [Google Scholar]
  27. Scolnik P. A., Haselkorn R. 1984; Activation of extra copies of genes coding for nitrogenase in Rbodopseudomonas capsulata. . Nature 307:289–292
    [Google Scholar]
  28. Strimmer K., von Haeseler A. 1996; Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969
    [Google Scholar]
  29. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w : improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
    [Google Scholar]
  30. Viale A. M., Kobayashi H., Akazawa T., Henikoff S. 1991; rbcR, a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in the photosynthetic bacterium Chromatium vinosum . J Bacteriol 173:5224–5229
    [Google Scholar]
  31. Walker J. E., Saraste M., Runswick M. J., Gay N. J. 1982; Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–951
    [Google Scholar]
  32. Watson G. M. F., Tabita F. R. 1996; Regulation, unique organization, and unusual primary structure of carbon fixation genes from a marine phycoerythrin-containing cyanobacterium. Plant Mol Biol 32:1103–1115
    [Google Scholar]
  33. Watson G. M. F., Tabita F. R. 1997; Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol Lett 146:13–22
    [Google Scholar]
  34. Windhovel U., Bowien B. 1991; Identification of cfxR, an activator gene of autotrophic O2 fixation in Alcaligenes eutrophus. . Mol Microbiol 5:2695–2705
    [Google Scholar]
  35. Woese C. R., Gibson J., Fox G. E. 1980; Do genealogical patterns in purple photosynthetic bacteria reflect interspecific gene transfer ?. Nature 283:212–214
    [Google Scholar]
  36. Woese C. R., Stackebrandt E., Weisburg W. G. 8 other authors 1984; The phylogeny of purple bacteria: the alpha subdivision. Syst Appl Microbiol 5:315–326
    [Google Scholar]
  37. Yokoyama K., Hayashi N. R., Arai H., Chung S. Y., Igarashi Y., Kodama T. 1995; Genes encoding RubisCO in Pseudomonas hydrogenothermophila are followed by a novel cbbQ gene similar to nirQ of the denitrification gene cluster from Pseudomonas species. Gene 153:75–79
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-144-1-219
Loading
/content/journal/micro/10.1099/00221287-144-1-219
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error