RNA structures regulating ribosomal protein biosynthesis in bacilli

RNA Biology

Volumn 10, Issue 7, 2013, Pages 1180-1184

  Deiorio Haggar, Kaila ^a   Anthony, Jon ^a   Meyer, Michelle M ^a  

^a BOSTON COLLEGE   (United States)

Author keywords

Bacillus subtilis; Geobacillus stearothermophilus; Gram positive; Infernal; Rfam; Ribosomal leader sequence; Ribosomal protein

Indexed keywords

RIBOSOME PROTEIN;

ARTICLE; BACILLI; BASE PAIRING; GENE FUNCTION; GENOMICS; NONHUMAN; PHYLOGENY; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; RNA BINDING; RNA STRUCTURE; TRANSCRIPTION INITIATION;

BACILLI (CLASS); BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS; POSIBACTERIA;

BACILLUS SUBTILIS; GEOBACILLUS STEAROTHERMOPHILUS; GRAM-POSITIVE; INFERNAL; RFAM; RIBOSOMAL LEADER SEQUENCE; RIBOSOMAL PROTEIN;

BACILLUS; BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RIBOSOMAL PROTEINS; RNA, BACTERIAL;

EID: 84880853882     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.24151     Document Type: Article

References (34)

1. Serganov A, Patel DJ. Molecular recognition and function of riboswitches. Curr Opin Struct Biol 2012; 22:279-86; PMID:22579413; http://dx.doi.org/10. 1016/j.sbi.2012.04.005.
2. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880-91; PMID:21925377; http://dx.doi.org/10.1016/j.molcel.2011.08.022.
3. Desnoyers G, Bouchard MP, Massé E. New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet 2013; 29:92-8; PMID:23141721; http://dx.doi.org/10.1016/j.tig.2012.10.004.
4. Nomura M, Yates JL, Dean D, Post LE. Feedback regulation of ribosomal protein gene expression in Escherichia coli: structural homology of ribosomal RNA and ribosomal protein mRNA. Proc Natl Acad Sci USA 1980; 77:7084-8; PMID:7012833; http://dx.doi.org/10.1073/pnas.77.12.7084.
5. Zengel JM, Lindahl L. Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli. Prog Nucleic Acid Res Mol Biol 1994; 47:331-70; PMID:7517053; http://dx.doi.org/10.1016/S0079-6603(08)60256-1.
6. Zengel JM, Lindahl L. Ribosomal protein L4 stimulates in vitro termination of transcription at a NusAdependent terminator in the S10 operon leader. Proc Natl Acad Sci USA 1990; 87:2675-9; PMID:2157208; http://dx.doi.org/10.1073/pnas.87.7.2675.
7. Guillier M, Allemand F, Raibaud S, Dardel F, Springer M, Chiaruttini C. Translational feedback regulation of the gene for L35 in Escherichia coli requires binding of ribosomal protein L20 to two sites in its leader mRNA: A possible case of ribosomal RNA-messenger RNA molecular mimicry. RNA 2002; 8:878-89; PMID:12166643; http://dx.doi.org/10.1017/S1355838202029084.
8. Marzi S, Myasnikov AG, Serganov A, Ehresmann C, Romby P, Yusupov M, et al. Structured mRNAs regulate translation initiation by binding to the platform of the ribosome. Cell 2007; 130:1019-31; PMID:17889647; http://dx.doi.org/10. 1016/j.cell.2007.07.008.
9. Schlax PJ, Xavier KA, Gluick TC, Draper DE. Translational repression of the Escherichia coli alpha operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex. J Biol Chem 2001; 276:38494-501; PMID:11504736; http://dx.doi.org/10.1074/jbc.M106934200.
10. Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM. Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria. Nucleic Acids Res 2013; 41:3491-503; PMID:23396277; http://dx.doi.org/10.1093/nar/gkt055.
11. Yutin N, Puigbò P, Koonin EV, Wolf YI. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 2012; 7:e36972; PMID:22615861; http://dx.doi.org/10.1371/journal.pone.0036972.
12. Coenye T, Vandamme P. Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes. FEMS Microbiol Lett 2005; 242:117-26; PMID:15621428; http://dx.doi.org/10.1016/j.femsle.2004.10.050.
13. Iben JR, Draper DE. Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11. Biochemistry 2008; 47:2721-31; PMID:18247578; http://dx.doi.org/10.1021/bi701838y.
14. Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, et al. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics 2009; 10:268; PMID:19531245; http://dx.doi.org/10.1186/1471-2164-10-268.
15. Grundy FJ, Henkin TM. The rpsD gene, encoding ribosomal protein S4, is autogenously regulated in Bacillus subtilis. J Bacteriol 1991; 173:4595-602; PMID:1906866.
16. Scott LG, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5'-translational operator mRNA. J Mol Biol 2001; 314:413-22; PMID:11846555; http://dx.doi.org/10.1006/jmbi.2001.5165.
17. Choonee N, Even S, Zig L, Putzer H. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res 2007; 35:1578-88; PMID:17289755; http://dx.doi.org/10.1093/nar/gkm011.
18. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 2013; 41(Database issue):D226-32; PMID:23125362; http://dx.doi.org/10.1093/nar/gks1005.
19. Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, et al. A computational pipeline for highthroughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 2007; 3:e126; PMID:17616982; http://dx.doi.org/10.1371/journal.pcbi.0030126.
20. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335-7; PMID:19307242; http://dx.doi.org/10. 1093/bioinformatics/btp157.
21. Miller CA, Anthony J, Meyer MM, Marth G. Scribl: An HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics 2013; 29:381-3; PMID:23172864; http://dx.doi.org/10.1093/bioinformatics/bts677.
22. Wolf M, Müller T, Dandekar T, Pollack JD. Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol 2004; 54:871-5; PMID:15143038; http://dx.doi.org/10.1099/ijs.0.02868-0.
23. Scott LG, Williamson JR. The binding interface between Bacillus stearothermophilus ribosomal protein S15 and its 5'-translational operator mRNA. J Mol Biol 2005; 351:280-90; PMID:16005889; http://dx.doi.org/10.1016/j.jmb. 2005.06.030.
24. Philippe C, Portier C, Mougel M, Grunberg-Manago M, Ebel JP, Ehresmann B, et al. Target site of Escherichia coli ribosomal protein S15 on its messenger RNA. Conformation and interaction with the protein. J Mol Biol 1990; 211:415-26; PMID:2407855; http://dx.doi.org/10.1016/0022-2836(90)90362-P.
25. Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, et al. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int J Syst Evol Microbiol 2001; 51:433-46; PMID:11321089.
26. Jinks-Robertson S, Nomura M. Ribosomal protein S4 acts in trans as a translational repressor to regulate expression of the alpha operon in Escherichia coli. J Bacteriol 1982; 151:193-202; PMID:6211432.
27. Grundy FJ, Henkin TM. Cloning and analysis of the Bacillus subtilis rpsD gene, encoding ribosomal protein S4. J Bacteriol 1990; 172:6372-9; PMID:1699930.
28. Li X, Lindahl L, Sha Y, Zengel JM. Analysis of the Bacillus subtilis S10 ribosomal protein gene cluster identifies two promoters that may be responsible for transcription of the entire 15-kilobase S10-spc-Alpha cluster. J Bacteriol 1997; 179:7046-54; PMID:9371452.
29. Grundy FJ, Henkin TM. Characterization of the Bacillus subtilis rpsD regulatory target site. J Bacteriol 1992; 174:6763-70; PMID:1400226.
30. Stern S, Wilson RC, Noller HF. Localization of the binding site for protein S4 on 16 S ribosomal RNA by chemical and enzymatic probing and primer extension. J Mol Biol 1986; 192:101-10; PMID:3820298; http://dx.doi.org/10.1016/ 0022-2836(86)90467-5.
31. Vartikar JV, Draper DE. S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region. J Mol Biol 1989; 209:221-34; PMID:2685320; http://dx.doi.org/10.1016/0022-2836(89)90274-X.
32. Serganov A, Polonskaia A, Ehresmann B, Ehresmann C, Patel DJ. Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J 2003; 22:1898-908; PMID:12682022; http://dx.doi.org/10. 1093/emboj/cdg170.
33. Naville M, Gautheret D. Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. Genome Biol 2010; 11:R97; PMID:20920266http://dx.doi.org/10.1186/gb-2010-11-9-r97.
34. Weinberg Z, Breaker RR. R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics 2011; 12:3; PMID:21205310; http://dx.doi.org/10.1186/1471-2105-12-3.