Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011.
BACKGROUND
Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobacteria and thus relatively little is known about the role of RNA-mediated regulation in most other bacterial genera. Here we have conducted a computational prediction of putative sRNA genes in intergenic regions (IgRs) of the symbiotic alpha-proteobacterium S. meliloti 1021 and experimentally confirmed the expression of dozens of these candidate loci in the closely related strain S. meliloti 2011.


RESULTS
Our first sRNA candidate compilation was based mainly on the output of the sRNAPredictHT algorithm. A thorough manual sequence analysis of the curated list rendered an initial set of 18 IgRs of interest, from which 14 candidates were detected in strain 2011 by Northern blot and/or microarray analysis. Interestingly, the intracellular transcript levels varied in response to various stress conditions. We developed an alternative computational method to more sensitively predict sRNA-encoding genes and score these predicted genes based on several features to allow identification of the strongest candidates. With this novel strategy, we predicted 60 chromosomal independent transcriptional units that, according to our annotation, represent strong candidates for sRNA-encoding genes, including most of the sRNAs experimentally verified in this work and in two other contemporary studies. Additionally, we predicted numerous candidate sRNA genes encoded in megaplasmids pSymA and pSymB. A significant proportion of the chromosomal- and megaplasmid-borne putative sRNA genes were validated by microarray analysis in strain 2011.


CONCLUSIONS
Our data extend the number of experimentally detected S. meliloti sRNAs and significantly expand the list of putative sRNA-encoding IgRs in this and closely related alpha-proteobacteria. In addition, we have developed a computational method that proved useful to predict sRNA-encoding genes in S. meliloti. We anticipate that this predictive approach can be flexibly implemented in many other bacterial species.
Valverde
Claudio
C
Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, B1876BXD, Argentina. cvalver@unq.edu.ar
Livny
Jonathan
J
Schlüter
Jan-Philip
JP
Reinkensmeier
Jan
J
Becker
Anke
A
Parisi
Gustavo
G
D002876:Chromosomes, Bacterial / Q000235:genetics; D019295:Computational Biology; D021901:DNA, Intergenic / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D008957:Models, Genetic; D012329:RNA, Bacterial / Q000032:analysis / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated / Q000032:analysis / Q000737:chemistry / Q000235:genetics*; D016962:Sinorhizobium meliloti / Q000145:classification / Q000235:genetics* / Q000254:growth & development
D021901:DNA, Intergenic; D012329:RNA, Bacterial; D022661:RNA, Untranslated
Curr Opin Microbiol. 2007 Apr;10(2):96-101
17383222
Appl Environ Microbiol. 1999 Apr;65(4):1420-7
10103231
FEMS Microbiol Lett. 2004 May 15;234(2):357-70
15135544
Genome Biol. 2005;6(8):R70
16086852
Comput Chem. 2001 Dec;26(1):51-6
11765852
Science. 2001 Jul 27;293(5530):668-72
11474104
Biol Chem. 2008 Mar;389(3):285-97
18177266
Mol Plant Microbe Interact. 2002 Dec;15(12):1245-52
12481997
Annu Rev Biochem. 2005;74:199-217
15952886
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9889-94
11481431
BMC Genomics. 2007 Dec 19;8:467
18093320
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20454-9
18042713
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4
15608160
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
BMC Bioinformatics. 2001;2:8
11801179
Nat Rev Genet. 2007 Nov;8(11):884-96
17943195
Trends Genet. 2005 Jul;21(7):399-404
15913835
Mol Microbiol. 2007 Jun;64(5):1260-73
17542919
Microbiol Mol Biol Rev. 2004 Jun;68(2):280-300
15187185
Microbiology (Reading). 2006 Jun;152(Pt 6):1751-1763
16735738
Nucleic Acids Res. 2006 Jul 05;34(11):3361-9
16822857
Curr Biol. 2001 Jun 26;11(12):941-50
11448770
J Gen Microbiol. 1974 Sep;84(1):188-98
4612098
Nucleic Acids Res. 2003 Nov 15;31(22):6435-43
14602901
Curr Opin Microbiol. 2007 Apr;10(2):125-33
17395525
Nucleic Acids Res. 2005 Oct 31;33(19):6268-76
16260475
Trends Genet. 2000 Jun;16(6):276-7
10827456
J Bacteriol. 1991 Oct;173(20):6373-82
1717438
Curr Opin Microbiol. 2007 Apr;10(2):134-9
17383928
Proc Natl Acad Sci U S A. 1977 May;74(5):2076-8
266730
Mol Microbiol. 1998 May;28(3):603-13
9632262
Annu Rev Microbiol. 2004;58:303-28
15487940
Mol Microbiol. 2007 Dec;66(5):1080-91
17971083
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6421-6
15096624
Nucleic Acids Res. 2005 Feb 17;33(3):1040-50
15718303
Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7778-83
10884408
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9883-8
11481432
Mol Genet Genomics. 2004 Aug;272(1):1-17
15221452
Genes Dev. 2003 Oct 1;17(19):2374-83
12975324
FEMS Microbiol Lett. 2003 Mar 28;220(2):207-13
12670682
J Bacteriol. 1995 Oct;177(19):5485-94
7559334
Genome Biol. 2007;8(2):R22
17313685
Nucleic Acids Res. 2006;34(14):3842-52
16899451
Nucleic Acids Res. 2006 May 22;34(9):2686-97
16717279
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337
Adv Exp Med Biol. 2008;631:54-79
18792682
Genome Biol. 2005;6(9):R73
16168080
Curr Opin Microbiol. 2007 Apr;10(2):156-63
17383221
Curr Opin Microbiol. 2007 Apr;10(2):164-8
17383220
Biol Chem. 2005 Dec;386(12):1219-38
16336117
Genome Biol. 2002;3(12):RESEARCH0076
12537565
RNA. 2005 May;11(5):774-84
15811922
Mol Microbiol. 2005 Jan;55(2):611-23
15659174
In Silico Biol. 2007;7(6):601-11
18467773
Nucleic Acids Res. 2006;34(12):3484-93
16870723
Curr Biol. 2001 Sep 4;11(17):1369-73
11553332
J Biotechnol. 2008 Jun 30;135(3):309-17
18538881
FEMS Microbiol Lett. 2007 Apr;269(1):117-23
17241239
RNA. 2004 Oct;10(10):1533-40
15337843
Cell. 2000 Jun 9;101(6):613-23
10892648
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9877-82
11481430
Genes Dev. 2001 Jul 1;15(13):1637-51
11445539
Biosystems. 2002 Mar-May;65(2-3):157-77
12069726