{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,29]],"date-time":"2024-01-29T14:41:45Z","timestamp":1706539305742},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,3]],"date-time":"2014-11-03T00:00:00Z","timestamp":1414972800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0111802","type":"journal-article","created":{"date-parts":[[2014,11,3]],"date-time":"2014-11-03T18:59:03Z","timestamp":1415041143000},"page":"e111802","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Towards Novel Amino Acid-Base Contacts in Gene Regulatory Proteins: AraR \u2013 A Case Study"],"prefix":"10.1371","volume":"9","author":[{"given":"Isabel Lopes","family":"Correia","sequence":"first","affiliation":[]},{"given":"Irina Saraiva","family":"Franco","sequence":"additional","affiliation":[]},{"given":"Isabel","family":"de S\u00e1-Nogueira","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,11,3]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1126\/science.2842864","article-title":"DNA binding by proteins","volume":"241","author":"R Schleif","year":"1988","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1146\/annurev.bi.53.070184.001453","article-title":"Protein-DNA recognition","volume":"53","author":"CO Pabo","year":"1984","journal-title":"Annu Rev Biochem"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1146\/annurev.bi.61.070192.005201","article-title":"Transcriptions factors: structural families and principles of DNA recognition","volume":"61","author":"CO Pabo","year":"1992","journal-title":"Annu Rev Biochem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1093\/nar\/29.13.2860","article-title":"Amino acid\u2013base interactions: a three-dimensional analysis of protein\u2013DNA interactions at an atomic level","volume":"29","author":"NM Luscombe","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1016\/S0022-2836(02)00571-5","article-title":"Protein\u2013DNA interactions: Amino acid conservation and the effects of mutations on binding specificity","volume":"320","author":"NM Luscombe","year":"2002","journal-title":"J Mol Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1955","DOI":"10.1002\/jcc.20954","article-title":"Energy-based prediction of amino acid-nucleotide base recognition","volume":"12","author":"A Marabotti","year":"2008","journal-title":"J Comput Chem"},{"issue":"9","key":"ref7","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/nrg2842","article-title":"Genome editing with engineered zinc finger nucleases","volume":"11","author":"FD Urnov","year":"2010","journal-title":"Nat Rev Genet"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1126\/science.1204094","article-title":"TAL Effectors: Customizable Proteins for DNA Targeting","volume":"333","author":"AJ Bogdanove","year":"2011","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1128\/jb.179.5.1598-1608.1997","article-title":"Negative regulation of L-arabinose metabolism in <italic>Bacillus subtilis<\/italic>: characterization of the <italic>araR<\/italic> (<italic>araC<\/italic>) gene","volume":"179","author":"I S\u00e1-Nogueira","year":"1997","journal-title":"J Bacteriol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1046\/j.1365-2958.1999.01484.x","article-title":"Mode of action of AraR, the key regulator of L-arabinose metabolism in <italic>Bacillus subtilis<\/italic>","volume":"33","author":"LJ Mota","year":"1999","journal-title":"Mol Microbiol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/j.1574-6968.1991.tb04544.x","article-title":"A new family of bacterial regulatory proteins","volume":"63","author":"DJ Haydon","year":"1991","journal-title":"FEMS Microbiol Lett"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"15869","DOI":"10.1016\/S0021-9258(19)49615-4","article-title":"A family of bacterial regulators homologous to Gal and Lac repressors","volume":"267","author":"MJ Weickert","year":"1992","journal-title":"J Biol Chem"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1107\/S090744491105414X","article-title":"Structure of the effector-binding domain of the arabinose repressor AraR from <italic>Bacillus subtilis<\/italic>","volume":"68","author":"K Proch\u00e1zkov\u00e1","year":"2012","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1093\/nar\/gks962","article-title":"Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators","volume":"41","author":"D Jain","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-2164(09)69001-8","article-title":"Chapter 1. Variation in form and function the helix-turn-helix regulators of the GntR superfamily","volume":"69","author":"PA Hoskisson","year":"2009","journal-title":"Adv Appl Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1099\/00221287-143-3-957","article-title":"The <italic>Bacillus subtilis<\/italic> L-arabinose (<italic>ara<\/italic>) operon: nucleotide sequence, genetic organization and expression","volume":"143","author":"I S\u00e1-Nogueira","year":"1997","journal-title":"Microbiology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"7705","DOI":"10.1128\/jb.179.24.7705-7711.1997","article-title":"Cloning, functional analysis, and transcriptional regulation of the <italic>Bacillus subtilis araE<\/italic> gene involved in L-arabinose utilization","volume":"179","author":"I S\u00e1-Nogueira","year":"1997","journal-title":"J Bacteriol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1128\/JB.186.5.1287-1296.2004","article-title":"Transcriptional regulation of genes encoding arabinan-degrading enzymes in <italic>Bacillus subtilis<\/italic>","volume":"186","author":"MP Raposo","year":"2004","journal-title":"J Bacteriol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"4190","DOI":"10.1128\/JB.183.14.4190-4201.2001","article-title":"Control of the arabinose regulon in Bacillus subtilis by AraR in vivo: crucial roles of operators, cooperativity, and DNA looping","volume":"183","author":"LJ Mota","year":"2001","journal-title":"J Bacteriol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3024","DOI":"10.1128\/JB.188.8.3024-3036.2006","article-title":"Functional domains of <italic>Bacillus subtilis<\/italic> transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector-binding","volume":"188","author":"IS Franco","year":"2006","journal-title":"J Bacteriol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4755","DOI":"10.1093\/nar\/gkm509","article-title":"Probing key DNA contacts in AraR-mediated transcriptional repression of the <italic>Bacillus subtilis<\/italic> arabinose regulon","volume":"35","author":"IS Franco","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref22","unstructured":"Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory. Cold Spring Harbor. NY."},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/S0300-9084(71)80193-1","article-title":"Characterization of two sucrase activities in <italic>Bacillus subtilis<\/italic> Marburg","volume":"53","author":"M Pascal","year":"1971","journal-title":"Biochimie"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1073\/pnas.44.10.1072","article-title":"Transformation of biochemically deficient strains of <italic>Bacillus subtilis<\/italic> by deoxyribonucleotide","volume":"22","author":"J Spizizen","year":"1958","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref25","unstructured":"Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY."},{"issue":"1\u20132","key":"ref26","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0378-1119(96)00404-0","article-title":"Plasmids for ectopic integration in <italic>Bacillus subtilis<\/italic>","volume":"180","author":"AM Gu\u00e9rout-Fleury","year":"1996","journal-title":"Gene"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/0076-6879(91)08032-D","article-title":"Identification of amino acid-base pair contacts by genetic methods","volume":"208","author":"RH Ebright","year":"1991","journal-title":"Methods Enzymol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"6673","DOI":"10.1073\/pnas.84.19.6673","article-title":"Missing contact probing of DNA-protein interactions","volume":"84","author":"A Brunelle","year":"1987","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/0022-2836(89)90598-6","article-title":"Determining residue-base interactions between AraC protein and <italic>araI<\/italic> DNA","volume":"209","author":"A Brunelle","year":"1989","journal-title":"J Mol Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/8195","article-title":"Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease","volume":"6","author":"AM Martin","year":"1999","journal-title":"Nat Struct Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1074\/jbc.272.3.1646","article-title":"DNA-based loss of specificity mutations","volume":"272","author":"SP Hilchey","year":"1997","journal-title":"J Biol Chem"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1093\/emboj\/20.8.2041","article-title":"The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR","volume":"20","author":"DM van Aalten","year":"2001","journal-title":"EMBO J"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"17373","DOI":"10.1074\/jbc.M100195200","article-title":"The FadR-DNA complex. Transcriptional control of fatty acid metabolism in <italic>Escherichia coli<\/italic>","volume":"276","author":"Y Xu","year":"2001","journal-title":"J Biol Chem"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/S0959-440X(99)00057-3","article-title":"Winged helix proteins","volume":"10","author":"KS Gajiwala","year":"2000","journal-title":"Curr Opin Struct Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1002\/j.1460-2075.1995.tb07204.x","article-title":"The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase I probing of inosine\/diaminopurine substituted DNA","volume":"14","author":"C Bailly","year":"1995","journal-title":"EMBO J"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jmbi.1995.0530","article-title":"Effects of base substitutions on the binding of a DNA-bending protein","volume":"253","author":"C Bailly","year":"1995","journal-title":"J Mol Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/25.17.3497","article-title":"Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3\u2032-A-tract junction","volume":"25","author":"NE M\u00f8llegaard","year":"1997","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"ref38","doi-asserted-by":"crossref","first-page":"4797","DOI":"10.1093\/nar\/gkn452","article-title":"Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system","volume":"36","author":"S Lindemose","year":"2008","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0111802","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T03:43:21Z","timestamp":1650512601000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0111802"}},"subtitle":[],"editor":[{"given":"Albert","family":"Jeltsch","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,11,3]]},"references-count":38,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0111802","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,3]]}}}