The transcriptionally active regions in the genome of Bacillus subtilis.
The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non-coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22, is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA. Through this work we have discovered a long conserved 3' untranslated region (UTR) in a group of membrane-associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system.
Rasmussen
Simon
S
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Nielsen
Henrik Bjørn
HB
Jarmer
Hanne
H
D001412:Bacillus subtilis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D001483:Base Sequence; D003470:Culture Media / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016372:RNA, Antisense / Q000096:biosynthesis; D022661:RNA, Untranslated / Q000096:biosynthesis; D014158:Transcription, Genetic
D003470:Culture Media; D016372:RNA, Antisense; D022661:RNA, Untranslated
Mol Microbiol. 2003 Sep;49(6):1685-97
12950930
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
FEMS Microbiol Rev. 1994 Dec;15(4):355-67
7848659
Bioinformatics. 2006 Aug 15;22(16):1963-70
16787969
J Bacteriol. 2004 Aug;186(15):4875-84
15262924
Nucleic Acids Res. 2005 Feb 17;33(3):1040-50
15718303
Nucleic Acids Res. 2007;35(19):e128
17897965
Nucleic Acids Res. 2006 May 22;34(9):2791-802
16717284
Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11927-32
18697947
J Bacteriol. 2006 Sep;188(17):6387-95
16923906
J Bacteriol. 2006 Jan;188(2):532-41
16385044
Mol Cell. 2006 Dec 8;24(5):747-757
17157257
J Bacteriol. 2009 Feb;191(3):1101-5
19047346
Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6
17901208
J Bacteriol. 1961 May;81(5):741-6
16561900
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4
18424795
Nature. 2009 Feb 19;457(7232):1033-7
19169243
J Mol Biol. 1995 Jun 23;249(5):843-56
7540694
Microbiology (Reading). 1999 May;145 ( Pt 5):1055-1067
10376821
Mol Microbiol. 2005 Oct;58(1):189-206
16164558
Curr Opin Microbiol. 2007 Jun;10(3):262-70
17574901
J Bacteriol. 2006 May;188(10):3664-73
16672620
Science. 2004 Dec 24;306(5705):2242-6
15539566
J Bacteriol. 2003 Aug;185(15):4450-60
12867454
J Bacteriol. 1977 Jan;129(1):556-8
401505
Microbiology (Reading). 2001 Sep;147(Pt 9):2417-2424
11535782
Microbiology (Reading). 2005 Feb;151(Pt 2):399-420
15699190
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W611-5
15980547
Genome Biol. 2007;8(2):R22
17313685
Nucleic Acids Res. 2002 Mar 15;30(6):1418-26
11884641
BMC Genomics. 2005 Mar 08;6:31
15755320
J Bacteriol. 1950 Jan;59(1):93-104
15408888
Microbiol Rev. 1995 Mar;59(1):1-30
7708009
Annu Rev Genet. 2005;39:47-68
16285852
J Bacteriol. 2005 Oct;187(19):6641-50
16166525
J Bacteriol. 2005 Apr;187(8):2758-67
15805522
Science. 2008 Jun 6;320(5881):1344-9
18451266
Microbiology (Reading). 2002 Aug;148(Pt 8):2591-2598
12177353
Microbiology (Reading). 2009 Jun;155(Pt 6):1758-1775
19383706
Nat Genet. 2006 Jan;38(1):124-9
16369532
Nature. 1997 Nov 20;390(6657):249-56
9384377
J Bacteriol. 2001 Dec;183(24):7318-28
11717291
J Biol Chem. 2000 May 12;275(19):14031-7
10799476
Am J Bot. 1947 Jun;34(6):345-8
20252518
Proc Natl Acad Sci U S A. 1958 Oct 15;44(10):1072-8
16590310
Proc Natl Acad Sci U S A. 2003 May 13;100(10):6115-20
12721369
Microbiology (Reading). 1995 Feb;141 ( Pt 2):323-7
7704261
J Bacteriol. 2004 Apr;186(8):2240-52
15060025
J Bacteriol. 2006 Jul;188(14):5273-85
16816200
J Bacteriol. 2008 Nov;190(21):6983-95
18723616
Bioinformatics. 2005 Dec 15;21(24):4322-9
16249266
Genome Res. 2002 Apr;12(4):656-64
11932250
Nucleic Acids Res. 2002 Sep 1;30(17):3732-8
12202758
Mol Microbiol. 2007 Jun;64(6):1605-20
17555441
FEMS Immunol Med Microbiol. 2008 Jul;53(2):195-203
18430003
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
16569694
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
J Biol Chem. 2007 Jul 27;282(30):21738-45
17535816
Gene. 2009 Jan 1;428(1-2):2-8
18948176
Microbiology (Reading). 1996 Aug;142 ( Pt 8):2031-40
8760915
Mol Microbiol. 1998 Nov;30(4):737-49
10094622
Trends Biochem Sci. 2003 Feb;28(2):91-8
12575997
J Bacteriol. 1999 Jan;181(1):353-6
9864351
Mol Microbiol. 2004 Dec;54(5):1319-25
15554971
PLoS Comput Biol. 2005 Aug;1(3):e25
16110342
Science. 1988 Jun 3;240(4857):1285-93
3287615
Mol Microbiol. 2005 Jun;56(6):1549-59
15916605
Bioinformatics. 2004 Dec 12;20(18):3682-6
15256401
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6
17962296
J Bacteriol. 1990 May;172(5):2667-74
2110147
FEMS Microbiol Lett. 2002 Jan 22;207(1):29-33
11886746