Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator

BMC Microbiology

Volumn 12, Issue , 2012, Pages

  Caballero, Valeria C ^a,d   Toledo, Viviana P ^a   Maturana, Cristian ^a,b   Fisher, Carolyn R ^c   Payne, Shelley M ^c   Salazar, Juan Carlos ^a  

^a UNIVERSITY OF CHILE   (Chile)

^b UNIVERSITY OF CHILE   (Chile)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

Author keywords

Gene expression; Osmotic stress; Stringent response; tRNA modification

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; BACTERIAL PROTEIN; BETA GALACTOSIDASE; DKSA PROTEIN; GLUTAMYL QUEUOSINE TRNA SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; BIOINFORMATICS; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE FUSION; GENETIC TRANSCRIPTION; NONHUMAN; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SHIGELLA FLEXNERI;

AMINO ACYL-TRNA SYNTHETASES; ARTIFICIAL GENE FUSION; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION, BACTERIAL; GENE ORDER; GENES, REPORTER; PROMOTER REGIONS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE DELETION; SHIGELLA FLEXNERI; SYNTENY; TRANSCRIPTION FACTORS; TRANSCRIPTION TERMINATION, GENETIC;

BACTERIA (MICROORGANISMS); SHIGELLA FLEXNERI;

EID: 84867009425     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-12-226     Document Type: Article

References (44)

1. Aminoacyl-tRNA synthesis. Ibba M, Söll D, Annu Rev Biochem 2000 69 617 650 10.1146/annurev.biochem.69.1.617 10966471
2. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Eriani G, Delarue M, Poch O, Gangloff J, Moras D, Nature 1990 347 203 206 10.1038/347203a0 2203971
3. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Woese CR, Olsen GJ, Ibba M, Söll D, Microbiol Mol Biol Rev 2000 64 202 236 10.1128/MMBR.64.1.202-236.2000 10704480
4. A noncognate aminoacyl-tRNA synthetase that may resolve a missing link in protein evolution. Skouloubris S, de Pouplana LR, de Reuse H, Hendrickson H, Proc Natl Acad Sci USA 2003 100 11297 11302 10.1073/pnas.1932482100 13679580
5. Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates. Salazar JC, Ahel I, Orellana O, Tumbula-Hansen D, Krieger R, Daniels L, Söll D, Proc Natl Acad Sci USA 2003 100 13863 13868 10.1073/pnas.1936123100 14615592
6. Modular design of components of the operational RNA code for alanine in evolution. Schimmel P, Ripmaster T, Trends Biochem Sci 1995 20 333 334 10.1016/S0968-0004(00)89067-2 7482695
7. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Sissler M, Delorme C, Bond J, Ehrlich SD, Renault P, Francklyn C, Proc Natl Acad Sci USA 1999 96 8985 8990 10.1073/pnas.96.16.8985 10430882
8. PoxA, YjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica. Navarre WW, Zou SB, Roy H, Xie JL, Savchenko A, Singer A, Edvokimova E, Prost LR, Kumar R, Ibba M, Fang FC, Mol Cell 2010 39 209 221 10.1016/j.molcel.2010.06.021 20670890
9. A mutation in the poxA gene of Salmonella enterica serovar Typhimurium alters protein production, elevates susceptibility to environmental challenges, and decreases swine colonization. Bearson SM, Bearson BL, Brunelle BW, Sharma VK, Lee IS, Foodborne Pathog Dis 2011 8 725 732 10.1089/fpd.2010.0796 21348575
10. A truncated aminoacyl-tRNA synthetase modifies RNA. Salazar JC, Ambrogelly A, Crain PF, McCloskey JA, Söll D, Proc Natl Acad Sci USA 2004 101 7536 7541 10.1073/pnas.0401982101 15096612
11. An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp. Dubois DY, Blaise M, Becker HD, Campanacci V, Keith G, Giegé R, Cambillau C, Lapointe J, Kern D, Proc Natl Acad Sci USA 2004 101 7530 7535 10.1073/pnas.0401634101 15096594
12. Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Iwata-Reuyl D, Bioorg Chem 2003 31 24 43 10.1016/S0045-2068(02) 00513-8 12697167
13. tRNA's modifications bring order to gene expression. Gustilo EM, Vendeix FA, Agris PF, Curr Opin Microbiol 2008 11 134 140 10.1016/j.mib.2008.02.003 18378185
14. The effect of queuosine on tRNA structure and function. Morris RC, Brown KG, Elliott MS, J Biomol Struct Dyn 1999 4 757 77414
15. Possible anticodon sequences of tRNAHis, tRNAAsnand tRNAAspfromEscherichia coliB. Universal presence of nucleoside Q in the first position of the anticodons of these transfer ribonucleic acids. Harada F, Nishimura S, Biochem 1972 11 301 308 10.1021/bi00752a024
16. vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase (Tgt) of Escherichia coli K-12. Durand JM, Okada N, Tobe T, Watarai M, Fukuda I, Suzuki T, Nakata N, Komatsu K, Yoshikawa M, Sasakawa C, J Bacteriol 1994 176 4627 4634 8045893
17. The modified nucleoside 2-methylthio-N6-isopentenyladenosine in tRNA of Shigella flexneri is required for expression of virulence genes. Durand JM, Björk GR, Kuwae A, Yoshikawa M, Sasakawa C, J Bacteriol 1997 179 5777 5782 9294434
18. Improvement of reading frame maintenance is a common function for several tRNA modifications. Urbonaviĉius J, Qian Q, Durand JM, Hagervall TG, Björk GR, EMBO J 2001 20 4863 4873 10.1093/emboj/20.17.4863 11532950
19. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, Mering C, Nucleic Acids Res 2011 39 561 D568 10.1093/nar/gkq973 21045058
20. Linking databases and organisms: GenomeNet resources in Japan. Kanehisa M, TIBS 1997 22 442 444 9397687
21. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
22. Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation. Kang PJ, Craig EA, J Bacteriol 1990 172 2055 2064 2180916
23. Construction of broad-host-range plasmid vectors for easy visible selection and analysis of promoters. Farinha MA, Kropinski AM, J Bacteriol 1990 172 3496 3499 2111810
24. Sambrook J, Fritsch EF, Maniatis T, Molecular Cloning: A Laboratory Manual USA: Cold Spring Harbor Laboratory Press 2 1989
25. The dksA promoter is negatively feedback regulated by DksA and ppGpp. Chandrangsu P, Lemke JJ, Gourse RL, Mol Microbiol 2011 80 1337 1348 10.1111/j.1365-2958.2011.07649.x 21496125
26. Mfold web server for nucleic acid folding and hybridization prediction. Zuker M, Nucleic Acids Res 2003 31 3406 3415 10.1093/nar/gkg595 12824337
27. dksA is required for intercellular spread of Shigella flexneri via an RpoS-independent mechanism. Mogull SA, Runyen-Janecky LJ, Hong M, Payne SM, Infect Immun 2001 69 5742 5751 10.1128/IAI.69.9.5742-5751.2001 11500451
28. Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity. Sharma UK, Chatterji D, FEMS Microbiol Rev 2010 34 646 657 20491934
29. Coregulation of gene expression by sigma factors RpoE and RpoS in Salmonella enterica serovar Typhi during hyperosmotic stress. Du H, Wang M, Luo Z, Ni B, Wang F, Meng Y, Xu S, Huang X, Curr Microbiol 2011 62 1483 1489 10.1007/s00284-011-9890-8 21311887
30. Transcription profiling of the stringent response in Escherichia coli. Durfee T, Hansen A-M, Zhi H, Blattner FR, Jin DJ, J Bacteriol 2008 190 1084 1096 10.1128/JB.01092-07 18039766
31. Enteric bacteria and osmotic stress: intracellular potassium glutamate as a secondary signal of osmotic stress? Booth IR, Higgins CF, FEMS Microbiol Rev 1990 6 239 246 1974769
32. The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val (cmo5UAC). Golovina AY, Sergiev PV, Golovin AV, Serebryakova MV, Demina I, Govoru VM, Dontsova OA, RNA 2009 15 1134 1141 10.1261/rna.1494409 19383770
33. Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. Smiley BL, Lupski JR, Svec PS, McMacken R, Godson GN, Proc Natl Acad Sci USA 1982 79 4550 4554 10.1073/pnas.79.15.4550 6750604
34. recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli. Pagès V, Koffel-Schwartz N, Fuchs RPP, DNA Repair 2003 2 273 284 10.1016/S1568-7864(02)00217-3 12547390
35. Riboswitches: structures and mechanisms. Garst AD, Edwards AL, Batey RT, Cold Spring Harbor Perspect Biol 2011 3 003533 10.1101/cshperspect.a003533
36. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Roth A, Winkler WC, Regulski EE, Lee BWK, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR, Nat Struct Mol Biol 2007 14 308 317 10.1038/nsmb1224 17384645
37. Computational identification of riboswitches based on RNA conserved functional sequences and conformations. Chang TH, Huang HD, Wu LC, Yeh CT, Liu BJ, Horng JT, RNA 2009 15 1426 1430 10.1261/rna.1623809 19460868
38. Genetics and virulence association of the Shigella flexneri sit iron transport system. Fisher CR, Davies NM, Wyckoff EE, Feng Z, Oaks EV, Payne SM, Infect Immun 2009 77 1992 1999 10.1128/IAI.00064-09 19289511
39. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
40. Comparisons of different hypervariable regions of rrs genes for use if fingerprinting of microbial communities by PCR-Denaturing Gel Electrophoresis. Yu Z, Morrison M, Appl Environ Microbiol 2004 70 4800 4806 10.1128/AEM.70.8. 4800-4806.2004 15294817
41. Single multiplex PCR assay to identify simultaneously the six categories of diarrheagenic Escherichia coli associated with enteric infections. Vidal M, Kruger E, Durán C, Lagos R, Levine M, Prado V, Toro C, Vidal R, J Clin Microbiol 2005 43 5362 5365 10.1128/JCM.43.10.5362-5365.2005 16208019
42. Miller J, Experiments in Molecular Genetics NY: Cold Spring Harbor Laboratory 1972 352 355
43. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR, Gene 1989 77 51 59 10.1016/0378-1119(89)90358-2 2744487
44. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Datsenko KA, Wanner BL, Proc Natl Acad Sci USA 2000 97 6640 6645 10.1073/pnas.120163297 10829079