Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase

RNA

Volumn 18, Issue 4, 2012, Pages 795-806

  Benítez Páez, Alfonso ^a,b   Villarroya, Magda ^a   Armengod, M Eugenia ^a  

^a CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^b Bioinformatic Analysis Group GABi   (Colombia)

Author keywords

Catalytic mechanism; Mutational analysis; rRNA modification; RsmG stability; Transcriptional regulatory elements

Indexed keywords

METHYLTRANSFERASE; RIBOSOME RNA; RSMG METHYLTRANSFERASE; S ADENOSYLMETHIONINE; STREPTOMYCIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DOWN REGULATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME REGULATION; ENZYME STABILITY; ENZYME STRUCTURE; ESCHERICHIA COLI; INVERTED REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROTEIN EXPRESSION; RIBOSOME; RNA BINDING; RNA SYNTHESIS; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

BIOCATALYSIS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; METHYLTRANSFERASES; OPERON;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84858650505     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.029868.111     Document Type: Article

References (50)

1. Andrup L, Atlung T, Ogasawara N, Yoshikawa H, Hansen FG. 1988. Interaction of the Bacillus subtilis DnaA-like protein with the Escherichia coli DnaA protein. J Bacteriol 170: 1333-1338.
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2: 2006.0008. doi: 10.1038/ msb4100050.
3. Leu isoacceptors. RNA 16: 2131-2143.
4. Benítez-Páez A, Cardenas-Brito S, Gutierrez AJ. 2011. A practical guide for the computational selection of residues to be experimentally characterized in protein families. Brief Bioinform doi: 10.1093/bib/bbr052.
5. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci 99: 9697-9702. (Pubitemid 34831110)
6. Bregeon D, Colot V, Radman M, Taddei F. 2001. Translational misreading: A tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 15: 2295-2306. (Pubitemid 32843841)
7. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340-348.
8. Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763. (Pubitemid 28552108)
9. Edgar RC. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. doi: 10.1186/1471-2105-5- 113.
10. Elseviers D, Petrullo LA, Gallagher PJ. 1984. Novel E. coli mutants deficient in biosynthesis of 5-methylaminomethyl-2-thiouridine. Nucleic Acids Res 12: 3521-3534.
11. Emilsson V, Kurland CG. 1990. Growth rate dependence of transfer RNA abundance in Escherichia coli. EMBO J 9: 4359-4366. (Pubitemid 120025992)
12. Gregory ST, Demirci H, Belardinelli R, Monshupanee T, Gualerzi C, Dahlberg AE, Jogl G. 2009. Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG. RNA 15: 1693-1704.
13. Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss- PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723. (Pubitemid 28059943)
14. Gummesson B, Magnusson LU, Lovmar M, Kvint K, Persson O, Ballesteros M, Farewell A, Nystrom T. 2009. Increased RNA polymerase availability directs resources towards growth at the expense of maintenance. EMBO J 28: 2209-2219.
15. Hansen F, Koefoed S, von Meyenburg K, Atlung T. 1981. Transcription and translation events in the oriC region of the E. coli chromosome. ICN-UCLA Symp Mol Cell Biol 22: 37-55.
16. Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravic-Vlahovicek G, Bujnicki JM, Sivaraman J. 2010. Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: A diversity of active sites in m7G methyltransferases. Nucleic Acids Res 38: 4120-4132.
17. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D. 2008. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9: 102. doi: 10.1186/1471-2164-9-102.
18. Jin DJ, Cagliero C, Zhou YN. 2011. Growth rate regulation in Escherichia coli. FEMS Microbiol Rev doi: 10.1111/j.1574-6976.2011.00279.x.
19. Keener J, Nomura M. 1996. Regulation of ribosome synthesis. In Escherichia coli and Salmonella: Cellular and molecular biology (ed. F Neidhardt et al.), pp. 1417-1431. ASM Press, Washington DC.
20. Kolling R, Gielow A, Seufert W, Kucherer C, Messer W. 1988. AsnC, a multifunctional regulator of genes located around the replication origin of Escherichia coli, oriC. Mol Gen Genet 212: 99-104.
21. Macian F, Perez-Roger I, Armengod ME. 1994. An improved vector system for constructing transcriptional lacZ fusions: Analysis of regulation of the dnaA, dnaN, recF, and gyrB genes of Escherichia coli. Gene 145: 17-24. (Pubitemid 24224958)
22. Magnusson LU, Farewell A, Nystrom T. 2005. ppGpp: A global regulator in Escherichia coli. Trends Microbiol 13: 236-242. (Pubitemid 40603907)
23. Miller JH. 1992. A short course in bacterial genetics: A laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
24. Moukadiri I, Prado S, Piera J, Velazquez-Campoy A, Bjork GR, Armengod ME. 2009. Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res 37: 7177-7193.
25. S subunit of RNA polymerase in E. coli. EMBO J 15: 1333-1339.
26. Nishimura K, Hosaka T, Tokuyama S, Okamoto S, Ochi K. 2007a. Mutations in rsmG, encoding a 16S rRNA methyltransferase, result in low-level streptomycin resistance and antibiotic overproduction in Streptomyces coelicolor A3(2). J Bacteriol 189: 3876-3883. (Pubitemid 46740185)
27. Nishimura K, Johansen SK, Inaoka T, Hosaka T, Tokuyama S, Tahara Y, Okamoto S, Kawamura F, Douthwaite S, Ochi K. 2007b. Identification of the RsmG methyltransferase target as 16S rRNA nucleotide G527 and characterization of Bacillus subtilis rsmG mutants. J Bacteriol 189: 6068-6073. (Pubitemid 47236159)
28. Ochi K, Kim JY, Tanaka Y, Wang G, Masuda K, Nanamiya H, Okamoto S, Tokuyama S, Adachi Y, Kawamura F. 2009. Inactivation of KsgA, a 16S rRNA methyltransferase, causes vigorous emergence of mutants with high-level kasugamycin resistance. Antimicrob Agents Chemother 53: 193-201.
29. Ogawa T, Okazaki T. 1991. Concurrent transcription from the gid and mioC promoters activates replication of an Escherichia coli mini-chromosome. Mol Gen Genet 230: 193-200.
30. Ogawa T, Okazaki T. 1994. Cell cycle-dependent transcription from the gid and mioC promoters of Escherichia coli. J Bacteriol 176: 1609-1615. (Pubitemid 24100209)
31. Ogle JM, Ramakrishnan V. 2005. Structural insights into translational fidelity. Annu Rev Biochem 74: 129-177. (Pubitemid 40995504)
32. Ogle JM, Carter AP, Ramakrishnan V. 2003. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28: 259-266. (Pubitemid 36588668)
33. Okamoto S, Tamaru A, Nakajima C, Nishimura K, Tanaka Y, Tokuyama S, Suzuki Y, Ochi K. 2007. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol Microbiol 63: 1096-1106. (Pubitemid 46188264)
34. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
35. Potrykus K, Cashel M. 2008. (p)ppGpp: Still magical? Annu Rev Microbiol 62: 35-51.
36. Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM. 2005. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 59: 482-488. (Pubitemid 40598104)
37. Reese MG. 2001. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26: 51-56. (Pubitemid 33034559)
38. Romanowski MJ, Bonanno JB, Burley SK. 2002. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 47: 563-567. (Pubitemid 34614737)
39. Schubert HL, Blumenthal RM, Cheng X. 2003. Many paths to methyltransfer: A chronicle of convergence. Trends Biochem Sci 28: 329-335. (Pubitemid 36776296)
40. Schuster-Bockler B, Bateman A. 2005. Visualizing profile-profile alignment: Pairwise HMM logos. Bioinformatics 21: 2912-2913. (Pubitemid 40862293)
41. Srivatsan A, Wang JD. 2008. Control of bacterial transcription, translation, and replication by (p)ppGpp. Curr Opin Microbiol 11: 100-105.
42. Suzuki T, Suzuki T. 2007. Chaplet column chromatography: Isolation of a large set of individual RNAs in a single step. Methods Enzymol 425: 231-239.
43. Theisen PW, Grimwade JE, Leonard AC, Bogan JA, Helmstetter CE. 1993. Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli. Mol Microbiol 10: 575-584. (Pubitemid 23334438)
44. Uniprot Consortium. 2010. The Universal Protein Resource (Uni- Prot) in 2010. Nucleic Acids Res 38: D142-D148.
45. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P. 2007. STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-D362. (Pubitemid 46056231)
46. von Meyenburg K, Jorgensen BB, Nielsen J, Hansen FG. 1982. Promoters of the atp operon coding for the membrane-bound ATP synthase of Escherichia coli mapped by Tn10 insertion mutations. Mol Gen Genet 188: 240-248. (Pubitemid 13177172)
47. Walker JE, Saraste M, Gay NJ. 1984. The unc operon. Nucleotide sequence, regulation, and structure of ATP-synthase. Biochim Biophys Acta 768: 164-200.
48. Wong SY, Lee JS, Kwak HK, Via LE, Boshoff HI, Barry CE 3rd. 2011. Mutations in gidB confer low-level streptomycin resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 55: 2515-2522.
49. Yim L, Moukadiri I, Bjork GR, Armengod ME. 2006. Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Nucleic Acids Res 34: 5892-5905. (Pubitemid 44941168)
50. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)