title: Protein:protein interactions in control of a transcriptional switch.
abstract: Protein partner exchange plays a key role in regulating many biological switches. Although widespread, the mechanisms dictating protein partner identity and, therefore, the outcome of a switch have been determined for a limited number of systems. The Escherichia coli protein BirA undergoes a switch between posttranslational biotin attachment and transcription repression in response to cellular biotin demand. Moreover, the functional switch reflects formation of alternative mutually exclusive protein:protein interactions by BirA. Previous studies provided a set of alanine-substituted BirA variants with altered kinetic and equilibrium parameters of forming these interactions. In this work, DNase I footprinting measurements were employed to investigate the consequences of these altered properties for the outcome of the BirA functional switch. The results support a mechanism in which BirA availability for DNA binding and, therefore, transcription repression is controlled by the rate of the competing protein:protein interaction. However, occupancy of the transcriptional regulatory site on DNA by BirA is exquisitely tuned by the equilibrium constant governing its homodimerization.
authors.affiliation: Department of Chemistry and Biochemistry, College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
authors.forename: Poorni R
authors.initials: PR
authors.lastname: Adikaram
authors.forename: Dorothy
authors.initials: D
authors.lastname: Beckett
mesh_terms: D000103:Acetyl-CoA Carboxylase / Q000378:metabolism; D001710:Biotin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019731:Carbon-Nitrogen Ligases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D054889:Fatty Acid Synthase, Type II / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D009876:Operon; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D011506:Proteins; D012097:Repressor Proteins; D001710:Biotin; D054889:Fatty Acid Synthase, Type II; D019731:Carbon-Nitrogen Ligases; C058125:birA protein, E coli; D000103:Acetyl-CoA Carboxylase; C079633:biotin carboxyl carrier protein
keywords: BCCP; BCCP87; BirA:biotinoyl-5′-AMP complex; C-terminal fragment of BCCP; bio-5′-AMP; bioO; biological switch; biotin carboxyl carrier protein; biotin operator; biotinoyl-5′-adenylate; holoBirA; kinetic versus equilibrium control; protein:protein interactions
references.citation: Biochemistry. 2002 Dec 3;41(48):14263-71
references.pmid: 12450391
references.citation: J Mol Biol. 2009 Jun 5;389(2):336-48
references.pmid: 19361526
references.citation: EMBO J. 2013 Apr 3;32(7):938-53
references.pmid: 23474895
references.citation: Biochemistry. 1993 Sep 21;32(37):9649-56
references.pmid: 8373769
references.citation: J Mol Biol. 2007 Oct 12;373(1):96-111
references.pmid: 17765263
references.citation: Structure. 2006 Feb;14(2):265-74
references.pmid: 16472746
references.citation: J Biol Chem. 2013 Apr 12;288(15):10766-78
references.pmid: 23430750
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W569-75
references.pmid: 20462859
references.citation: J Mol Biol. 1981 Mar 15;146(4):469-92
references.pmid: 6456358
references.citation: Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1415-23
references.pmid: 22550172
references.citation: Methods Mol Biol. 1995;37:379-91
references.pmid: 7780518
references.citation: J Biol Chem. 2008 May 23;283(21):14739-50
references.pmid: 18372281
references.citation: J Biol Chem. 2011 Apr 15;286(15):13071-8
references.pmid: 21343300
references.citation: Protein Sci. 2013 Jun;22(6):762-73
references.pmid: 23559560
references.citation: Anal Biochem. 1989 Nov 1;182(2):319-26
references.pmid: 2610349
references.citation: Proc Natl Acad Sci U S A. 1979 Nov;76(11):5592-5
references.pmid: 392507
references.citation: J Mol Biol. 2006 Mar 24;357(2):509-23
references.pmid: 16438984
references.citation: J Mol Biol. 2012 Jun 8;419(3-4):223-33
references.pmid: 22446587
references.citation: J Mol Biol. 2008 Jul 18;380(4):742-56
references.pmid: 18547585
references.citation: J Biol Chem. 1988 Jul 25;263(21):10332-6
references.pmid: 3134346
references.citation: J Mol Biol. 2008 Jun 27;380(1):223-36
references.pmid: 18508076
references.citation: Protein Sci. 2001 Dec;10(12):2618-22
references.pmid: 11714930
references.citation: Proc Natl Acad Sci U S A. 2001 May 22;98(11):6045-50
references.pmid: 11353844
references.citation: J Bacteriol. 1993 Jan;175(2):332-40
references.pmid: 7678242
references.citation: J Mol Biol. 1981 Mar 15;146(4):451-67
references.pmid: 7024555
references.citation: Methods Enzymol. 1986;130:132-81
references.pmid: 3773731
references.citation: J Biol Chem. 1964 Sep;239:2865-71
references.pmid: 14216437
references.citation: J Mol Biol. 2000 Dec 15;304(5):821-33
references.pmid: 11124029
references.citation: Biophys Chem. 2011 Nov;159(1):142-51
references.pmid: 21715082
references.citation: J Biol Chem. 1996 Mar 29;271(13):7559-67
references.pmid: 8631788
references.citation: Biochemistry. 1999 Oct 5;38(40):13077-84
references.pmid: 10529178
references.citation: J Mol Biol. 2013 Jul 10;425(13):2382-92
references.pmid: 23499887
references.citation: Biochemistry. 2006 May 23;45(20):6417-25
references.pmid: 16700552
references.citation: J Mol Biol. 1998 May 15;278(4):787-800
references.pmid: 9614942
references.citation: Cell. 1989 Aug 11;58(3):427-9
references.pmid: 2667763
references.citation: J Mol Biol. 2003 Jan 31;325(5):937-48
references.pmid: 12527300