Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi.
We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR-DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense-antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi.
Chinni
Suresh V
SV
Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany.
Raabe
Carsten A
CA
Zakaria
Robaiza
R
Randau
Gerrit
G
Hoe
Chee Hock
CH
Zemann
Anja
A
Brosius
Juergen
J
Tang
Thean-Hock
TH
Rozhdestvensky
Timofey S
TS
D021901:DNA, Intergenic / Q000737:chemistry; D015723:Gene Library; D044404:Genomic Islands; D016366:Open Reading Frames; D009876:Operon; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism*; D012485:Salmonella typhi / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity
D021901:DNA, Intergenic; D016372:RNA, Antisense; D012329:RNA, Bacterial; D022661:RNA, Untranslated
Curr Opin Microbiol. 2007 Apr;10(2):102-9
17387036
J Bioinform Comput Biol. 2006 Apr;4(2):443-54
16819794
J Biol Chem. 1992 May 5;267(13):8778-84
1533620
Mol Microbiol. 2006 Oct;62(2):469-79
17020583
Microbiology (Reading). 1995 Aug;141 ( Pt 8):1909-1920
7551053
Trends Biotechnol. 2001 Mar;19(3):109-14
11179804
Proc Natl Acad Sci U S A. 1989 Mar;86(5):1593-7
2646639
Nature. 2008 Nov 6;456(7218):130-4
18820678
PLoS Genet. 2009 Jul;5(7):e1000569
19609351
J Bacteriol. 2003 Apr;185(7):2330-7
12644504
J Gen Microbiol. 1990 Mar;136(3):455-62
2167922
BMC Bioinformatics. 2001;2:8
11801179
Mol Microbiol. 2002 Jul;45(2):333-49
12123448
Mol Microbiol. 2007 Jan;63(1):193-217
17163975
Nat Biotechnol. 2000 Dec;18(12):1262-8
11101804
Cell. 1982 Jul;29(3):939-44
6217898
Antimicrob Agents Chemother. 2002 Feb;46(2):360-6
11796342
Nucleic Acids Res. 1999 Sep 15;27(18):3690-5
10471738
Nucleic Acids Res. 2007;35(3):1018-37
17264113
Proc Natl Acad Sci U S A. 2006 May 2;103(18):7054-8
16636284
Mol Microbiol. 2008 Feb;67(3):475-81
18086200
Science. 2007 Jun 8;316(5830):1484-8
17510325
J Mol Biol. 1994 May 6;238(3):302-8
8176726
Clin Infect Dis. 2007 Jul 15;45 Suppl 1:S29-33
17582565
Cell. 2002 Apr 19;109(2):141-4
12007399
Curr Biol. 2001 Jun 26;11(12):941-50
11448770
Proc Natl Acad Sci U S A. 1989 May;86(10):3484-8
2471187
Nucleic Acids Res. 2003 Nov 15;31(22):6435-43
14602901
PLoS Genet. 2008 Aug 29;4(8):e1000173
18769676
Nat Genet. 2009 May;41(5):572-8
19377478
J Bacteriol. 1995 Dec;177(24):7141-9
8522521
Curr Opin Microbiol. 2007 Apr;10(2):134-9
17383928
Nature. 1986 Jul 17-23;322(6076):273-5
3736654
Annu Rev Biophys. 2008;37:117-33
18573075
Nucleic Acids Res. 2005 Feb 17;33(3):1040-50
15718303
Curr Opin Microbiol. 2006 Apr;9(2):229-36
16529986
Biochemistry. 2008 Mar 4;47(9):2721-31
18247578
Cell. 1997 Jul 11;90(1):43-53
9230301
BMC Genomics. 2008 Apr 13;9:167
18405392
Nucleic Acids Res. 2010 Jan;38(2):608-17
19864253
BMC Genomics. 2008 May 13;9:217
18477385
J Biol Chem. 1988 Jun 5;263(16):7776-84
2836397
Mol Microbiol. 2003 Nov;50(4):1111-24
14622403
RNA. 2000 May;6(5):668-79
10836788
J Biol Chem. 1994 Oct 28;269(43):26959-68
7929435
EMBO J. 1990 Apr;9(4):1267-74
1691097
J Bacteriol. 2004 Oct;186(20):6698-705
15466020
PLoS Genet. 2008 Aug 22;4(8):e1000163
18725932
Nat Biotechnol. 2003 Apr;21(4):371-2
12665819
EMBO J. 2002 Feb 15;21(4):715-24
11847119
Biochim Biophys Acta. 2002 May 3;1575(1-3):15-25
12020814
Nucleic Acids Res. 2008 Apr;36(6):1913-27
18267966
J Biol Chem. 1977 May 25;252(10):3286-94
324994
Mol Microbiol. 1999 Jun;32(5):1090-102
10361310
Methods Enzymol. 1987;155:335-50
3431465
Mol Microbiol. 2006 Aug;61(4):1013-22
16859494
Annu Rev Microbiol. 1994;48:713-42
7826024
Crit Rev Biochem Mol Biol. 2005 Mar-Apr;40(2):93-113
15814430
Mol Microbiol. 2009 Jan;71(1):1-11
19007416
Nucleic Acids Res. 2007;35(2):529-39
17175535
EMBO J. 1989 Aug;8(8):2403-10
2551682
Nucleic Acids Res. 2003 Feb 1;31(3):869-77
12560482
Curr Opin Microbiol. 2006 Dec;9(6):605-11
17055775
Antimicrob Agents Chemother. 2008 Jul;52(7):2428-34
18443112
Mol Microbiol. 2007 Dec;66(5):1174-91
17971080
Biol Cell. 2008 Feb;100(2):83-95
18199047
OMICS. 2007 Spring;11(1):58-73
17411396
EMBO J. 1996 Aug 1;15(15):3993-4000
8670904
Nature. 2004 Jun 3;429(6991):571-4
15175754
Antimicrob Agents Chemother. 2004 Jul;48(7):2518-23
15215103
J Antimicrob Chemother. 2009 Jan;63(1):95-102
18984645
J Bacteriol. 1989 Mar;171(3):1739-41
2646296
J Mol Biol. 1981 May 15;148(2):107-27
7028991