Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum

Environmental Microbiology Reports

Volumn 7, Issue 2, 2015, Pages 204-210

  Rodionova, Irina A ^a   Li, Xiaoqing ^a   Plymale, Andrew E ^b   Motamedchaboki, Khatereh ^a   Konopka, Allan E ^b   Romine, Margaret F ^b   Fredrickson, James K ^b   Osterman, Andrei L ^a   Rodionov, Dmitry A ^a,c  

^a BURNHAM INSTITUTE   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROFLEXI; CHLOROFLEXI (CLASS); CHLOROFLEXUS AURANTIACUS;

CARRIER PROTEIN; VITAMIN B COMPLEX;

CHLOROFLEXI; GENETIC COMPLEMENTATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; ORGANISMAL INTERACTION; PHYSIOLOGY; SYMBIOSIS;

CHLOROFLEXI; ENVIRONMENTAL MICROBIOLOGY; GENETIC COMPLEMENTATION TEST; MEMBRANE TRANSPORT PROTEINS; METABOLIC NETWORKS AND PATHWAYS; MICROBIAL INTERACTIONS; SYMBIOSIS; VITAMIN B COMPLEX;

EID: 84924694174     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/1758-2229.12227     Document Type: Article

References (27)

1. Bunge, M., and Lechner, U. (2009) Anaerobic reductive dehalogenation of polychlorinated dioxins. Appl Microbiol Biotechnol 84: 429-444.
2. Castenholz, R.W. (1969) Thermophilic blue-green algae and the thermal environment. Bacteriol Rev 33: 476-504.
3. Eitinger, T., Rodionov, D.A., Grote, M., and Schneider, E. (2011) Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev 35: 3-67.
4. Frigaard, N.U., and Bryant, D.A. (2004) Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol 182: 265-276.
5. Gelfand, M.S., and Rodionov, D.A. (2008) Comparative genomics and functional annotation of bacterial transporters. Phys Life Rev 5: 22-49.
6. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
7. Gupta, R.S., Chander, P., and George, S. (2013) Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] 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.
8. Hanada, S., and Pierson, B.K. (2006) The family Chloroflexaceae. In The Prokaryotes. Dworkin, M. etal. (eds). New York, NY, USA: Springer, pp. 815-842.
9. Hanada, S., Hiraishi, A., Shimada, K., and Matsuura, K. (1995) Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int J Syst Bacteriol 45: 676-681.
10. Hanada, S., Takaichi, S., Matsuura, K., and Nakamura, K. (2002) Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52: 187-193.
11. Jaehme, M., and Slotboom, D.J. (2014) Diversity of membrane transport proteins for vitamins in bacteria and archaea. Biochim Biophys Acta. DOI: 10.1016/j.bbagen.2014.05.006.
12. Kaiser, J., Illarionov, B., Rohdich, F., Eisenreich, W., Saller, S., den Brulle, J.V., etal. (2007) A high-throughput screening platform for inhibitors of the riboflavin biosynthesis pathway. Anal Biochem 365: 52-61.
13. Klatt, C.G., Bryant, D.A., and Ward, D.M. (2007) Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ Microbiol 9: 2067-2078.
14. Klatt, C.G., Inskeep, W.P., Herrgard, M.J., Jay, Z.J., Rusch, D.B., Tringe, S.G., etal. (2013) Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol 4: 106.
15. LeBlanc, J.G., Laino, J.E., del Valle, M.J., Vannini, V., van Sinderen, D., Taranto, M.P., etal. (2011) B-group vitamin production by lactic acid bacteria - current knowledge and potential applications. J Appl Microbiol 111: 1297-1309.
16. van der Meer, M.T., Schouten, S., Bateson, M.M., Nubel, U., Wieland, A., Kuhl, M., etal. (2005) Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park. Appl Environ Microbiol 71: 3978-3986.
17. Novichkov, P.S., Rodionov, D.A., Stavrovskaya, E.D., Novichkova, E.S., Kazakov, A.E., Gelfand, M.S., etal. (2010) RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res 38: W299-W307.
18. Novichkov, P.S., Kazakov, A.E., Ravcheev, D.A., Leyn, S.A., Kovaleva, G.Y., Sutormin, R.A., etal. (2013) RegPrecise 3.0 - a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics 14: 745.
19. Osterman, A.L., Overbeek, R., and Rodionov, D.A. (2010) The use of subsystems to encode biosynthesis of vitamins and cofactors. In Comprehensive Natural Products II: Chemistry and Biology. Mander, L.N., and Liu, H. (eds). Kidlington, UK: Elsevier, pp. 141-159.
20. Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., etal. (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42: D206-D214.
21. Pierson, B.K., and Castenholz, R.W. (1974) A phototrophic gliding filamentous bacterium of hot springs, Chloroflexus aurantiacus, gen. and sp. nov. Arch Microbiol 100: 5-24.
22. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S. (2002) Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem 277: 48949-48959.
23. Rodionov, D.A., Hebbeln, P., Eudes, A., ter Beek, J., Rodionova, I.A., Erkens, G.B., etal. (2009) A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol 191: 42-51.
24. Schipp, C.J., Marco-Urrea, E., Kublik, A., Seifert, J., and Adrian, L. (2013) Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. Philos Trans R Soc Lond B Biol Sci 368: 20120321.
25. Stolyar, S., Liu, Z., Thiel, V., Tomsho, L.P., Pinel, N., Nelson, W.C., etal. (2014) Genome sequence of the thermophilic cyanobacterium Thermosynechococcus sp. Strain NK55a. Genome Announc 2: e01060-13.
26. Sun, E.I., Leyn, S.A., Kazanov, M.D., Saier, M.H., Jr, Novichkov, P.S., and Rodionov, D.A. (2013) Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics 14: 597.
27. Zarzycki, J., and Fuchs, G. (2011) Coassimilation of organic substrates via the autotrophic 3-hydroxypropionate bi-cycle in Chloroflexus aurantiacus. Appl Environ Microbiol 77: 6181-6188.