Erratum to Transcription attenuation in bacteria: theme and variations, [Brief Funct Genomic Proteomic 2009; 8 : 482-492, doi:10.1093/bfgp/elp025];Transcription attenuation in bacteria: Theme and variations

Briefings in Functional Genomics and Proteomics

Volumn 8, Issue 6, 2009, Pages 482-492

  Naville, Magali ^a   Gautheret, Daniel ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Attenuation; Bacteria; Evolution; Gene regulation; Transcriptional termination

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; CIS ACTING ELEMENT; COLD SHOCK PROTEIN; MESSENGER RNA; RHO FACTOR; RNA POLYMERASE; T BOX TRANSCRIPTION FACTOR; THREONINE TRANSFER RNA; TRANSFER RNA; BACTERIAL RNA; RNA BINDING PROTEIN;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BIOSYNTHESIS; CODON; FUNCTIONAL GENOMICS; GENE CONTROL; GENE EXPRESSION REGULATION; GENE TRANSFER; GENETIC ASSOCIATION; GENETIC CODE; HOUSEKEEPING GENE; MOLECULAR EVOLUTION; NONHUMAN; OPERON; PROTEIN RNA BINDING; RIBOSWITCH; RNA BINDING; RNA STRUCTURE; RNA TRANSCRIPTION; RNA TRANSLATION; TEMPERATURE SENSITIVITY; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; BACTERIUM; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENETICS; METABOLISM; REVIEW;

BACTERIA (MICROORGANISMS);

BACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC VARIATION; RNA, BACTERIAL; RNA-BINDING PROTEINS; TRANSCRIPTION, GENETIC;

EID: 70449729788     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elq008     Document Type: Erratum

References (51)

1. Yanofsky C, Platt T, Crawford IP, et al. The complete nucleotide sequence of the tryptophan operon of Escherichia coli. Nucleic Acids Res 1981;9:6647-68.
2. Merino E, Yanofsky C. Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet 2005;21:260-4.
3. Nudler E, Gottesman ME. Transcription termination and anti-termination in E.coli. Genes Cells 2002;7:755-68.
4. Neal RJ, Chater KF. Bidirectional promoter and terminator regions bracket mmr, a resistance gene embedded in the Streptomyces coelicolor A3(2) gene cluster encoding methylenomycin production. Gene 1991;100:75-83.
5. Unniraman S, Prakash R, Nagaraja V. Conserved economics of transcription termination in eubacteria. Nucleic Acids Res 2002;30:675-84.
6. Narberhaus F, Waldminghaus T, Chowdhury S. RNA thermometers. FEMS Microbiol Rev 2006;30:3-16.
7. Waldminghaus T, Gaubig LC, Narberhaus F. Genome-wide bioinformatics prediction and experimental evaluation of potential RNA thermometers. Mol Genet Genomics 2007; 278:555-64.
8. Chowdhury S, Maris C, Allain FH, etal. Molecular basis for temperature sensing by an RNA thermometer. EMBO J 2006;25:2487-97.
9. Uppal S, Rao Akkipeddi VSN, Jawali N. Posttranscriptional regulation of cspE in Escherichia coli: involvement of the short 50-untranslated region. FEMS Microbiol Lett 2008; 279:83-91.
10. Bae W, Xia B, Inouye M, et al. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc Natl Acad Sci USA 2000;97:7784-9.
11. Vitreschak A, Rodionov D, Mironov A, etal. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet 2004;20:44-50.
12. Coppins L, Hall KB, Groisman EA. The intricate world of riboswitches. Curr Opin Microbiol 2007;10:176-81.
13. Henkin TM. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev 2009;22:3383-90.
14. Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs. Curr Opin Microbiol 2009;12:161-9.
15. Sudarsan N, Lee ER, Weinberg Z, et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 2008;321:411-13.
16. Regulski EE, Moy RH, Weinberg Z, et al. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol 2008;68:918-32.
17. Dann CD, Wakeman CA, Sieling CL, et al. Structure and mechanism of a metal-sensing regulatory RNA. Cell 2007; 130:878-92.
18. Serganov A, Huang L, Patel DJ. Structural insights into amino acid and gene control by a lysine riboswitch. Nature 2008;455:1263-7.
19. Garst AD, Heroux A, Rambo RP, et al. Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 2008;283:22347-51.
20. Sudarsan N, Hammond MC, Block KF, et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 2006;314:300-4.
21. Kim JN, Breaker RR. Purine sensing by riboswitches. Biol Cell 2008;100:1-11.
22. Gutiérrez-Preciado A, Henkin TM, Grundy FJ, et al. Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev 2009;73:36-61.
23. Vitreschak AG, Mironov AA, Lyubetsky VA, et al. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA 2008;14:717-35.
24. Vitreschak AG, Lyubetskaya EV, Shirshinet MA, et al. Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett 2004;234:357-70.
25. Lyubetskaya EV, Leont'ev LA, Gelfand MS, etal. Search for alternative RNA secondary structures regulating expression of bacterial genes. Mol Biol 2003;37:707-16.
26. Nomura M, Yates JL, Dean D, et al. Feedback regulation of ribosomal protein gene expression in Escherichia coli: structural homology of ribosomal RNA and ribosomal protein mRNA. Proc Natl Acad Sci 1980;77:7084-8.
27. Draper DE. How do proteins recognize specific RNA sites? New clues from autogenously regulated ribosomal proteins. Trends Biochem Sci 1989;14:335-8.
28. Romby P, Springer M. Bacterial translational control at atomic resolution. Trends Genet 2003;19:155-61.
29. Bonner ER, D'Elia JN, Billips BK, etal. Molecular recognition of pyr mRNA by the Bacillus subtilis attenuation regulatory protein PyrR. Nucleic Acids Res 2001;29:4851-65.
30. Amster-Choder O. The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination. Curr Opin Microbiol 2005;8:127-34.
31. de Hoon MJL, Makita Y, Nakai K, et al. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comp Biol 2005;1:e25.
32. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007;8:R22.
33. Konan KV, Yanofsky C. Rho-dependent transcription termination in the tna operon of Escherichia coli: Roles of the boxA sequence and the rut site. J Bacteriol 2000;182:3981-8.
34. Tsubouchi T, Mineki R, Taka H, et al. Leader peptide-mediated transcriptional attenuation of lysine biosynthetic gene cluster in Thermus thermophilus. J Biol Chem 2005;280:18511-16.
35. Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 2007;8:R239.
36. Yao Z, Barrick J, Weinberg Z, etal. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 2007;3:e126.
37. Dufayard JF, Duret L, Penel S, et al. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005;21:2596-603.
38. Turnbough CL Jr, Switzer RL. Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 2008;72:266-300.
39. Jensen-MacAllister IE, Meng Q, Switzer RL. Regulation of pyrG expression in Bacillus subtilis: CTP-regulated antitermination and reiterative transcription with pyrG templates in vitro. Mol Microbiol 2007;63:1440-52.
40. Fox KA, Ramesh A, Stearns JE, etal. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc Natl Acad Sci 2009;106:4435-40.
41. André G, Even S, Putzer H, et al. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res 2008; 36:5955-69.
42. Rodionov DA, Vitreschak AG, Mironov AA, et al. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 2004;32:3340-53.
43. Merino E, Jensen RA, Yanofsky C. Evolution of bacterial trp operons and their regulation. Curr Opin Microbiol 2008; 11:78-86.
44. Devalckenaere A, Odaert M, Trieu-Cuot P, et al. Characterization of IS1541-like elements in Yersinia enterocolitica and Yersinia pseudotuberculosis. FEMS Microbiol Lett 1999;176:229-33.
45. Odaert M, Devalckenaere A, Trieu-Cuot P, et al. Molecular characterization of IS1541 insertions in the genome of Yersinia pestis. J Bacteriol 1998;180:178-81.
46. Davis MA, Simons RW, Kleckner N. Tn10 protects itself at two levels from fortuitous activation by external promoters. Cell 1985;43:379-87.
47. Beuzon CR, Marques S, Casadesus J. Repression of IS200 transposase synthesis by RNA secondary structures. Nucleic Acids Res 1999;27:3690-3695.
48. Leonhartsberger S, Huber A, Lottspeich F, etal. The hydH/G genes from Escherichiacoli code for a zinc and lead responsive two-component regulatory system. J Mol Biol 2001;307:93-105.
49. Schell MA. Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 1993;47:597-626.
50. Babitzke P, Romeo T. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 2007;10:156-63.
51. Yarus M, Caporaso JG, Knight R. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 2005;74:179-98.