title: The Sulfolobus initiator element is an important contributor to promoter strength.
abstract: Basal elements in archaeal promoters, except for putative initiator elements encompassing transcription start sites, are well characterized. Here, we employed the Sulfolobus araS promoter as a model to study the function of the initiator element (Inr) in archaea. We have provided evidence for the presence of a third core promoter element, the Sulfolobus Inr, whose action depends on a TATA box and the TFB recognition element (BRE). Substitution mutations in the araS Inr did not alter the location of the transcription start site. Using systematic mutagenesis, the most functional araS Inr was defined as +1 GAGAMK +6 (where M is A/C and K is G/T). Furthermore, WebLogo analysis of a subset of promoters with coding sequences for 5' untranslated regions (UTRs) larger than 4 nucleotides (nt) in Sulfolobus solfataricus P2 identified an Inr consensus that exactly matches the functional araS Inr sequence. Moreover, mutagenesis of 3 randomly selected promoters confirmed the Inr sequences to be important for basal promoter strength in the subgroup. Importantly, the result of the araS Inr being added to the Inr-less promoters indicates that the araS Inr, the core promoter element, is able to enhance the strength of Inr-less promoters. We infer that transcription factor B (TFB) and subunits of RNA polymerase bind the Inr to enhance promoter strength. Taken together, our data suggest that the presence or absence of an Inr on basal promoters is important for global gene regulation in Sulfolobus.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Ao
authors.forename: Yingjun
authors.initials: Y
authors.lastname: Li
authors.forename: Fan
authors.initials: F
authors.lastname: Wang
authors.forename: Mingxia
authors.initials: M
authors.lastname: Feng
authors.forename: Yanxu
authors.initials: Y
authors.lastname: Lin
authors.forename: Shumiao
authors.initials: S
authors.lastname: Zhao
authors.forename: Yunxiang
authors.initials: Y
authors.lastname: Liang
authors.forename: Nan
authors.initials: N
authors.lastname: Peng
mesh_terms: D004252:DNA Mutational Analysis; D019641:DNA, Archaeal / Q000235:genetics; D050436:Regulatory Elements, Transcriptional; D048229:Sulfolobus solfataricus / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D019641:DNA, Archaeal
references.citation: Mol Microbiol. 2003 May;48(3):587-98
references.pmid: 12694606
references.citation: Annu Rev Microbiol. 2013;67:113-39
references.pmid: 23768203
references.citation: J Biol Chem. 2012 May 25;287(22):18863-71
references.pmid: 22496454
references.citation: Nucleic Acids Res. 2008 Feb;36(2):598-606
references.pmid: 18056077
references.citation: Extremophiles. 2006 Oct;10(5):383-91
references.pmid: 16604273
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: J Bacteriol. 1995 Apr;177(7):1844-9
references.pmid: 7896710
references.citation: J Bacteriol. 1999 Apr;181(8):2513-8
references.pmid: 10198017
references.citation: EMBO J. 1997 May 15;16(10):2927-36
references.pmid: 9184236
references.citation: Curr Opin Microbiol. 2011 Jun;14(3):328-34
references.pmid: 21596617
references.citation: J Biol Chem. 2002 Aug 16;277(33):29537-49
references.pmid: 12042311
references.citation: J Bacteriol. 2008 Jan;190(1):157-67
references.pmid: 17965161
references.citation: Nucleic Acids Res. 2009 Jun;37(11):3588-601
references.pmid: 19359364
references.citation: Mol Microbiol. 1999 Oct;34(2):377-84
references.pmid: 10564480
references.citation: Curr Opin Genet Dev. 2004 Apr;14(2):133-8
references.pmid: 15196459
references.citation: PLoS Genet. 2007 Dec;3(12):e229
references.pmid: 18159946
references.citation: Proc Natl Acad Sci U S A. 1990 Dec;87(24):9509-13
references.pmid: 2124695
references.citation: Biochem Soc Trans. 2013 Feb 1;41(1):326-31
references.pmid: 23356306
references.citation: Cell. 1989 Apr 7;57(1):103-13
references.pmid: 2467742
references.citation: Appl Microbiol Biotechnol. 2013 Jan;97(1):171-9
references.pmid: 22322871
references.citation: Mol Microbiol. 2004 Jan;51(2):579-88
references.pmid: 14756795
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4630-5
references.pmid: 17360575
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835-40
references.pmid: 11427726
references.citation: J Biol Chem. 2004 Jan 23;279(4):2825-31
references.pmid: 14597623
references.citation: Nucleic Acids Res. 2012 Oct;40(19):9941-52
references.pmid: 22848102
references.citation: Mol Microbiol. 1999 Mar;31(5):1295-305
references.pmid: 10200952
references.citation: Trends Microbiol. 2005 Jun;13(6):262-5
references.pmid: 15936657
references.citation: Mol Cell Biol. 2005 Sep;25(18):8344-55
references.pmid: 16135821
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5097-102
references.pmid: 12692306
references.citation: EMBO J. 1999 Sep 1;18(17):4835-45
references.pmid: 10469661
references.citation: Mol Microbiol. 2007 Sep;65(6):1395-404
references.pmid: 17697097
references.citation: Mol Cell. 1998 Feb;1(3):389-400
references.pmid: 9660923
references.citation: Insect Biochem Mol Biol. 1993 Jan;23(1):81-90
references.pmid: 8485519
references.citation: Cold Spring Harb Symp Quant Biol. 1998;63:21-31
references.pmid: 10384267
references.citation: Science. 1980 Sep 19;209(4463):1406-14
references.pmid: 6251548
references.citation: J Mol Biol. 1991 Dec 5;222(3):495-508
references.pmid: 1748992
references.citation: Nucleic Acids Res. 1992 Oct 25;20(20):5423-8
references.pmid: 1279520
references.citation: Mol Microbiol. 2009 Nov;74(4):928-39
references.pmid: 19818017
references.citation: Biochim Biophys Acta. 1997 Mar 20;1351(1-2):73-88
references.pmid: 9116046
references.citation: Genome Res. 2010 Jan;20(1):133-41
references.pmid: 19884261
references.citation: Can J Microbiol. 2006 Nov;52(11):1136-40
references.pmid: 17215906
references.citation: Gene. 1996 Dec 5;182(1-2):13-22
references.pmid: 8982062
references.citation: Extremophiles. 2009 Jul;13(4):735-46
references.pmid: 19513584
references.citation: Biochem Soc Trans. 2011 Jan;39(1):99-103
references.pmid: 21265754
references.citation: Curr Opin Microbiol. 2005 Dec;8(6):677-84
references.pmid: 16249119
references.citation: J Biol Chem. 2007 Apr 13;282(15):11047-57
references.pmid: 17311916