Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis

BMC Research Notes

Volumn 6, Issue 1, 2013, Pages

  Jeßberger, Nadja ^a   Lu, Yinhua ^a,b   Amon, Johannes ^a   Titgemeyer, Fritz ^c   Sonnewald, Sophia ^a   Reid, Stephen ^a   Burkovski, Andreas ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c Fachbereich Oecotrophologie   (Germany)

Author keywords

AmtR; GlnR; Nitrogen control; Nitrogen metabolism; OmpR EnvZ

Indexed keywords

BACTERIA (MICROORGANISMS); CORYNEBACTERIACEAE; CORYNEBACTERIUM; MYCOBACTERIUM SMEGMATIS; STREPTOMYCETACEAE; STREPTOMYCINEAE;

BACTERIAL PROTEIN; NITROGEN; REPRESSOR PROTEIN; TRANSACTIVATOR PROTEIN; TRANSCRIPTOME;

ARTICLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; MYCOBACTERIUM SMEGMATIS; REGULATOR GENE;

BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, REGULATOR; MOLECULAR SEQUENCE ANNOTATION; MYCOBACTERIUM SMEGMATIS; NITROGEN; REPRESSOR PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84887873037     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-6-482     Document Type: Article

References (37)

1. Common patterns-unique features: nitrogen metabolism and regulation in Gram-positive bacteria. Amon J, Titgemeyer F, Burkovski A, FEMS Microbiol Rev 2010 34 588 605 20337720
2. Two transcriptional regulators GlnR and GlnRII are involved in regulation of nitrogen metabolism in Streptomyces coelicolor A3(2). Fink D, Weissschuh N, Reuther J, Wohlleben W, Engels A, Mol Microbiol 2002 46 331 347 10.1046/j.1365-2958.2002.03150.x 12406212 (Pubitemid 35340947)
3. The Streptomyces coelicolor GlnR regulon: identification of new GlnR targets and evidence for a central role of GlnR in nitrogen metabolism in actinomycetes. Tiffert Y, Supra P, Wurm R, Wohlleben W, Wagner R, Reuther J, Mol Microbiol 2008 67 861 880 10.1111/j.1365-2958.2007.06092.x 18179599 (Pubitemid 351143689)
4. Proteomic analysis of the GlnR-mediated response to nitrogen limitation in Streptomyces coelicolor M145. Tiffert Y, Franz-Wachtel M, Fladerer C, Nordheim A, Reuther J, Wohlleben W, Mast Y, Appl Microbiol Biotechnol 2011 89 1149 1159 10.1007/s00253-011-3086-9 21229241
5. Nitrogen metabolism in Streptomyces coelicolor: transcriptional and post-translational regulation. Reuther J, Wohlleben W, J Mol Microbiol Biotechnol 2007 12 139 146 10.1159/000096469 17183221 (Pubitemid 46011135)
6. AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum. Jakoby M, Nolden L, Meier-Wagner J, Krämer R, Burkovski A, Mol Microbiol 2000 37 964 977 10.1046/j.1365-2958.2000.02073.x 10972815 (Pubitemid 30618155)
7. Nitrogen assimilation in Corynebacterium diphtheriae: pathways and regulatory cascades. Nolden L, Beckers G, Burkovski A, FEMS Microbiol Lett 2002 208 287 293 10.1111/j.1574-6968.2002.tb11096.x 11959451 (Pubitemid 34310610)
8. Nitrogen metabolism and nitrogen control in corynebacteria: variations of a common theme. Walter B, Hänßler E, Kalinowski J, Burkovski A, J Mol Microbiol Biotechnol 2007 12 131 138 10.1159/000096468 17183220 (Pubitemid 46011134)
9. Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon. Beckers G, Strösser J, Hildebrandt U, Kalinowski J, Farwick M, Krämer R, Burkovski A, Mol Microbiol 2005 58 580 595 10.1111/j.1365-2958.2005.04855.x 16194241 (Pubitemid 41476170)
10. A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR. Buchinger S, Strösser J, Rehm N, Hänßler E, Hans S, Bathe B, Schomburg D, Krämer R, Burkovski A, J Biotechnol 2009 140 68 74 10.1016/j.jbiotec.2008. 10.009 19041910
11. Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR. Amon J, Bräu T, Grimrath A, Hänßler E, Hasselt K, Höller M, Jeßberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A, J Bacteriol 2008 190 7108 7106 10.1128/JB.00855-08 18689485
12. A genomic view on nitrogen metabolism and nitrogen control in mycobacteria. Amon J, Titgemeyer F, Burkovski A, J Mol Microbiol Biotechnol 2009 17 20 29 10.1159/000159195 18824837
13. The COG database: an updated version includes eukaryotes. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. BMC Bioinformatics 2003 4 41 10.1186/1471-2105-4-41 12969510 (Pubitemid 38751229)
14. DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum. Silberbach M, Hüser A, Kalinowski J, Pühler A, Walter B, Krämer R, Burkovski A, J Biotechnol 2005 119 357 367 10.1016/j.jbiotec.2005.04.007 15935503 (Pubitemid 41330754)
15. Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. Pullan ST, Chandra G, Bibb MJ, Merrick M, BMC Genomics 2011 12 175 10.1186/1471-2164- 12-175 21463507
16. Changes in the enzyme activities involved in nitrogen assimilation in Mycobacterium smegmatis under various growth conditions. Ahmad S, Bhatnagar RK, Venkitasubramanian TA, Ann Inst Pasteur Microbiol 1986 137B 231 237 2891360 (Pubitemid 17210134)
17. The nitrogen metabolism of mycobacteria. Iwainsky H, Sehrt I, Z Tuberk Erkr Thoraxorg 1968 128 145 150 5755175
18. Effect of homoserine on growth of Mycobacterium smegmatis: inhibition of glutamate transport by homoserine. Sritharan V, Ratledge C, Wheeler PR, J Gen Microbiol 1987 133 2781 2785 2896760
19. Urease of Corynebacterium glutamicum: organization of corresponding genes and investigation of activity. Nolden L, Beckers G, Möckel B, Pfefferle W, Nampoothiri KM, Krämer R, Burkovski A, FEMS Microbiol Lett 2000 189 305 310 10.1111/j.1574-6968.2000.tb09248.x 10930756 (Pubitemid 30642910)
20. Structure of the urease operon of Corynebacterium glutamicum. Puskás LG, Inui M, Yukawa H, DNA Seq 2000 11 383 394 467 11328647 (Pubitemid 32398612)
21. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, et al. PLoS Genet 2006 2 214 10.1371/journal.pgen.0020214 17194220 (Pubitemid 46045189)
22. Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T, Genome Res 2003 13 1572 1579 10.1101/gr.1285603 12840036 (Pubitemid 36874473)
23. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, et al. J Bacteriol 2008 190 2138 2149 10.1128/JB.01595-07 18192381 (Pubitemid 351355337)
24. Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. Bagwell CE, Bhat S, Hawkins GM, Smith BW, Biswas T, Hoover TR, Saunders E, Han CS, Tsodikov OV, Shimkets LJ, PLoS One 2008 3 3878 10.1371/journal.pone.0003878 19057647
25. The complete genomic sequence of Nocardia farcinica IFM 10152. Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, Hotta K, Shiba T, Hattori M, Proc Natl Acad Sci USA 2004 101 14925 14930 10.1073/pnas.0406410101 15466710 (Pubitemid 39410776)
26. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, et al. Proc Natl Acad Sci USA 2001 98 12215 12220 10.1073/pnas.211433198 11572948 (Pubitemid 32959853)
27. The TetR family of transcriptional repressors. Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R, Microbiol Mol Biol Rev 2005 69 326 356 10.1128/MMBR.69.2.326-356.2005 15944459 (Pubitemid 40847943)
28. Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques. Silberbach M, Schäfer M, Hüser AT, Kalinowski J, Pühler A, Krämer R, Burkovski A, Appl Environ Microbiol 2005 71 2391 23402 10.1128/AEM.71.5.2391- 2402.2005 15870326 (Pubitemid 40646981)
29. The mechanisms of carbon catabolite repression in bacteria. Deutscher J, Curr Opin Microbiol 2008 11 87 93 10.1016/j.mib.2008.02.007 18359269
30. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Görke B, Stülke J, Nat Rev Microbiol 2008 6 613 624 10.1038/nrmicro1932 18628769 (Pubitemid 352006104)
31. Sambrook J, Fritsch EF, Maniatis T, Molecular Cloning. A Laboratory Handbook Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press 2 1989
32. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Grant SG, Jessee J, Bloom FR, Hanahan D, Proc Natl Acad Sci USA 1990 87 4645 4649 10.1073/pnas.87.12.4645 2162051 (Pubitemid 20204159)
33. Isolation of genomic DNA from mycobacteria. Belisle JT, Sonnenberg MG, Methods Mol Biol 1998 101 31 44 9921467
34. Consecutive gene deletions in Mycobacterium smegmatis using the yeast FLP recombinase. Stephan J, Stemmer V, Niederweis M, Gene 2004 343 181 190 10.1016/j.gene.2004.08.028 15563844 (Pubitemid 39551042)
35. The growth rate of Mycobacterium smegmatis depends on sufficient porin-mediated influx of nutrients. Stephan J, Bender J, Wolschendorf F, Hoffmann C, Roth E, Mailänder C, Engelhardt H, Niederweis M, Mol Microbiol 2005 58 714 730 10.1111/j.1365-2958.2005.04878.x 16238622 (Pubitemid 41532470)
36. Amplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions. Moreno-Paz M, Parro V, Environ Microbiol 2006 8 1064 1073 10.1111/j.1462-2920.2006.00998.x 16689727 (Pubitemid 43901773)
37. polR, a pathway-specific transcriptional regulatory gene, positively controls polyoxin biosynthesis in Streptomyces cacaoi subsp. asoensis. Li R, Xie Z, Tian Y, Yang H, Chen W, You D, Liu G, Deng Z, Tan H, Microbiology 2009 155 1819 1831 10.1099/mic.0.028639-0 19383687