title: A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
abstract: BACKGROUND
  Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations.
  
  
  RESULTS
  A total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173), cis-encoded antisense sRNAs (117), mRNA leader transcripts (379), and sense sRNAs overlapping coding regions (456) were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus sigma70 promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences from S. meliloti already known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria.
  
  
  CONCLUSIONS
  The screening data suggests that in S. meliloti about 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.
authors.affiliation: Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.
authors.forename: Jan-Philip
authors.initials: JP
authors.lastname: Schlüter
authors.forename: Jan
authors.initials: J
authors.lastname: Reinkensmeier
authors.forename: Svenja
authors.initials: S
authors.lastname: Daschkey
authors.forename: Elena
authors.initials: E
authors.lastname: Evguenieva-Hackenberg
authors.forename: Stefan
authors.initials: S
authors.lastname: Janssen
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jänicke
authors.forename: Jörg D
authors.initials: JD
authors.lastname: Becker
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
mesh_terms: D004251:DNA Transposable Elements; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D016962:Sinorhizobium meliloti / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D004251:DNA Transposable Elements; D012329:RNA, Bacterial; D022661:RNA, Untranslated
references.citation: FEMS Microbiol Rev. 2006 Jan;30(1):3-16
references.pmid: 16438677
references.citation: Nat Rev Microbiol. 2006 Oct;4(10):729-40
references.pmid: 16980936
references.citation: J Gen Microbiol. 1974 Sep;84(1):188-98
references.pmid: 4612098
references.citation: J Biotechnol. 2009 Mar 10;140(1-2):45-50
references.pmid: 19103235
references.citation: Genome Biol. 2005;6(8):R70
references.pmid: 16086852
references.citation: Mol Microbiol. 2000 Aug;37(4):856-68
references.pmid: 10972807
references.citation: EMBO J. 1990 Apr;9(4):1259-66
references.pmid: 1691096
references.citation: FEBS Lett. 2009 Jul 21;583(14):2339-42
references.pmid: 19540834
references.citation: J Mol Biol. 1989 Sep 5;209(1):79-90
references.pmid: 2478715
references.citation: Annu Rev Biochem. 2005;74:199-217
references.pmid: 15952886
references.citation: Biol Chem. 1997 Dec;378(12):1421-31
references.pmid: 9461341
references.citation: J Biol Chem. 1989 Oct 25;264(30):17961-70
references.pmid: 2478539
references.citation: Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16636-41
references.pmid: 15542588
references.citation: Curr Opin Microbiol. 2007 Jun;10(3):257-61
references.pmid: 17553733
references.citation: Comput Syst Bioinformatics Conf. 2006;:111-21
references.pmid: 17369630
references.citation: Curr Opin Struct Biol. 2009 Jun;19(3):251-9
references.pmid: 19303767
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):102-9
references.pmid: 17387036
references.citation: Mol Microbiol. 2007 Jun;64(5):1260-73
references.pmid: 17542919
references.citation: Cell. 2009 Feb 20;136(4):615-28
references.pmid: 19239884
references.citation: RNA. 2009 Dec;15(12):2075-82
references.pmid: 19861422
references.citation: Microbiology (Reading). 2006 Jun;152(Pt 6):1751-1763
references.pmid: 16735738
references.citation: Mol Microbiol. 2008 Nov;70(4):896-907
references.pmid: 18808382
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):579-89, Table of Contents
references.pmid: 19052321
references.citation: Cell. 2002 Apr 19;109(2):141-4
references.pmid: 12007399
references.citation: Curr Biol. 2001 Jun 26;11(12):941-50
references.pmid: 11448770
references.citation: Bioinformatics. 2007 Jul 1;23(13):i392-400
references.pmid: 17646322
references.citation: Nucleic Acids Res. 2004 Sep 15;32(16):4843-51
references.pmid: 15371549
references.citation: Mol Microbiol. 2008 May;68(3):600-14
references.pmid: 18373523
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11394-9
references.pmid: 9736747
references.citation: Mol Microbiol. 2007 Dec;66(5):1080-91
references.pmid: 17971083
references.citation: Mol Syst Biol. 2009;5:305
references.pmid: 19756044
references.citation: Mol Genet Genomics. 2007 Nov;278(5):555-64
references.pmid: 17647020
references.citation: Curr Opin Microbiol. 2009 Oct;12(5):536-46
references.pmid: 19758836
references.citation: Nucleic Acids Res. 2009 Apr;37(6):e46
references.pmid: 19223322
references.citation: Cell. 2004 Jul 9;118(1):69-82
references.pmid: 15242645
references.citation: Genes Dev. 2003 Oct 1;17(19):2374-83
references.pmid: 12975324
references.citation: J Bacteriol. 1995 Oct;177(19):5485-94
references.pmid: 7559334
references.citation: BMC Genomics. 2008 Sep 16;9:416
references.pmid: 18793445
references.citation: Nucleic Acids Res. 2001 Nov 15;29(22):4724-35
references.pmid: 11713323
references.citation: BMC Bioinformatics. 2008 Feb 29;9:131
references.pmid: 18312625
references.citation: Cell. 1987 Dec 24;51(6):1131-43
references.pmid: 2446776
references.citation: Annu Rev Genet. 2008;42:541-64
references.pmid: 18713030
references.citation: Science. 2001 Jul 27;293(5530):668-72
references.pmid: 11474104
references.citation: BMC Bioinformatics. 2009 Feb 06;10:50
references.pmid: 19200358
references.citation: J Bacteriol. 2004 Oct;186(20):6698-705
references.pmid: 15466020
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):140-5
references.pmid: 17383226
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):499-516
references.pmid: 21233528
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4620-5
references.pmid: 11917098
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):164-8
references.pmid: 17383220
references.citation: Biochim Biophys Acta. 2002 May 3;1575(1-3):15-25
references.pmid: 12020814
references.citation: Environ Microbiol. 2003 Mar;5(3):143-51
references.pmid: 12588294
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):156-63
references.pmid: 17383221
references.citation: Mol Microbiol. 2005 Jan;55(2):611-23
references.pmid: 15659174
references.citation: Mol Microbiol. 2007 Jul;65(2):373-85
references.pmid: 17590231
references.citation: Annu Rev Biochem. 2007;76:101-24
references.pmid: 17291191
references.citation: Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12462-7
references.pmid: 9770508
references.citation: Curr Opin Microbiol. 2006 Dec;9(6):605-11
references.pmid: 17055775
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: BMC Genomics. 2007 Dec 19;8:467
references.pmid: 18093320
references.citation: Mol Microbiol. 2004 Dec;54(5):1431-44
references.pmid: 15554980
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20454-9
references.pmid: 18042713
references.citation: Nucleic Acids Res. 1990 Jul 11;18(13):3941-52
references.pmid: 2197600
references.citation: Cell. 1983 Sep;34(2):683-91
references.pmid: 6311438
references.citation: BMC Bioinformatics. 2006 Aug 24;7:389
references.pmid: 16930469
references.citation: Structure. 2009 Mar 11;17(3):472-81
references.pmid: 19278661
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40
references.pmid: 18953034
references.citation: J Biotechnol. 2008 Jun 30;135(3):309-17
references.pmid: 18538881
references.citation: FEMS Microbiol Lett. 2007 Apr;269(1):117-23
references.pmid: 17241239
references.citation: BMC Microbiol. 2008 May 02;8:72
references.pmid: 18454850
references.citation: PLoS Comput Biol. 2006 May;2(5):e57
references.pmid: 16710451
references.citation: Mol Microbiol. 1994 Apr;12(1):61-70
references.pmid: 8057840
references.citation: Mol Microbiol. 2009 Oct;74(1):139-158
references.pmid: 19732340
references.citation: Methods Enzymol. 2008;447:381-416
references.pmid: 19161853
references.citation: Mol Cell. 2007 Jul 6;27(1):79-90
references.pmid: 17612492
references.citation: PLoS Comput Biol. 2009 Sep;5(9):e1000502
references.pmid: 19750212
references.citation: Nature. 2008 Jan 17;451(7176):355-8
references.pmid: 18202662
references.citation: Structure. 2009 Mar 11;17(3):317-9
references.pmid: 19278643
references.citation: EMBO J. 1998 Oct 15;17(20):6069-75
references.pmid: 9774350
references.citation: Nat Rev Microbiol. 2007 Aug;5(8):619-33
references.pmid: 17632573
references.citation: J Bacteriol. 2004 Oct;186(20):6689-97
references.pmid: 15466019