title: Study of PcaV from Streptomyces coelicolor yields new insights into ligand-responsive MarR family transcription factors.
abstract: MarR family proteins constitute a group of >12 000 transcriptional regulators encoded in bacterial and archaeal genomes that control gene expression in metabolism, stress responses, virulence and multi-drug resistance. There is much interest in defining the molecular mechanism by which ligand binding attenuates the DNA-binding activities of these proteins. Here, we describe how PcaV, a MarR family regulator in Streptomyces coelicolor, controls transcription of genes encoding β-ketoadipate pathway enzymes through its interaction with the pathway substrate, protocatechuate. This transcriptional repressor is the only MarR protein known to regulate this essential pathway for aromatic catabolism. In in vitro assays, protocatechuate and other phenolic compounds disrupt the PcaV-DNA complex. We show that PcaV binds protocatechuate in a 1:1 stoichiometry with the highest affinity of any MarR family member. Moreover, we report structures of PcaV in its apo form and in complex with protocatechuate. We identify an arginine residue that is critical for ligand coordination and demonstrate that it is also required for binding DNA. We propose that interaction of ligand with this arginine residue dictates conformational changes that modulate DNA binding. Our results provide new insights into the molecular mechanism by which ligands attenuate DNA binding in this large family of transcription factors.
authors: Department of Molecular Pharmacology and Physiology, Brown University, Providence, RI 02912, USA.
authors: Jennifer R
authors: JR
authors: Davis
authors: Breann L
authors: BL
authors: Brown
authors: Rebecca
authors: R
authors: Page
authors: Jason K
authors: JK
authors: Sello
mesh_terms: D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D062385:Hydroxybenzoates / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D009875:Operator Regions, Genetic; D010636:Phenols / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D048372:Streptomyces coelicolor / Q000235:genetics*
chemical_list: C520290:3,4-dihydroxybenzoate; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D062385:Hydroxybenzoates; D008024:Ligands; D010636:Phenols; D012097:Repressor Proteins; D001120:Arginine
references: Appl Environ Microbiol. 2007 Jan;73(1):232-42
references: 17085716
references: Appl Microbiol Biotechnol. 2010 Apr;86(3):921-9
references: 20012281
references: J Mol Biol. 2008 Mar 28;377(3):655-67
references: 18272181
references: Nat Rev Microbiol. 2011 Oct 03;9(11):803-16
references: 21963803
references: Biochemistry. 2009 Mar 17;48(10):2099-108
references: 19166356
references: Curr Issues Mol Biol. 2006 Jan;8(1):51-62
references: 16450885
references: J Bacteriol. 1995 May;177(9):2328-34
references: 7730261
references: Appl Microbiol Biotechnol. 2012 Jan;93(2):891-900
references: 22159607
references: Genet Mol Res. 2006 Dec 07;5(4):773-89
references: 17183485
references: J Biol Chem. 2011 Jun 24;286(25):22178-85
references: 21550983
references: Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):439-50
references: 16552146
references: J Bacteriol. 1999 Aug;181(15):4669-72
references: 10419969
references: Nucleic Acids Res. 2003 Jul 1;31(13):3580-5
references: 12824370
references: Annu Rev Microbiol. 1996;50:553-90
references: 8905091
references: J Bacteriol. 2010 Mar;192(6):1565-72
references: 20081038
references: Appl Environ Microbiol. 2003 Sep;69(9):5398-409
references: 12957928
references: Antioxid Redox Signal. 2011 Mar 15;14(6):1049-63
references: 20626317
references: J Bacteriol. 2012 Apr;194(8):1960-7
references: 22328668
references: Nucleic Acids Res. 2003 Nov 15;31(22):6598-609
references: 14602920
references: Nature. 2008 Aug 14;454(7206):841-5
references: 18704079
references: Nucleic Acids Res. 2009 Mar;37(4):1211-24
references: 19129225
references: Appl Microbiol Biotechnol. 2007 Aug;76(1):159-68
references: 17483937
references: J Mol Biol. 1998 Jul 17;280(3):463-74
references: 9665849
references: Biosci Biotechnol Biochem. 2007 Jan;71(1):1-15
references: 17213657
references: Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5456-60
references: 7777530
references: Antimicrob Agents Chemother. 2000 Oct;44(10):2905-7
references: 10991887
references: Methods Enzymol. 1997;276:307-26
references: 27754618
references: Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1541-6
references: 12563033
references: FEMS Microbiol Lett. 2012 Jul;332(1):68-75
references: 22515452
references: J Biol Chem. 2012 Nov 2;287(45):37703-12
references: 22992749
references: J Am Chem Soc. 2003 Dec 3;125(48):14859-66
references: 14640663
references: J Bacteriol. 1996 Jan;178(1):266-72
references: 8550427
references: Mol Cell. 2005 Oct 7;20(1):131-41
references: 16209951
references: Proc Natl Acad Sci U S A. 2010 May 11;107(19):8617-22
references: 20421503
references: J Bacteriol. 2010 Sep;192(18):4786-9
references: 20639340
references: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references: 20383002
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D344-8
references: 16381883
references: Appl Environ Microbiol. 2003 Mar;69(3):1598-606
references: 12620848
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: Proteins. 2013 Jan;81(1):176-82
references: 23042442
references: J Biol Chem. 2009 Aug 28;284(35):23517-24
references: 19586910
references: Protein Sci. 2010 Apr;19(4):680-92
references: 20095047
references: J Biol Chem. 2004 Dec 3;279(49):51442-50
references: 15448166
references: J Mol Cell Biol. 2010 Oct;2(5):243-54
references: 20716550
references: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references: 20124702
references: Biochem Biophys Res Commun. 2007 Oct 19;362(2):275-80
references: 17707338
references: J Mol Biol. 2009 May 8;388(3):559-69
references: 19298823
references: J Biol Chem. 2002 Aug 9;277(32):29253-9
references: 12034710
references: Microbiology (Reading). 2010 May;156(Pt 5):1313-1322
references: 20110298
references: J Biol Chem. 2005 Apr 1;280(13):13055-61
references: 15632111
references: BMC Microbiol. 2010 Feb 08;10:36
references: 20137101
references: Appl Environ Microbiol. 2001 Aug;67(8):3530-41
references: 11472929
references: Appl Environ Microbiol. 2006 Aug;72(8):5403-13
references: 16885292
references: J Bacteriol. 2001 Jul;183(14):4134-41
references: 11418552
references: Nucleic Acids Res. 2012 May;40(9):4178-92
references: 22238377
references: Nucleic Acids Res. 2009 Aug;37(14):4723-35
references: 19509310
references: Microbiol Mol Biol Rev. 2004 Sep;68(3):474-500, table of contents
references: 15353566
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8
references: 15980471