Searching for small σb-regulated genes in Staphylococcus aureus

Archives of Microbiology

Volumn 193, Issue 1, 2011, Pages 23-34

  Nielsen, Jesper S ^a   Christiansen, Mie H G ^a   Bonde, Mette ^a   Gottschalk, Sanne ^b   Frees, Dorte ^b   Thomsen, Line E ^b   Kallipolitis, Birgitte H ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

B; S. aureus; SRNA

Indexed keywords

SIGMA B DEPENDENT SMALL RNA A; SIGMA B DEPENDENT SMALL RNA B; SIGMA B DEPENDENT SMALL RNA C; SIGMA FACTOR; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; GENE FUNCTION; GENETIC CONSERVATION; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN EXPRESSION; REGULATOR GENE; REGULON; STAPHYLOCOCCUS AUREUS; TRANSCRIPTION INITIATION SITE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DNA, INTERGENIC; GENE EXPRESSION REGULATION, BACTERIAL; HOST FACTOR 1 PROTEIN; MOLECULAR SEQUENCE DATA; RNA, BACTERIAL; RNA, SMALL UNTRANSLATED; SEQUENCE ALIGNMENT; SIGMA FACTOR; STAPHYLOCOCCUS AUREUS; TRANSCRIPTION INITIATION SITE;

STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

EID: 78650909811     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-010-0641-1     Document Type: Article

References (49)

1. H Aiba 2007 Mechanism of RNA silencing by Hfq-binding small RNAs Curr Opin Microbiol 10 134 139 1:CAS:528:DC%2BD2sXksFait7k%3D 10.1016/j.mib.2007.03. 010 17383928 (Pubitemid 46590050)
2. AureoList (2010) AureoList. World Wide Web. http://genolist.pasteur.fr/ AureoList/
3. M Bischoff P Dunman J Kormanec D Macapagal E Murphy W Mounts B Berger-Bachi S Projan 2004 Microarray-based analysis of the Staphylococcus aureus sigmaB regulon J Bacteriol 186 4085 4099 1:CAS:528:DC%2BD2cXlt1Onu7c%3D 10.1128/JB.186.13.4085-4099.2004 15205410 (Pubitemid 38802556)
4. C Bohn C Rigoulay P Bouloc 2007 No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus BMC Microbiol 7 10 10.1186/1471-2180-7-10 17291347 (Pubitemid 46277050)
5. Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezee-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res. doi: 10.1093/nar/gkq462
6. S Boisset T Geissmann E Huntzinger P Fechter N Bendridi M Possedko C Chevalier AC Helfer Y Benito A Jacquier C Gaspin F Vandenesch P Romby 2007 Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism Genes Dev 21 1353 1366 1:CAS:528:DC%2BD2sXmsFSgsbs%3D 10.1101/gad.423507 17545468 (Pubitemid 46871039)
7. J Cassat PM Dunman E Murphy SJ Projan KE Beenken KJ Palm SJ Yang KC Rice KW Bayles MS Smeltzer 2006 Transcriptional profiling of a Staphylococcus aureus clinical isolate and its isogenic agr and sarA mutants reveals global differences in comparison to the laboratory strain RN6390 Microbiology 152 3075 3090 1:CAS:528:DC%2BD28XhtFWqtbzK 10.1099/mic.0.29033-0 17005987 (Pubitemid 44542387)
8. JK Christiansen MH Larsen H Ingmer L Sogaard-Andersen BH Kallipolitis 2004 The RNA-binding protein Hfq of Listeria monocytogenes: role in stress tolerance and virulence J Bacteriol 186 3355 3362 1:CAS:528:DC%2BD2cXks1Cqsb8%3D 10.1128/JB.186.11.3355-3362.2004 15150220 (Pubitemid 38661530)
9. ClustalW (2010) ClustalW. World Wide Web. http://www.ebi.ac.uk/Tools/ clustalw2/index.html
10. H de Lencastre A Tomasz 1994 Reassessment of the number of auxiliary genes essential for expression of high-level methicillin resistance in Staphylococcus aureus Antimicrob Agents Chemother 38 2590 2598 7872753
11. ES Duthie LL Lorenz 1952 Staphylococcal coagulase; mode of action and antigenicity J Gen Microbiol 6 95 107 1:CAS:528:DyaG3sXisFKhsQ%3D%3D 14927856
12. EM Fozo M Kawano F Fontaine Y Kaya KS Mendieta KL Jones A Ocampo KE Rudd G Storz 2008 Repression of small toxic protein synthesis by the Sib and OhsC small RNAs Mol Microbiol 70 1076 1093 1:CAS:528:DC%2BD1cXhsVKitb%2FF 10.1111/j.1365-2958.2008.06394.x 18710431
13. A Gaballa H Antelmann C Aguilar SK Khakh KB Song GT Smaldone JD Helmann 2008 The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins Proc Natl Acad Sci USA 105 11927 11932 1:CAS:528:DC%2BD1cXhtVCnurjE 10.1073/pnas.0711752105 18697947
14. E Geisinger RP Adhikari R Jin HF Ross RP Novick 2006 Inhibition of rot translation by RNAIII, a key feature of agr function Mol Microbiol 61 1038 1048 1:CAS:528:DC%2BD28XovVWmtL0%3D 10.1111/j.1365-2958.2006.05292.x 16879652 (Pubitemid 44134179)
15. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37:7239-7257
16. S Gertz S Engelmann R Schmid AK Ziebandt K Tischer C Scharf J Hacker M Hecker 2000 Characterization of the sigma(B) regulon in Staphylococcus aureus J Bacteriol 182 6983 6991 1:CAS:528:DC%2BD3MXitVCmurY%3D 10.1128/JB.182.24.6983- 6991.2000 11092859 (Pubitemid 32259602)
17. P Giachino S Engelmann M Bischoff 2001 Sigma(B) activity depends on RsbU in Staphylococcus aureus J Bacteriol 183 1843 1852 1:CAS:528: DC%2BD3MXhvVeks7g%3D 10.1128/JB.183.6.1843-1852.2001 11222581 (Pubitemid 32225979)
18. AF Gillaspy SG Hickmon RA Skinner JR Thomas CL Nelson MS Smeltzer 1995 Role of the accessory gene regulator (agr) in pathogenesis of staphylococcal osteomyelitis Infect Immun 63 3373 3380 1:CAS:528:DyaK2MXnvVWns74%3D 7642265
19. M Gimpel N Heidrich U Mader H Krugel S Brantl 2010 A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon Mol Microbiol 76 990 1009 1:CAS:528:DC%2BC3cXnt1Klt7o%3D 10.1111/j.1365-2958.2010. 07158.x 20444087
20. MR Hemm BJ Paul TD Schneider G Storz KE Rudd 2008 Small membrane proteins found by comparative genomics and ribosome binding site models Mol Microbiol 70 1487 1501 1:CAS:528:DC%2BD1cXhsFaks7bM 10.1111/j.1365-2958.2008.06495.x 19121005
21. MR Hemm BJ Paul J Miranda-Rios A Zhang N Soltanzad G Storz 2010 Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies J Bacteriol 192 46 58 1:CAS:528:DC%2BC3cXisVKhtb4%3D 10.1128/JB.00872-09 19734316
22. EC Hobbs JL Astarita G Storz 2010 Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection J Bacteriol 192 59 67 1:CAS:528:DC%2BC3cXisVKhtb8%3D 10.1128/JB.00873-09 19734312
23. MJ Horsburgh JL Aish IJ White L Shaw JK Lithgow SJ Foster 2002 sigmaB modulates virulence determinant expression and stress resistance: characterization of a functional rsbU strain derived from Staphylococcus aureus 8325-4 J Bacteriol 184 5457 5467 1:CAS:528:DC%2BD38Xnt1ehtrk%3D 10.1128/JB.184.19.5457-5467.2002 12218034 (Pubitemid 35024393)
24. MJ Horsburgh SJ Wharton AG Cox E Ingham S Peacock SJ Foster 2002 MntR modulates expression of the PerR regulon and superoxide resistance in Staphylococcus aureus through control of manganese uptake Mol Microbiol 44 1269 1286 1:CAS:528:DC%2BD38XksFGquro%3D 10.1046/j.1365-2958.2002.02944.x 12028379 (Pubitemid 34595758)
25. IM Jonsson S Arvidson S Foster A Tarkowski 2004 Sigma factor B and RsbU are required for virulence in Staphylococcus aureus-induced arthritis and sepsis Infect Immun 72 6106 6111 1:CAS:528:DC%2BD2cXotFaksL0%3D 10.1128/IAI.72.10. 6106-6111.2004 15385515 (Pubitemid 39303726)
26. JK Klitgaard MN Skov BH Kallipolitis HJ Kolmos 2008 Reversal of methicillin resistance in Staphylococcus aureus by thioridazine J Antimicrob Chemother 62 1215 1221 1:CAS:528:DC%2BD1cXhtl2gs7zI 10.1093/jac/dkn417 18836185
27. GR Kraemer JJ Iandolo 1990 High-frequency transformation of Staphylococcus aureus by electroporation Curr Microbiol 21 373 376 1:CAS:528:DyaK3MXhsFyntb4%3D 10.1007/BF02199440
28. BN Kreiswirth S Lofdahl MJ Betley M O'Reilly PM Schlievert MS Bergdoll RP Novick 1983 The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage Nature 305 709 712 1:CAS:528:DyaL3sXlvVyrsLY%3D 10.1038/305709a0 6226876
29. I Kullik P Giachino 1997 The alternative sigma factor sigmaB in Staphylococcus aureus: regulation of the sigB operon in response to growth phase and heat shock Arch Microbiol 167 151 159 1:CAS:528:DyaK2sXhvFOqu7s%3D 10.1007/s002030050428 9042755 (Pubitemid 27141765)
30. I Kullik P Giachino T Fuchs 1998 Deletion of the alternative sigma factor sigmaB in Staphylococcus aureus reveals its function as a global regulator of virulence genes J Bacteriol 180 4814 4820 1:CAS:528:DyaK1cXmt1Snsr0%3D 9733682
31. U Lorenz C Huttinger T Schafer W Ziebuhr A Thiede J Hacker S Engelmann M Hecker K Ohlsen 2008 The alternative sigma factor sigma B of Staphylococcus aureus modulates virulence in experimental central venous catheter-related infections Microbes Infect 10 217 223 1:CAS:528:DC%2BD1cXktFemu7k%3D 10.1016/j.micinf.2007.11.006 18328762
32. FD Lowy 1998 Staphylococcus aureus infections N Engl J Med 339 520 532 1:STN:280:DyaK1czmtlKltw%3D%3D 10.1056/NEJM199808203390806 9709046 (Pubitemid 28384886)
33. PJ McNamara JJ Iandolo 1998 Genetic instability of the global regulator agr explains the phenotype of the xpr mutation in Staphylococcus aureus KSI9051 J Bacteriol 180 2609 2615 1:CAS:528:DyaK1cXjtVWlsrk%3D 9573143
34. MFOLDi (2010) MFOLD. World Wide Web. http://mfold.bioinfo.rpi.edu/cgi- bin/rna-form1.cgi
35. K Morikawa Y Inose H Okamura A Maruyama H Hayashi K Takeyasu T Ohta 2003 A new staphylococcal sigma factor in the conserved gene cassette: functional significance and implication for the evolutionary processes Genes Cells 8 699 712 1:CAS:528:DC%2BD3sXmsFylsb4%3D 10.1046/j.1365-2443.2003.00668.x 12875655 (Pubitemid 36974698)
36. JS Nielsen AS Olsen M Bonde P Valentin-Hansen BH Kallipolitis 2008 Identification of a sigma B-dependent small noncoding RNA in Listeria monocytogenes J Bacteriol 190 6264 6270 1:CAS:528:DC%2BD1cXhtFSrs7%2FP 10.1128/JB.00740-08 18621897
37. JS Nielsen LK Lei T Ebersbach AS Olsen JK Klitgaard P Valentin-Hansen BH Kallipolitis 2010 Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes Nucleic Acids Res 38 907 919 1:CAS:528:DC%2BC3cXitVSks7k%3D 10.1093/nar/gkp1081 19942685
38. RP Novick 2003 Autoinduction and signal transduction in the regulation of staphylococcal virulence Mol Microbiol 48 1429 1449 1:CAS:528: DC%2BD3sXkvFCmtL4%3D 10.1046/j.1365-2958.2003.03526.x 12791129 (Pubitemid 36751052)
39. J Pane-Farre B Jonas K Forstner S Engelmann M Hecker 2006 The sigmaB regulon in Staphylococcus aureus and its regulation Int J Med Microbiol 296 237 258 1:CAS:528:DC%2BD28XhtVamsbzI 10.1016/j.ijmm.2005.11.011 16644280 (Pubitemid 44016170)
40. A Petersohn J Bernhardt U Gerth D Hoper T Koburger U Volker M Hecker 1999 Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization J Bacteriol 181 5718 5724 1:CAS:528:DyaK1MXmtFKit7Y%3D 10482513
41. C Pichon B Felden 2005 Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains Proc Natl Acad Sci USA 102 14249 14254 1:CAS:528: DC%2BD2MXhtFChu7fO 10.1073/pnas.0503838102 16183745 (Pubitemid 41429684)
42. C Poyart P Trieu-Cuot 1997 A broad-host-range mobilizable shuttle vector for the construction of transcriptional fusions to beta-galactosidase in gram-positive bacteria FEMS Microbiol Lett 156 193 198 1:CAS:528: DyaK2sXmvFWjtL8%3D 10.1016/S0378-1097(97)00423-0 9513264 (Pubitemid 28252818)
43. MA Schumacher RF Pearson T Moller P Valentin-Hansen RG Brennan 2002 Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein EMBO J 21 3546 3556 1:CAS:528: DC%2BD38XlsFCgur0%3D 10.1093/emboj/cdf322 12093755 (Pubitemid 34760584)
44. CM Sharma J Vogel 2009 Experimental approaches for the discovery and characterization of regulatory small RNA Curr Opin Microbiol 12 536 546 1:CAS:528:DC%2BD1MXht1CmtLfK 10.1016/j.mib.2009.07.006 19758836
45. LN Shaw C Lindholm TK Prajsnar HK Miller MC Brown E Golonka GC Stewart A Tarkowski J Potempa 2008 Identification and characterization of sigma, a novel component of the Staphylococcus aureus stress and virulence responses PLoS One 3 e3844 10.1371/journal.pone.0003844 19050758
46. P Valentin-Hansen M Eriksen C Udesen 2004 The bacterial Sm-like protein Hfq: a key player in RNA transactions Mol Microbiol 51 1525 1533 1:CAS:528:DC%2BD2cXivFCrsr0%3D 10.1111/j.1365-2958.2003.03935.x 15009882 (Pubitemid 38406529)
47. CS Wadler CK Vanderpool 2007 A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide Proc Natl Acad Sci USA 104 20454 20459 1:CAS:528: DC%2BD1cXjt1agug%3D%3D 10.1073/pnas.0708102104 18042713
48. LS Waters G Storz 2009 Regulatory RNAs in bacteria Cell 136 615 628 1:CAS:528:DC%2BD1MXkvFGksb8%3D 10.1016/j.cell.2009.01.043 19239884
49. S Wu H de Lencastre A Tomasz 1996 Sigma-B, a putative operon encoding alternate sigma factor of Staphylococcus aureus RNA polymerase: molecular cloning and DNA sequencing J Bacteriol 178 6036 6042 1:CAS:528: DyaK28XmtFOksb4%3D 8830703