1887

Abstract

The phylogenetic placement of the rumen bacterium was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among [Gupta, R. S. (2000) 24, 367–402]. For this purpose, segments of the Hsp60 (), Hsp70 (), CTP synthase and alanyl-tRNA synthetase genes, which are known to contain signature sequences that are useful for phylogenetic deterministic purposes, were cloned. Using degenerate oligonucleotide primers for highly conserved regions in these proteins, 14 kb, 075 kb, 401 bp and 171 bp fragments of the Hsp70, Hsp60, CTP synthase and alanyl-tRNA synthetase genes respectively were amplified by PCR, and these fragments were cloned and sequenced. These primers, because of their high degree of conservation, could also be used for cloning these genes from other bacterial species. The Hsp70 homologues from different Gram-negative bacteria contain a 21–23 aa insert that is not found in any Gram-positive bacteria. The presence of this insert in the Hsp70 supports its placement within the Gram-negative group of bacteria. A conserved insert in Hsp60 that is commonly present in all bacterial species, except various Gram-positive bacteria, groups and green non-sulphur bacteria, provides evidence that does not belong to these taxa. A particularly useful signature consisting of a 4 aa insert is found in Ala-tRNA synthetase. This insert is present in all proteobacterial homologues as well as in homologues from species belonging to the and (CFB) groups, but it is not found in homologues from any other groups of bacteria. The presence of this insert in Ala-tRNA synthetase provides evidence that this species is related to these groups. However, two other signatures in CTP synthase and Hsp70 proteins, that are distinctive of the proteobacterial species, are not present in the homologues. These results provide evidence that does not belong to the proteobacterial division and thus should be placed in a similar position as the and CFB groups of species.

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2001-09-01
2019-12-10
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References

  1. Amann, R. L., Lin, C., Key, R., Montgomery, L. & Stahl, D. A. ( 1992; ). Diversity among Fibrobacter isolates: towards a phylogenetic classification. Syst Appl Microbiol 15, 23-31.
    [Google Scholar]
  2. Asanuma, N., Iwamoto, M. & Hino, T. ( 1999; ). Effect of the addition of fumarate on methane production by ruminal microorganisms in vitro. J Dairy Sci 82, 780-787.[CrossRef]
    [Google Scholar]
  3. Brown, J. R. & Doolittle, W. F. ( 1995; ). Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92, 2441-2445.[CrossRef]
    [Google Scholar]
  4. Cheng, K. J., Forsberg, C. W., Minato, H. & Costerton, J. W. ( 1991; ). Microbial ecology and physiology of feed degradation within the rumen. In Physiological Aspects of Digestion and Metabolism in Ruminants , pp. 595-624. Edited by T. Tsuda, Y. Sasaki & R. Kawahima. New York:Academic Press.
  5. Debroas, D. & Blanchart, G. ( 1993; ). Interactions between proteolytic and cellulolytic rumen bacteria during hydrolysis of plant cell wall protein. Reprod Nutr Dev 33, 283-288.[CrossRef]
    [Google Scholar]
  6. Doolittle, W. F. ( 1999; ). Phylogenetic classification and the universal tree. Science 284, 2124-2128.[CrossRef]
    [Google Scholar]
  7. Fields, M. W., Mallik, S. & Russell, J. B. ( 2000; ). Fibrobacter succinogenes S85 ferments ball-milled cellulose as fast as cellobiose until cellulose surface area is limiting. Appl Microbiol Biotechnol 54, 570-574.[CrossRef]
    [Google Scholar]
  8. Fraser, C. M., Gocayne, J. D., White, O. & 7 other authors ( 1995; ). The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.[CrossRef]
    [Google Scholar]
  9. Galley, K. A., Singh, B. & Gupta, R. S. ( 1992; ). Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach. Biochim Biophys Acta 1130, 203-208.[CrossRef]
    [Google Scholar]
  10. Garcia-Vallve, S., Romeu, A. & Palau, J. ( 2000; ). Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17, 352-361.[CrossRef]
    [Google Scholar]
  11. Gokarn, R. R., Eitnan, M. A., Martin, S. A. & Eriksson, K. E. ( 1997; ). Production of succinate from glucose, cellobiose, and various cellulosic materials by the ruminal anaerobic bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens. Appl Biochem Biotechnol 68, 69-80.[CrossRef]
    [Google Scholar]
  12. Gupta, R. S. ( 1995; ). Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol 15, 1-11.[CrossRef]
    [Google Scholar]
  13. Gupta, R. S. ( 1998a; ). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol Mol Biol Rev 62, 1435-1491.
    [Google Scholar]
  14. Gupta, R. S. ( 1998b; ). What are archaebacteria: life’s third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol 29, 695-708.[CrossRef]
    [Google Scholar]
  15. Gupta, R. S. ( 2000a; ). The phylogeny of Proteobacteria: relationships to other Eubacterial phyla and eukaryotes. FEMS Microbiology Reviews 24, 367-402.[CrossRef]
    [Google Scholar]
  16. Gupta, R. S. ( 2000b; ). The natural relationships among prokaryotes. CRC Crit Rev Microbiol 26, 111-131.[CrossRef]
    [Google Scholar]
  17. Gupta, R. S. ( 2000c; ). Evolutionary relationships among bacteria: does 16S rRNA provide all the answers? ASM News 66, 189-190.
    [Google Scholar]
  18. Gupta, R. S. & Golding, G. B. ( 1993; ). Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 37, 573-582.
    [Google Scholar]
  19. Gupta, R. S. & Singh, B. ( 1992; ). Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene. J Bacteriol 17, 4594-4605.
    [Google Scholar]
  20. Gupta, R. S., Mukhtar, T. & Singh, B. ( 1999; ). Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, Cyanobacteria, Chlorobium tepidum and Proteobacteria): implications regarding the origin of photosynthesis. Mol Microbiol 32, 893-906.[CrossRef]
    [Google Scholar]
  21. Holdeman, L. V., Kelley, R. W. & Moore, W. E. C. ( 1984; ). Family I. Bacteroidaceae Pribam 1933. In Bergey’s Manual of Systematic Bacteriology , pp. 602-662. Edited by N. R. Krieg & J. G. Holt. Baltimore:Williams & Wilkins.
  22. Huang, L. & Forsberg, C. W. ( 1990; ). Cellulose digestion and cellulase regulation and distribution in Fibrobacter succinogenes subsp. succinogenes S85. Appl Environ Microbiol 56, 1221-1228.
    [Google Scholar]
  23. Hugenholtz, P., Pitulle, C., Hershberger, K. L. & Pace, N. ( 1998; ). Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180, 366-376.
    [Google Scholar]
  24. Hungate, R. E. ( 1950; ). The anaerobic mesophilic cellulolytic bacteria. Bacteriol Rev 14, 1-49.
    [Google Scholar]
  25. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S. & Miyata, T. ( 1989; ). Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86, 9355-9359.[CrossRef]
    [Google Scholar]
  26. Lindquist, S. & Craig, E. A. ( 1988; ). The heat-shock proteins. Annu Rev Genet 22, 631-677.[CrossRef]
    [Google Scholar]
  27. Ludwig, W. & Schleifer, K. H. ( 1999; ). Phylogeny of Bacteria beyond the 16S rRNA Standard. ASM News 65, 752-757.
    [Google Scholar]
  28. Maidak, B. L., Cole, J. R., Parker, C. T., Jr and 11 other authors ( 1999; ). A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27, 171–173.[CrossRef]
    [Google Scholar]
  29. Montgomery, L., Flesher, B. & Stahl, D. ( 1988; ). Transfer of Bacteroides succinogenes (Hungate) to Fibrobacter gen. nov. as Fibrobacter succinogenes comb. nov. and description of Fibrobacter intestinalis sp. nov. Int J Syst Bacteriol 38, 430-435.[CrossRef]
    [Google Scholar]
  30. Olsen, G. J. & Woese, C. R. ( 1993; ). Ribosomal RNA: a key to phylogeny. FASEB J 7, 113-123.
    [Google Scholar]
  31. Paster, B. J., Dewhirst, F. E., Olsen, I. & Fraser, G. J. ( 1994; ). Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. J Bacteriol 176, 725-732.
    [Google Scholar]
  32. Reichenbach, H. ( 1992; ). The Order Cytophagales. In The Prokaryotes , pp. 3631-3675. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York:Springer.
  33. Rusanganwa, E., Singh, B. & Gupta, R. S. ( 1992; ). Cloning of HSP60 (GroEL) operon from Clostridium perfringens using a polymerase chain reaction based approach. Biochim Biophys Acta 1130, 90-94.[CrossRef]
    [Google Scholar]
  34. Shah, R. N. ( 1992; ). The genus Bacteroides and related taxa. In The Prokaryotes , pp. 3593-3607. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York:Springer.
  35. Shi, Y., Odt, C. L. & Weimer, P. J. ( 1997; ). Competition for cellulose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. Appl Environ Microbiol 63, 734-742.
    [Google Scholar]
  36. Wang, Y., McAllister, T. A., Yanke, L. J. & Cheeke, P. R. ( 2000; ). Effect of steroidal saponin from Yucca schidigera extract on ruminal microbes. J Appl Microbiol 88, 887-896.[CrossRef]
    [Google Scholar]
  37. Weimer, P. J., Waghorn, G. C., Odt, C. L. & Mertens, D. R. ( 1999; ). Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J Dairy Sci 82, 122-134.[CrossRef]
    [Google Scholar]
  38. Weisburg, W. G., Oyaizu, Y., Oyaizu, H. & Woese, C. R. ( 1985; ). Natural relationship between Bacteroides and Flavobacteria. J Bacteriol 164, 230-236.
    [Google Scholar]
  39. Woese, C. R. ( 1987; ). Bacterial evolution. Microbiol Rev 51, 221-271.
    [Google Scholar]
  40. Woese, C. R. ( 1998; ). The universal ancestor. Proc Natl Acad Sci USA 95, 6854-6859.[CrossRef]
    [Google Scholar]
  41. Zinder, S. H. ( 1998; ). Bacterial diversity. In Topley and Wilson’s Microbiology and Microbial Infections , pp. 125-147. Edited by A. Balows & B. I. Duerden. London:Arnold.
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