RNA polymerase trafficking in Bacillus subtilis cells.
To obtain insight into the in vivo dynamics of RNA polymerase (RNAP) on the Bacillus subtilis genome, we analyzed the distribution of the σ(A) and β' subunits of RNAP and the NusA elongation factor on the genome in exponentially growing cells using chromatin affinity precipitation coupled with gene chip mapping (ChAP-chip). In contrast to Escherichia coli RNAP, which often accumulates at the promoter-proximal region, B. subtilis RΝΑP is evenly distributed from the promoter to the coding sequences. This finding suggests that, in general, B. subtilis RNAP recruited to the promoter promptly translocates away from the promoter to form the elongation complex and proceeds without intragenic transcription attenuation. We detected RNAP accumulation in the promoter-proximal regions of some genes, most of which can be identified as transcription attenuation systems in the leader region. Our findings suggest that the differences in RNAP behavior between E. coli and B. subtilis during initiation and elongation steps might result in distinct strategies for postinitiation control of transcription. The E. coli mechanism involves trapping at the promoter and promoter-proximal pausing of RNAP in addition to transcription attenuation, whereas transcription attenuation in leader sequences is mainly employed in B. subtilis.
Ishikawa
Shu
S
Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan.
Oshima
Taku
T
Kurokawa
Ken
K
Kusuya
Yoko
Y
Ogasawara
Naotake
N
D001412:Bacillus subtilis / Q000166:cytology* / Q000201:enzymology*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D015971:Gene Expression Regulation, Enzymologic / Q000502:physiology; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D021381:Protein Transport / Q000502:physiology*; D014158:Transcription, Genetic
D012321:DNA-Directed RNA Polymerases
J Bacteriol. 2004 Aug;186(16):5392-9
15292140
Mol Microbiol. 1999 Jan;31(2):651-63
10027981
Annu Rev Biochem. 1985;54:171-204
3896120
Bioinformatics. 2006 Aug 15;22(16):1963-70
16787969
Curr Opin Genet Dev. 2008 Apr;18(2):130-6
18282700
EMBO J. 2009 Nov 18;28(22):3523-33
19779461
J Bacteriol. 2000 Nov;182(21):6027-35
11029421
J Mol Biol. 1992 Jan 20;223(2):399-414
1310745
J Biol Chem. 2000 Aug 18;275(33):25516-22
10811806
Cell. 2007 Jul 13;130(1):77-88
17632057
Cell. 2003 May 30;113(5):577-86
12787499
Bioessays. 2002 Aug;24(8):700-7
12210530
Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11067-72
12161562
Mol Microbiol. 2006 Jun;60(6):1364-80
16796675
J Mol Biol. 1991 Jul 20;220(2):307-24
1856861
Mol Cell. 2006 Dec 8;24(5):747-757
17157257
Mol Cell. 2005 Apr 15;18(2):171-83
15837421
Nucleic Acids Res. 1993 Feb 25;21(4):935-40
8451193
Microbiology (Reading). 2006 Sep;152(Pt 9):2515-2528
16946247
Biochemistry. 1987 Dec 15;26(25):8206-13
3126800
Cell. 1981 May;24(2):421-8
6263495
Mol Microbiol. 2008 Apr;68(1):17-28
18333883
Nat Genet. 2007 Dec;39(12):1512-6
17994019
Nat Genet. 2007 Dec;39(12):1507-11
17994021
Nature. 1997 Nov 20;390(6657):249-56
9384377
Genes Dev. 2007 May 15;21(10):1258-72
17504942
Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15406-11
19706412
DNA Res. 2007 Aug 31;14(4):155-68
17932079
Mol Cell. 2009 Jan 16;33(1):97-108
19150431
EMBO J. 2009 Jul 8;28(13):1940-52
19494834
J Mol Biol. 1997 Sep 26;272(3):293-300
9325090
Mol Cell. 2005 Apr 1;18(1):49-60
15808508