Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae.
In eukaryotes, protein-coding genes are transcribed by RNA polymerase II (pol II) together with general transcription factors (GTFs). TFIID, the largest GTF composed of TATA element-binding protein (TBP) and 14 TBP-associated factors (TAFs), plays a critical role in transcription from TATA-less promoters. In metazoans, several core promoter elements other than the TATA element are thought to be recognition sites for TFIID. However, it is unclear whether functionally homologous elements also exist in TATA-less promoters in Saccharomyces cerevisiae. Here, we identify the cis-elements required to support normal levels of transcription and accurate initiation from sites within the TATA-less and TFIID-dependent RPS5 core promoter. Systematic mutational analyses show that multiple AT-rich sequences are required for these activities and appear to function as recognition sites for TFIID. A single copy of these sequences can support accurate initiation from the endogenous promoter, indicating that they carry highly redundant functions. These results show a novel architecture of yeast TATA-less promoters and support a model in which pol II scans DNA downstream from a recruited site, while searching for appropriate initiation site(s).
Sugihara
Fuminori
F
Division of Molecular and Cellular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan.
Kasahara
Koji
K
Kokubo
Tetsuro
T
D020856:AT Rich Sequence; D015966:Gene Expression Regulation, Fungal; D011401:Promoter Regions, Genetic; D012269:Ribosomal Proteins / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D016385:TATA Box; D015533:Transcriptional Activation
D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C030831:ribosomal protein S5
Biochemistry. 2002 Mar 5;41(9):3147-55
11863454
Genes Dev. 2010 Jan 15;24(2):135-47
20040571
EMBO J. 1999 Sep 1;18(17):4835-45
10469661
Genes Dev. 2001 Oct 1;15(19):2515-9
11581157
Mol Cell. 2004 Feb 27;13(4):573-85
14992726
Proc Natl Acad Sci U S A. 1985 Dec;82(24):8557-61
3909147
Genes Dev. 2008 Oct 15;22(20):2823-30
18923080
PLoS Biol. 2010 Mar 09;8(3):e1000329
20231876
Mol Cell Biol. 1995 Dec;15(12):7059-66
8524273
Nature. 1995 Sep 21;377(6546):254-7
7675113
J Mol Biol. 1986 Feb 5;187(3):363-78
3009831
Genes Dev. 1994 May 1;8(9):995-1006
7926793
Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4213-8
19251649
PLoS One. 2009;4(4):e5103
19337366
Crit Rev Biochem Mol Biol. 2009 Jun;44(2-3):117-41
19514890
Nucleic Acids Res. 2005 May 19;33(9):2838-51
15905473
Yeast. 1998 Jul;14(10):953-61
9717241
J Biol Chem. 2006 Aug 11;281(32):22665-73
16772290
Genes Dev. 1998 Feb 15;12(4):547-56
9472023
Genes Dev. 1999 Jan 1;13(1):49-63
9887099
Mol Cell Biol. 1990 Sep;10(9):4447-55
2201891
Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13475-80
9391050
EMBO J. 1985 Dec 1;4(12):3273-80
3912167
Genes Dev. 2002 Jul 15;16(14):1852-63
12130544
Proc Natl Acad Sci U S A. 1989 Aug;86(15):5718-22
2569738
Mol Cell. 1998 Nov;2(5):675-82
9844639
Nat Struct Mol Biol. 2004 May;11(5):394-403
15114340
Proc Natl Acad Sci U S A. 1985 Dec;82(24):8562-6
3001709
Mol Cell Biol. 2006 Jul;26(13):4853-62
16782874
Nat Rev Genet. 2007 Jun;8(6):424-36
17486122
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2691-5
3282236
Nat Methods. 2006 Nov;3(11):917-22
17124735
Curr Biol. 2003 Apr 29;13(9):772-7
12725737
Biochem Biophys Res Commun. 1999 Feb 5;255(1):157-63
10082672
Nature. 2004 Dec 23;432(7020):1054-8
15616568
Mol Cell Biol. 2004 Oct;24(20):9152-64
15456886
Mol Cell Biol. 1986 Nov;6(11):3847-53
3540601
Mol Cell Biol. 1989 Dec;9(12):5298-304
2685558
J Biol Chem. 2003 Nov 14;278(46):45888-902
12939271
Bioinformatics. 1999 Apr;15(4):267-77
10320394
Curr Opin Cell Biol. 2008 Jun;20(3):253-9
18436437
Genes Dev. 2002 Mar 15;16(6):673-5
11963920
Nat Struct Mol Biol. 2006 Jul;13(7):564-6
16826228
Cell. 2004 Mar 5;116(5):699-709
15006352
J Biol Chem. 2006 May 19;281(20):14119-28
16571719
Curr Biol. 2002 Jul 23;12(14):1240-4
12176335
Mol Cell Biol. 2002 Nov;22(21):7365-71
12370284
Adv Protein Chem. 2004;67:67-92
14969724
Mol Cell Biol. 2004 Sep;24(18):8104-12
15340072
Nucleic Acids Res. 2008 Mar;36(4):1343-57
18187511
EMBO J. 1992 Dec;11(12):4583-90
1425591
Annu Rev Biochem. 2003;72:449-79
12651739
Gene. 2007 Mar 1;389(1):52-65
17123746
Yeast. 2002 Jan 30;19(2):141-9
11788969
Nat Struct Mol Biol. 2009 Oct;16(10):1043-8
19767748
Mol Cell Biol. 2001 Jul;21(14):4427-40
11416123
Cell. 1997 Aug 22;90(4):615-24
9288742
Nucleic Acids Res. 2006 Apr 05;34(6):e51
16598072
Mol Cell Biol. 2008 Jun;28(11):3757-66
18362165
Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78
16858867
Mol Cell Biol. 2002 Aug;22(16):6000-13
12138208
Bioinformatics. 2005 Apr 15;21(8):1295-300
15572469
Mol Cell Biol. 2010 Jul;30(14):3471-9
20457814
Mol Cell Biol. 2005 Nov;25(21):9674-86
16227614
Mol Cell Biol. 2000 Apr;20(7):2385-99
10713163
Curr Biol. 2002 Oct 29;12(21):1828-32
12419182
Nucleic Acids Res. 2006;34(21):6225-32
17090597
J Biol Chem. 2001 Jul 13;276(28):25715-26
11337503
Curr Opin Struct Biol. 2009 Feb;19(1):65-71
19208466
Mol Cell Biol. 2002 Dec;22(24):8744-55
12446791
BMC Bioinformatics. 2006 Mar 07;7:114
16522199
Mol Cell Biol. 2007 Jan;27(1):297-311
17074814
Genome Res. 2009 Nov;19(11):2090-100
19652015
Science. 1993 Aug 6;261(5122):759-62
8342041
EMBO J. 2003 Jul 1;22(13):3395-402
12840001
Annu Rev Biochem. 1989;58:1051-77
2673007
Mol Cell. 2002 Apr;9(4):823-33
11983173
Nature. 2004 Dec 23;432(7020):1058-61
15616569
Nat Rev Genet. 2009 Mar;10(3):161-72
19204718
Mol Cell Biol. 2007 Jul;27(13):4815-24
17452446
Science. 2000 May 19;288(5469):1242-4
10817999
Nature. 1999 Jun 10;399(6736):605-9
10376604
Biochem Biophys Res Commun. 2010 Jan 29;392(1):77-82
20059977
Cell. 2004 Dec 29;119(7):969-79
15620355
Science. 2009 Apr 24;324(5926):513-6
19390046
EMBO J. 2005 Feb 9;24(3):533-42
15692568
Nucleic Acids Res. 2009 Jul;37(13):4234-46
19443449
Genes Dev. 1990 Apr;4(4):636-45
2163345
Development. 2010 Jan;137(1):15-26
20023156
Nature. 2004 Sep 2;431(7004):99-104
15343339