Rho and RNase play a central role in FMN riboswitch regulation in Corynebacterium glutamicum

Nucleic Acids Research

Volumn 43, Issue 1, 2015, Pages 520-529

  Takemoto, Norihiko ^a   Tanaka, Yuya ^a   Inui, Masayuki ^a,b  

^a RESEARCH INSTITUTE OF INNOVATIVE TECHNOLOGY FOR THE EARTH   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARRIER PROTEIN; FLAVINE MONONUCLEOTIDE; MESSENGER RNA; RHO FACTOR; RIBONUCLEASE; RIBONUCLEASE E; RIBOSWITCH;

ANTAGONISTS AND INHIBITORS; CORYNEBACTERIUM GLUTAMICUM; ENZYMOLOGY; GENE DELETION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; RIBOSWITCH; TRANSCRIPTION ELONGATION; TRANSCRIPTION TERMINATION;

BACTERIAL PROTEINS; CORYNEBACTERIUM GLUTAMICUM; ENDORIBONUCLEASES; FLAVIN MONONUCLEOTIDE; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; MEMBRANE TRANSPORT PROTEINS; RHO FACTOR; RIBOSWITCH; RNA, MESSENGER; TRANSCRIPTION ELONGATION, GENETIC; TRANSCRIPTION TERMINATION, GENETIC;

EID: 84941074547     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1281     Document Type: Article

References (38)

1. Roth,A. and Breaker,R.R. (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem., 78, 305-334.
2. Henkin,T.M. (2008) Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev., 22, 3383-3390.
3. Serganov,A. and Nudler,E. (2013) A decade of riboswitches. Cell, 152, 17-24.
4. Caron,M.P., Bastet,L., Lussier,A., Simoneau-Roy,M., Masse,E. and Lafontaine,D.A. (2012) Dual-acting riboswitch control of translation initiation and mRNA decay. Proc. Natl Acad. Sci. U.S.A., 109, E3444-E3453.
5. Hollands,K., Proshkin,S., Sklyarova,S., Epshtein,V., Mironov,A., Nudler,E. and Groisman,E.A. (2012) Riboswitch control of Rho-dependent transcription termination. Proc. Natl Acad. Sci. U.S.A., 109, 5376-5381.
6. Hermann,T. (2003) Industrial production of amino acids by coryneform bacteria. J. Biotechnol., 104, 155-172.
7. Inui,M., Kawaguchi,H., Murakami,S., Vertès,A.A. and Yukawa,H. (2004) Metabolic engineering of Corynebacterium glutamicum for fuel ethanol production under oxygen-deprivation conditions. J. Mol. Microbiol. Biotechnol., 8, 243-254.
8. Okino,S., Noburyu,R., Suda,M., Jojima,T., Inui,M. and Yukawa,H. (2008) An efficient succinic acid production process in a metabolically engineered Corynebacterium glutamicum strain. Appl. Microbiol. Biotechnol., 81, 459-464.
9. Inui,M., Murakami,S., Okino,S., Kawaguchi,H., Vertès,A.A. and Yukawa,H. (2004) Metabolic analysis of Corynebacterium glutamicum during lactate and succinate productions under oxygen deprivation conditions. J. Mol. Microbiol. Biotechnol., 7, 182-196.
10. Smith,K.M., Cho,K.M. and Liao,J.C. (2010) Engineering Corynebacterium glutamicum for isobutanol production. Appl. Microbiol. Biotechnol., 87, 1045-1055.
11. Baumbach,J. (2007) CoryneRegNet 4.0-a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8, 429.
12. Brune,I., Brinkrolf,K., Kalinowski,J., Puhler,A. and Tauch,A. (2005) The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC genomics, 6, 86.
13. Liebl,W. (2005) Corynebacterium Taxonomy. In: Eggeling,L and Bott,M (eds). Handbook of Corynebacterium glutamicum. CRC Press, Boca Raton, FL. pp. 9-34.
14. 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.
15. Vitreschak,A.G., Rodionov,D.A.,Mironov,A.A. and Gelfand,M.S. (2002) Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res., 30, 3141-3151.
16. Mentz,A., Neshat,A., Pfeifer-Sancar,K., Puhler,A., Ruckert,C. and Kalinowski,J. (2013) Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics, 14, 714.
17. Takemoto,N., Tanaka,Y., Inui,M. and Yukawa,H. (2014) The physiological role of riboflavin transporter and involvement of FMN-riboswitch in its gene expression in Corynebacterium glutamicum. Appl. Microbiol. Biotechnol., 98, 4159-4168.
18. Inui,M., Suda,M., Okino,S., Nonaka,H., Puskas,L.G., Vertès,A.A. and Yukawa,H. (2007) Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions. Microbiology, 153, 2491-2504.
19. Teramoto,H., Suda,M., Inui,M. and Yukawa,H. (2010) Regulation of the expression of genes involved in NAD de novo biosynthesis in Corynebacterium glutamicum. Appl. Environ. Microbiol., 76, 5488-5495.
20. Tanaka,Y., Teramoto,H., Inui,M. and Yukawa,H. (2011) Translation efficiency of antiterminator proteins is a determinant for the difference in glucose repression of two beta-glucoside phosphotransferase system gene clusters in Corynebacterium glutamicum R. J. Bacteriol., 193, 349-357.
21. Kushner,S.R. (2004) mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life, 56, 585-594.
22. Maeda,T. and Wachi,M. (2012) 3untranslated region-dependent degradation of the aceA mRNA, encoding the glyoxylate cycle enzyme isocitrate lyase, by RNase E/G in Corynebacterium glutamicum. Appl. Environ. Microbiol., 78, 8753-8761.
23. Deana,A. and Belasco,J.G. (2005) Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev., 19, 2526-2533.
24. Uplekar,S., Rougemont,J., Cole,S.T. and Sala,C. (2013) High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Res., 41, 961-977.
25. Nou,X. and Kadner,R.J. (2000) Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc. Natl Acad. Sci. U.S.A., 97, 7190-7195.
26. Nou,X. and Kadner,R.J. (1998) Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli. J. Bacteriol., 180, 6719-6728.
27. Ontiveros-Palacios,N., Smith,A.M., Grundy,F.J., Soberon,M., Henkin,T.M. and Miranda-Rios,J. (2008) Molecular basis of gene regulation by the THI-box riboswitch. Mol. Microbiol., 67, 793-803.
28. Barrick,J.E. and Breaker,R.R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol., 8, R239.
29. Winkler,W.C., Cohen-Chalamish,S. and Breaker,R.R. (2002) An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci. U.S.A., 99, 15908-15913.
30. Epshtein,V.,Mironov,A.S. and Nudler,E. (2003) The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci. U.S.A., 100, 5052-5056.
31. Sudarsan,N., Wickiser,J.K., Nakamura,S., Ebert,M.S. and Breaker,R.R. (2003) An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev., 17, 2688-2697.
32. Groisman,E.A., Cromie,M.J., Shi,Y. and Latifi,T. (2006) A Mg2+-responding RNA that controls the expression of a Mg2+ transporter. Cold Spring Harb. Symp. Quant. Biol., 71, 251-258.
33. Tezuka,T. and Ohnishi,Y. (2014) Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus. J. Bacteriol., 196, 1369-1376.
34. Bian,J., Shen,H., Tu,Y., Yu,A. and Li,C. (2011) The riboswitch regulates a thiamine pyrophosphate ABC transporter of the oral spirochete Treponema denticola. J. Bacteriol., 193, 3912-3922.
35. Cheng,J., Poduska,B., Morton,R.A. and Finan,T.M. (2011) An ABC-type cobalt transport system is essential for growth of Sinorhizobium meliloti at trace metal concentrations. J. Bacteriol., 193, 4405-4416.
36. Argaman,L., Elgrably-Weiss,M., Hershko,T., Vogel,J. and Altuvia,S. (2012) RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq. Proc. Natl Acad. Sci. U.S.A., 109, 4621-4626.
37. Bossi,L., Schwartz,A., Guillemardet,B., Boudvillain,M. and Figueroa-Bossi,N. (2012) A role for Rho-dependent polarity in gene regulation by a noncoding small RNA. Genes Dev., 26, 1864-1873.
38. Rabhi,M., Espeli,O., Schwartz,A., Cayrol,B., Rahmouni,A.R., Arluison,V. and Boudvillain,M. (2011) The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators. EMBO J., 30, 2805-2816.