title: Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
abstract: DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Horton
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Blumenthal
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA xcheng@emory.edu.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Cheng
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C499294:dam protein, E coli
references.citation: Nat Genet. 2001 Mar;27(3):304-8
references.pmid: 11242113
references.citation: J Biol Chem. 2007 Aug 3;282(31):22848-55
references.pmid: 17545164
references.citation: Mol Microbiol. 2002 Apr;44(2):509-20
references.pmid: 11972787
references.citation: J Mol Biol. 1978 Dec 15;126(3):367-80
references.pmid: 370402
references.citation: Chembiochem. 2009 Oct 12;10(15):2488-93
references.pmid: 19725089
references.citation: Cell. 1988 Sep 9;54(6):735-7
references.pmid: 2842065
references.citation: Mol Cell. 2003 Jun;11(6):1647-59
references.pmid: 12820976
references.citation: FEMS Microbiol Rev. 2009 May;33(3):488-503
references.pmid: 19175412
references.citation: Protein Expr Purif. 2005 May;41(1):207-34
references.pmid: 15915565
references.citation: Mol Microbiol. 2002 Aug;45(3):673-95
references.pmid: 12139615
references.citation: J Mol Biol. 1995 Nov 3;253(4):618-32
references.pmid: 7473738
references.citation: Nat Struct Biol. 1998 Aug;5(8):697-701
references.pmid: 9699633
references.citation: Gene. 1988 Dec 25;74(1):189-90
references.pmid: 3074008
references.citation: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references.pmid: 9757107
references.citation: J Mol Biol. 2011 Jun 10;409(3):311-32
references.pmid: 21338611
references.citation: Structure. 2008 Aug 6;16(8):1166-74
references.pmid: 18682218
references.citation: Cell. 2005 May 6;121(3):349-61
references.pmid: 15882618
references.citation: Nucleic Acids Res. 1983 Feb 11;11(3):837-51
references.pmid: 6300769
references.citation: J Mol Biol. 2014 Oct 23;426(21):3539-52
references.pmid: 25134757
references.citation: J Biol Chem. 2012 Jun 29;287(27):22873-81
references.pmid: 22570478
references.citation: Epigenetics. 2011 Sep 1;6(9):1078-84
references.pmid: 21814036
references.citation: J Bacteriol. 2010 Aug;192(15):3903-14
references.pmid: 20511501
references.citation: J Biol Chem. 1989 Mar 5;264(7):4064-70
references.pmid: 2645286
references.citation: EcoSal Plus. 2008 Jul 25;2008:
references.pmid: 25325076
references.citation: J Biol Chem. 2004 Dec 10;279(50):52075-81
references.pmid: 15456775
references.citation: Microbes Infect. 2014 Aug;16(8):615-22
references.pmid: 24947562
references.citation: J Mol Biol. 1977 Jul;114(1):153-68
references.pmid: 20509
references.citation: J Mol Biol. 2004 Aug 6;341(2):443-54
references.pmid: 15276835
references.citation: J Biol Chem. 2012 Dec 7;287(50):41576-82
references.pmid: 23048026
references.citation: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references.pmid: 2025413
references.citation: Annu Rev Biochem. 1996;65:101-33
references.pmid: 8811176
references.citation: Prog Nucleic Acid Res Mol Biol. 2004;77:67-126
references.pmid: 15196891
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references.pmid: 20383002
references.citation: Annu Rev Biochem. 1998;67:181-98
references.pmid: 9759487
references.citation: Res Microbiol. 2000 Sep;151(7):563-74
references.pmid: 11037134
references.citation: Nat Biotechnol. 2012 Dec;30(12):1232-9
references.pmid: 23138224
references.citation: Curr Opin Microbiol. 2005 Apr;8(2):154-60
references.pmid: 15802246
references.citation: Mol Microbiol. 1994 Feb;11(4):605-18
references.pmid: 7910935
references.citation: Mol Cell. 2003 Oct;12(4):947-57
references.pmid: 14580345
references.citation: Methods Enzymol. 1997;276:594-611
references.pmid: 9048382
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17140-5
references.pmid: 25313048
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references.pmid: 20124702
references.citation: J Mol Biol. 2008 Oct 31;383(1):92-105
references.pmid: 18706913
references.citation: J Biol Chem. 2008 Jul 18;283(29):20106-16
references.pmid: 18502761
references.citation: Nucleic Acids Res. 1995 Apr 25;23(8):1388-95
references.pmid: 7753630
references.citation: Nature. 2008 Oct 9;455(7214):826-9
references.pmid: 18772888
references.citation: Mol Microbiol. 1995 Jun;16(5):943-53
references.pmid: 7476191
references.citation: Mol Microbiol. 2014 Feb;91(4):665-78
references.pmid: 24308271
references.citation: J Biol Chem. 2007 Dec 21;282(51):36942-52
references.pmid: 17977824
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4672-7
references.pmid: 12682301
references.citation: J Bacteriol. 2003 Mar;185(6):1886-94
references.pmid: 12618452
references.citation: J Bacteriol. 2005 Oct;187(20):7027-37
references.pmid: 16199573
references.citation: J Mol Biol. 2006 Apr 28;358(2):559-70
references.pmid: 16524590
references.citation: Nat Struct Biol. 2003 Oct;10(10):849-55
references.pmid: 12937411
references.citation: Mol Gen Genet. 1985;201(1):14-9
references.pmid: 3932821
references.citation: PLoS One. 2007 Mar 07;2(3):e273
references.pmid: 17342207