1887

Abstract

The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin–Benson–Bassham cycle of autotrophic CO fixation, was investigated in the members of the genus and the relative genus , all obligately chemolithoautotrophic sulfur-oxidizing . The gene encoding the ‘green-like’ form I RubisCO large subunit was found in all analysed species, while the gene encoding form II RubisCO was present only in species. Furthermore, species belonging to the 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, and . Both 16S-rRNA- and -based phylogenies of the group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.28699-0
2006-07-01
2020-01-23
Loading full text...

Full text loading...

/deliver/fulltext/micro/152/7/2159.html?itemId=/content/journal/micro/10.1099/mic.0.28699-0&mimeType=html&fmt=ahah

References

  1. Boulygina E. S, Kuznetsov B. B, Marusina A. I, Tourova T. P, Kravchenko I. K, Bykova S. A, Kolganova T. V, Galchenko V. F. 2002; The study of nucleotide sequences of nifH genes from some methanotrophic bacteria. Microbiology71:425–432[CrossRef]
    [Google Scholar]
  2. Brinkhoff T, Muyzer G, Wirsen C. O, Kuever J. 1999a; Thiomicrospira kuenenii sp. nov. and Thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat. Int J Syst Bacteriol49:385–392[CrossRef]
    [Google Scholar]
  3. Brinkhoff T, Muyzer G, Wirsen C. O, Kuever J. 1999b; Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from a Thioploca mat. Int J Syst Bacteriol49:875–879[CrossRef]
    [Google Scholar]
  4. Brinkhoff T, Sievert S. M, Kuever J, Muyzer G. 1999c; Distribution and diversity of sulfur-oxidizing Thiomicrospira spp. at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece). Appl Environ Microbiol65:3843–3849
    [Google Scholar]
  5. Delwiche C. F, Palmer J. D. 1996; Rampant horizontal transfer and duplication of RubisCO genes in eubacteria and plastids. Mol Biol Evol13:873–882[CrossRef]
    [Google Scholar]
  6. Elsaied H, Naganuma T. 2001; Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. Appl Environ Microbiol67:1751–1765[CrossRef]
    [Google Scholar]
  7. English R. S, Williams C. A, Lorbach S. C, Shively J. M. 1992; Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans . FEMS Microbiol Lett94:111–119[CrossRef]
    [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376[CrossRef]
    [Google Scholar]
  9. Felsenstein J. 1993; phylip (phylogeny inference package), version 3.53c Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  10. Fennoy S. L, Bailey-Serres J. 1993; Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons. Nucleic Acids Res21:5294–5300[CrossRef]
    [Google Scholar]
  11. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool20:406–416[CrossRef]
    [Google Scholar]
  12. Fitch W. M, Margoliash E. 1967; Construction of phylogenetic trees. Science155:279–284[CrossRef]
    [Google Scholar]
  13. Gibson J. L, Tabita F. R. 1977a; Different molecular forms of ribulose-1,5-bisphosphate carboxylase from Rhodopseudomonas sphaeroides . J Biol Chem252:943–949
    [Google Scholar]
  14. Gibson J. L, Tabita F. R. 1977b; Isolation and preliminary characterization of two forms of ribulose 1,5-bisphosphate carboxylase from Rhodopseudomonas capsulata . J Bacteriol132:818–823
    [Google Scholar]
  15. Heinhorst S, Baker S. H, Johnson D. R, Davies P. S, Cannon G. C. 2002; Two copies of form I RubisCO genes in Acidithiobacillus ferrooxidans ATCC 23270. Curr Microbiol45:115–117[CrossRef]
    [Google Scholar]
  16. Hernandez J. M, Baker S. H, Lorbach S. C, Shively J. M, Tabita F. R. 1996; Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans . J Bacteriol178:347–356
    [Google Scholar]
  17. Hugler M, Wirsen C. O, Fuchs G, Taylor C. D, Sievert S. M. 2005; Evidence for autotrophic CO[sub]2[/sub] fixation via the reductive tricarboxylic acid cycle by members of the ε subdivision of proteobacteria. J Bacteriol187:3020–3027[CrossRef]
    [Google Scholar]
  18. Jannasch H. W, Wirsen C. O, Nelson D. C, Robertson L. A. 1985; Thiomicrospira crunogena sp. nov., a colorless sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J Syst Bacteriol35:422–424[CrossRef]
    [Google Scholar]
  19. Kobayashi H, Viale A. M, Takabe T, Akazawa T, Wada K, Shinozaki K, Kobayashi K, Sugiura M. 1991; Sequence and expression of genes encoding the large and small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum . Gene97:55–62[CrossRef]
    [Google Scholar]
  20. Kuenen J. G, Veldkamp H. 1972; Thiomicrospira pelophila, gen. n., sp. n., a new obligately chemolithotrophic colourless sulfur bacterium. Antonie van Leeuwenhoek38:241–256[CrossRef]
    [Google Scholar]
  21. Kusano T, Takeshima T, Inoue C, Sugawara K. 1991; Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans . J Bacteriol173:7313–7323
    [Google Scholar]
  22. Kusian B, Bednarski R, Husemann M, Bowien B. 1995; Characterization of the duplicate ribulose-1,5-bisphosphate carboxylase genes and cbb promoters of Alcaligenes eutrophus . J Bacteriol177:4442–4450
    [Google Scholar]
  23. Medigue C, Rouxel T, Vigier P, Henaut A, Danchin A. 1991; Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol222:851–856[CrossRef]
    [Google Scholar]
  24. Musto H, Romero H, Rodriguez-Maseda H. 1998; Heterogeneity in codon usage in the flatworm Schistosoma mansoni . J Mol Evol46:159–167[CrossRef]
    [Google Scholar]
  25. Nishihara H, Igarashi Y, Kodama T. 1991; Hydrogenovibrio marinus gen. nov., sp. nov., a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium. Int J Syst Bacteriol41:130–133[CrossRef]
    [Google Scholar]
  26. Nishihara H, Yaguchi T, Chung S. Y, Suzuki K, Yanagi M, Yamasato K, Kodama T, Igarashi Y. 1998; Phylogenetic position of an obligately chemoautotrophic, marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus , on the basis of 16S rRNA gene sequences and two form I RubisCO gene sequences. Arch Microbiol169:364–368[CrossRef]
    [Google Scholar]
  27. Ohtaka C, Ishikawa H. 1993; Accumulation of adenine and thymine in groE -homologous operon of an intracellular symbiont. J Mol Evol36:121–126[CrossRef]
    [Google Scholar]
  28. Paoli G. C, Morgan N. S, Tabita F. R, Shively J. M. 1995; Expression of the cbbLcbbS and cbbM genes and distinct organization of the cbb Calvin cycle structural genes of Rhodobacter capsulatus . Arch Microbiol164:396–405
    [Google Scholar]
  29. Robertson L. A, Kuenen J. G. 1999; The colourless sulfur bacteria. In The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community, 3rd edn. Release 3.0 21 May 1999 () New York: Springer;http://link.springer-ny.com/link/service/books/10125/
    [Google Scholar]
  30. Saitou N, Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425
    [Google Scholar]
  31. Sambrook J, Fritsch E. F, Maniatis T. 1989; Molecular Cloning: a Laboratory Manual, 2nd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  32. Shively J. M, Devore W, Stratford L, Porter L, Medlin L, Stevens S. E. 1986; Molecular evolution of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). FEMS Microbiol Lett37:251–257[CrossRef]
    [Google Scholar]
  33. Sorokin D. Y, Kuenen J. G. 2005; Alkaliphilic chemolithotrophs from soda lakes. FEMS Microbiol Ecol52:287–295[CrossRef]
    [Google Scholar]
  34. Sorokin D. Y, Lysenko A. M, Mityushina L. L, Tourova T. P, Jones B. E, Rainey F. A, Robertson L. A, Kuenen G. J. 2001; Thioalkalimicrobium aerophilum gen. nov., sp. nov. and Thioalkalimicrobium sibiricum sp. nov., and Thioalkalivibrio versutus gen. nov., sp. nov., Thioalkalivibrio nitratis sp. nov. and Thioalkalivibrio denitrificans sp. nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. Int J Syst Evol Microbiol51:565–580
    [Google Scholar]
  35. Sorokin D. Y, Gorlenko V. M, Tourova T. P, Tsapin A. I, Nealson K. H, Kuenen G. J. 2002; Thioalkalimicrobium cyclicum sp. nov. and Thioalkalivibrio jannaschii sp. nov., novel species of haloalkaliphilic, obligately chemolithoautotrophic sulfur-oxidizing bacteria from hypersaline alkaline Mono Lake (California). Int J Syst Evol Microbiol52:913–920[CrossRef]
    [Google Scholar]
  36. Spiridonova E. M, Berg I. A, Kolganova T. V, Ivanovsky R. N, Kuznetsov B. B, Tourova T. P. 2004; An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups. Microbiology73:316–325[CrossRef]
    [Google Scholar]
  37. Stoner M. T, Shively J. M. 1993; Cloning and expression of the d-ribulose-1,5-bisphosphate carboxylase/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli . FEMS Microbiol Lett107:287–292
    [Google Scholar]
  38. Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson K. H, Horikoshi K. 2004; Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. Int J Syst Evol Microbiol54:2325–2333[CrossRef]
    [Google Scholar]
  39. Thompson J. D, Higgins D. G, Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res9:3251–3270
    [Google Scholar]
  40. Tourova T. P, Spiridonova E. M, Berg I. A, Kuznetsov B. B, Sorokin D. Yu. 2005; Phylogeny of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in haloalkaliphilic obligately autotrophic sulfur-oxidizing bacteria of the genus Thioalkalivibrio . Microbiology74:321–328[CrossRef]
    [Google Scholar]
  41. Uchino Y, Yokota A. 2003; ‘Green-like’ and ‘red-like’ RubisCO cbbL genes in Rhodobacter azotoformans . Mol Biol Evol20:821–830[CrossRef]
    [Google Scholar]
  42. Van de Peer Y., De Wachter R. 1994; treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Applic Biosci10:569–570
    [Google Scholar]
  43. Viale A. M, Kobayashi H, Akazawa T. 1989; Expressed genes for plant-type ribulose 1,5-bisphosphate carboxylase/oxygenase in the photosynthetic bacterium Chromatium vinosum , which possesses two complete sets of the genes. J Bacteriol171:2391–2400
    [Google Scholar]
  44. Watson G. M. F, Tabita F. R. 1997; Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol Lett146:13–22[CrossRef]
    [Google Scholar]
  45. Wood A. P, Kelly D. P. 1989; Isolation and characterization of Thiobacillus thyasiris sp. nov., a novel marine facultative autotroph and the putative symbiont of Thyasira flexuosa . Arch Microbiol152:160–166[CrossRef]
    [Google Scholar]
  46. Wood A. P, Kelly D. P. 1993; Reclassification of Thiobacillus thyasiris as Thiomicrospira thyasirae comb. nov., an organism exhibiting pleomorphism in response to environmental conditions. Arch Microbiol159:45–47[CrossRef]
    [Google Scholar]
  47. Yaguchi T, Chung S. Y, Igarashi Y, Kodama T. 1994; Cloning and sequencing of the L2 form of RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. Biosci Biotechnol Biochem58:1733–1737[CrossRef]
    [Google Scholar]
  48. Yang Z. 2000; paml (phylogenetic analysis by maximum likelihood), version 3.0 London: University College London;
    [Google Scholar]
  49. Yang Z, Nielsen R. 2000; Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol17:32–43[CrossRef]
    [Google Scholar]
  50. Yoshizawa Y, Toyoda K, Arai H, Ishii M, Igarashi Y. 2004; CO[sub]2[/sub]- responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in Hydrogenovibrio marinus strain MH-110. J Bacteriol186:5685–5691[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.28699-0
Loading
/content/journal/micro/10.1099/mic.0.28699-0
Loading

Data & Media loading...

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