1887

Abstract

The bacteria belonging to the class , due to their ability to dehalogenate chlorinated compounds, are of much interest for bioremediation of contaminated sites. We report here comparative analyses on different genes/proteins from the genomes of members of the class These studies have identified numerous novel molecular markers in the forms of conserved signature indels (CSIs) in broadly distributed proteins and conserved signature genes/proteins (CSPs), which are uniquely found in members of the class , but except for an isolated exception, they are not found in other sequenced bacterial genomes. Of these molecular markers, nine CSIs in divergent proteins and 19 CSPs are specific for members of the genera and , providing potential molecular markers for the bacterial class . Additionally, four CSIs in divergent proteins and 28 CSPs are only found in all members of the genus for which genome sequences are available, but they are absent in and in other bacteria. The gene sequences of several of these CSPs exhibiting specificity for the genus or the class are highly conserved and PCR primers based upon them provide a novel means for identification of other related bacteria. Two other CSIs identified in this study in the SecD and aspartate carbomyltransferase proteins weakly support an affiliation of the class with the other members of the phylum .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.057919-0
2014-06-01
2019-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/6/2176.html?itemId=/content/journal/ijsem/10.1099/ijs.0.057919-0&mimeType=html&fmt=ahah

References

  1. Adrian L., Szewzyk U., Wecke J., Görisch H.. ( 2000;). Bacterial dehalorespiration with chlorinated benzenes. . Nature 408:, 580–583. [CrossRef][PubMed]
    [Google Scholar]
  2. Adrian L., Dudková V., Demnerová K., Bedard D. L.. ( 2009;). Dehalococcoides” sp. strain CBDB1 extensively dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. . Appl Environ Microbiol 75:, 4516–4524. [CrossRef][PubMed]
    [Google Scholar]
  3. Ahmod N. Z., Gupta R. S., Shah H. N.. ( 2011;). Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group. . J Microbiol Methods 87:, 278–285. [CrossRef][PubMed]
    [Google Scholar]
  4. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J.. ( 1997;). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25:, 3389–3402. [CrossRef][PubMed]
    [Google Scholar]
  5. Bhandari V., Naushad H. S., Gupta R. S.. ( 2012;). Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution. . Front Cell Infect Microbiol 2:, 98. [CrossRef][PubMed]
    [Google Scholar]
  6. Bowman K. S., Nobre M. F., da Costa M. S., Rainey F. A., Moe W. M.. ( 2013;). Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater. . Int J Syst Evol Microbiol 63:, 1492–1498. [CrossRef][PubMed]
    [Google Scholar]
  7. Cheng D., He J.. ( 2009;). Isolation and characterization of “Dehalococcoides” sp. strain MB, which dechlorinates tetrachloroethene to trans-1,2-dichloroethene. . Appl Environ Microbiol 75:, 5910–5918. [CrossRef][PubMed]
    [Google Scholar]
  8. Cheng D., Chow W. L., He J.. ( 2010;). A Dehalococcoides-containing co-culture that dechlorinates tetrachloroethene to trans-1,2-dichloroethene. . ISME J 4:, 88–97. [CrossRef][PubMed]
    [Google Scholar]
  9. Dutilh B. E., Snel B., Ettema T. J., Huynen M. A.. ( 2008;). Signature genes as a phylogenomic tool. . Mol Biol Evol 25:, 1659–1667. [CrossRef][PubMed]
    [Google Scholar]
  10. Fang G., Rocha E., Danchin A.. ( 2005;). How essential are nonessential genes?. Mol Biol Evol 22:, 2147–2156. [CrossRef][PubMed]
    [Google Scholar]
  11. Fennell D. E., Nijenhuis I., Wilson S. F., Zinder S. H., Häggblom M. M.. ( 2004;). Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. . Environ Sci Technol 38:, 2075–2081. [CrossRef][PubMed]
    [Google Scholar]
  12. Gao B., Gupta R. S.. ( 2005;). Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. . Int J Syst Evol Microbiol 55:, 2401–2412. [CrossRef][PubMed]
    [Google Scholar]
  13. Gao B., Gupta R. S.. ( 2012a;). Microbial systematics in the post-genomics era. . Antonie van Leeuwenhoek 101:, 45–54. [CrossRef][PubMed]
    [Google Scholar]
  14. Gao B., Gupta R. S.. ( 2012b;). Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. . Microbiol Mol Biol Rev 76:, 66–112. [CrossRef][PubMed]
    [Google Scholar]
  15. Griffiths E., Petrich A. K., Gupta R. S.. ( 2005;). Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification. . Microbiology 151:, 2647–2657. [CrossRef][PubMed]
    [Google Scholar]
  16. Gupta R. S., Mathews D. W.. ( 2010;). Signature proteins for the major clades of Cyanobacteria. . BMC Evol Biol 10:, 24. [CrossRef][PubMed]
    [Google Scholar]
  17. Gupta R. S., Mok A.. ( 2007;). Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups. . BMC Microbiol 7:, 106. [CrossRef][PubMed]
    [Google Scholar]
  18. Gupta R. S., Chander P., George S.. ( 2013;). Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.. Antonie van Leeuwenhoek 103:, 99–119. [CrossRef][PubMed]
    [Google Scholar]
  19. Hatt J. K., Löffler F. E.. ( 2012;). Quantitative real-time PCR (qPCR) detection chemistries affect enumeration of the Dehalococcoides 16S rRNA gene in groundwater. . J Microbiol Methods 88:, 263–270. [CrossRef][PubMed]
    [Google Scholar]
  20. Hug L. A., Maphosa F., Leys D., Löffler F. E., Smidt H., Edwards E. A., Adrian L.. ( 2013;). Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. . Philos Trans R Soc Lond B Biol Sci 368:, 20120322. [CrossRef][PubMed]
    [Google Scholar]
  21. Lerat E., Daubin V., Ochman H., Moran N. A.. ( 2005;). Evolutionary origins of genomic repertoires in bacteria. . PLoS Biol 3:, e130. [CrossRef][PubMed]
    [Google Scholar]
  22. Löffler F. E., Edwards E. A.. ( 2006;). Harnessing microbial activities for environmental cleanup. . Curr Opin Biotechnol 17:, 274–284. [CrossRef][PubMed]
    [Google Scholar]
  23. Löffler F. E., Sun Q., Li J., Tiedje J. M.. ( 2000;). 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. . Appl Environ Microbiol 66:, 1369–1374. [CrossRef][PubMed]
    [Google Scholar]
  24. Löffler F. E., Yan J., Ritalahti K. M., Adrian L., Edwards E. A., Konstantinidis K. T., Müller J. A., Fullerton H., Zinder S. H., Spormann A. M.. ( 2013;). Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. . Int J Syst Evol Microbiol 63:, 625–635. [CrossRef][PubMed]
    [Google Scholar]
  25. Maness A. D., Bowman K. S., Yan J., Rainey F. A., Moe W. M.. ( 2012;). Dehalogenimonas spp. can reductively dehalogenate high concentrations of 1,2-dichloroethane, 1,2-dichloropropane, and 1,1,2-trichloroethane. . AMB Express 2:, 54. [CrossRef][PubMed]
    [Google Scholar]
  26. McMurdie P. J., Behrens S. F., Müller J. A., Göke J., Ritalahti K. M., Wagner R., Goltsman E., Lapidus A., Holmes S.. & other authors ( 2009;). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. . PLoS Genet 5:, e1000714. [CrossRef][PubMed]
    [Google Scholar]
  27. Moe W. M., Yan J., Nobre M. F., da Costa M. S., Rainey F. A.. ( 2009;). Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. . Int J Syst Evol Microbiol 59:, 2692–2697. [CrossRef][PubMed]
    [Google Scholar]
  28. Naushad H. S., Lee B., Gupta R. S.. ( 2014;). Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. . Int J Syst Evol Microbiol 64:, 366–383. [CrossRef][PubMed]
    [Google Scholar]
  29. NCBI ( 2013;). NCBI Completed microbial genomes. . http://www.ncbi.nlm.nih.gov/genome/browse/.
  30. Pöritz M., Goris T., Wubet T., Tarkka M. T., Buscot F., Nijenhuis I., Lechner U., Adrian L.. ( 2013;). Genome sequences of two dehalogenation specialists – Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region. . FEMS Microbiol Lett 343:, 101–104. [CrossRef][PubMed]
    [Google Scholar]
  31. Schoeffler A. J., May A. P., Berger J. M.. ( 2010;). A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. . Nucleic Acids Res 38:, 7830–7844. [CrossRef][PubMed]
    [Google Scholar]
  32. Seshadri R., Adrian L., Fouts D. E., Eisen J. A., Phillippy A. M., Methe B. A., Ward N. L., Nelson W. C., Deboy R. T.. & other authors ( 2005;). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. . Science 307:, 105–108. [CrossRef][PubMed]
    [Google Scholar]
  33. Siddaramappa S., Challacombe J. F., Delano S. F., Green L. D., Daligault H., Bruce D., Detter C., Tapia R., Han S.. & other authors ( 2012;). Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains. . Stand Genomic Sci 6:, 251–264. [CrossRef][PubMed]
    [Google Scholar]
  34. Singh B., Gupta R. S.. ( 2009;). Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. . Mol Genet Genomics 281:, 361–373. [CrossRef][PubMed]
    [Google Scholar]
  35. Smidt H., de Vos W. M.. ( 2004;). Anaerobic microbial dehalogenation. . Annu Rev Microbiol 58:, 43–73. [CrossRef][PubMed]
    [Google Scholar]
  36. Yan J., Rash B. A., Rainey F. A., Moe W. M.. ( 2009;). Detection and quantification of Dehalogenimonas and “Dehalococcoides” populations via PCR-based protocols targeting 16S rRNA genes. . Appl Environ Microbiol 75:, 7560–7564. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.057919-0
Loading
/content/journal/ijsem/10.1099/ijs.0.057919-0
Loading

Data & Media loading...

Supplementary Material 

PDF

Most Cited This Month

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