Nag Repressor–Operator Interactions: Protein–DNA Contacts Cover More Than Two Turns of the DNA Helix
Identifieur interne : 000307 ( France/Analysis ); précédent : 000306; suivant : 000308Nag Repressor–Operator Interactions: Protein–DNA Contacts Cover More Than Two Turns of the DNA Helix
Auteurs : Jacqueline Plumbridge [France] ; Annie Kolb [France]Source :
- Journal of Molecular Biology [ 0022-2836 ] ; 1995.
English descriptors
- KwdEn :
- Teeft :
- Acrylamide, Bacillus subtilis, Bamhi, Binding proteins, Binding sites, Biol, Boxb, Boxe, Boxe operator, Boxm, Centre, Coli, Crystal structure, Cytr, Derepression, Different complexes, Dnasei, Double mutations, Ecori, Escherichia, Escherichia coli, Fragment, Glcnac, Glucose, Groove, Half sites, Helix, Hillen, Intergenic region, Kolb, Loop formation, Major groove, Minor groove, Mutagenesis, Mutant, Mutant operators, Mutation, Nagb, Nagb promoter, Nagb promoters, Nagc, Nagc operator, Nagc operator mutagenesis, Nagc operators, Nagc repressor, Nagc strain, Nage, Nage operator, Native acrylamide, Natl acad, Nucleotide sequence, Operator mutations, Operon, Plumbridge, Plumbridge kolb, Polynucleotide kinase, Prokaryotic, Promoter, Repressor, Repressor binding, Retardation analysis, Weickert adhya.
Abstract
Abstract: The NagC repressor binds to two sites in the intergenicnagE-Bregion overlapping the divergently expressednagEandnagBpromoters. In addition the NagC repressor binds to two sites upstream of themanXYZoperon. Although basically palindromic, there is little sequence consensus between the four operators. To identify the DNA sequence important for NagC recognition, we have taken advantage of the fact that repression of thenagEandnagBgenes requires the formation of a loop of DNA between molecules of the repressor bound to thenagEandnagBoperators. ThenagEoperator was systematically mutagenised and the effect of the mutations measured on the level of expression from anagB-lacZfusion. These experiments showed that the most important positions for recognition are the two A·T base-pairs at positions −5 and −6 from the centre of symmetry. These are the only absolutely conserved bases in the four operators. Certain changes of residues at position −3 and −4 have fairly strong effects while changes at −7 to −10 have only minor effects. However the presence of a G or C base at positions +11 or −11 produces a NagC binding site with considerably higher affinity than the wild-typenagEoperator bothin vitroandin vivo, a “super-operator”. The presence of a super-operator considerably increased the stability of the binary looped NagC-DNA complexin vitro. However in the presence of cAMP/CAP, NagC showed the same apparent binding affinity to wild-type and super-operators indicating that one role of cAMP/CAP in the repression complex is to reduce the need for high affinity sites. These super-operators allow a higher level of repression of thenagEpromoter compared to thenagB, presumably due to the existence of linear complexes of NagC bound to BoxE.
Url:
DOI: 10.1006/jmbi.1995.0346
Affiliations:
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ISTEX:DBFC8AB3CB007D9FDB43BEBACAD4BAFE7909C5D5Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Nag Repressor–Operator Interactions: Protein–DNA Contacts Cover More Than Two Turns of the DNA Helix</title><author><name sortKey="Plumbridge, Jacqueline" sort="Plumbridge, Jacqueline" uniqKey="Plumbridge J" first="Jacqueline" last="Plumbridge">Jacqueline Plumbridge</name></author><author><name sortKey="Kolb, Annie" sort="Kolb, Annie" uniqKey="Kolb A" first="Annie" last="Kolb">Annie Kolb</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:DBFC8AB3CB007D9FDB43BEBACAD4BAFE7909C5D5</idno><date when="1995" year="1995">1995</date><idno type="doi">10.1006/jmbi.1995.0346</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-Z9ZDR71N-K/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">003905</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">003905</idno><idno type="wicri:Area/Istex/Curation">002C77</idno><idno type="wicri:Area/Istex/Checkpoint">002A54</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">002A54</idno><idno type="wicri:doubleKey">0022-2836:1995:Plumbridge J:nag:repressor:operator</idno><idno type="wicri:Area/Main/Merge">003101</idno><idno type="wicri:Area/Main/Curation">002F31</idno><idno type="wicri:Area/Main/Exploration">002F31</idno><idno type="wicri:Area/France/Extraction">000307</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Nag Repressor–Operator Interactions: Protein–DNA Contacts Cover More Than Two Turns of the DNA Helix</title><author><name sortKey="Plumbridge, Jacqueline" sort="Plumbridge, Jacqueline" uniqKey="Plumbridge J" first="Jacqueline" last="Plumbridge">Jacqueline Plumbridge</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Institut de Biologie Physico-chimique (URA1139), 13, rue Pierre et Marie Curie, 75005, Paris, FranceInstitut Pasteur (URA1149), 25, rue de Dr Roux, 75015, Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Kolb, Annie" sort="Kolb, Annie" uniqKey="Kolb A" first="Annie" last="Kolb">Annie Kolb</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Institut de Biologie Physico-chimique (URA1139), 13, rue Pierre et Marie Curie, 75005, Paris, FranceInstitut Pasteur (URA1149), 25, rue de Dr Roux, 75015, Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Molecular Biology</title><title level="j" type="abbrev">YJMBI</title><idno type="ISSN">0022-2836</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1995">1995</date><biblScope unit="volume">249</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="890">890</biblScope><biblScope unit="page" to="902">902</biblScope></imprint><idno type="ISSN">0022-2836</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0022-2836</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>NagC repressor</term><term>cAMP/CAP</term><term>nagE-Boperator</term><term>protein–DNA recognition</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Acrylamide</term><term>Bacillus subtilis</term><term>Bamhi</term><term>Binding proteins</term><term>Binding sites</term><term>Biol</term><term>Boxb</term><term>Boxe</term><term>Boxe operator</term><term>Boxm</term><term>Centre</term><term>Coli</term><term>Crystal structure</term><term>Cytr</term><term>Derepression</term><term>Different complexes</term><term>Dnasei</term><term>Double mutations</term><term>Ecori</term><term>Escherichia</term><term>Escherichia coli</term><term>Fragment</term><term>Glcnac</term><term>Glucose</term><term>Groove</term><term>Half sites</term><term>Helix</term><term>Hillen</term><term>Intergenic region</term><term>Kolb</term><term>Loop formation</term><term>Major groove</term><term>Minor groove</term><term>Mutagenesis</term><term>Mutant</term><term>Mutant operators</term><term>Mutation</term><term>Nagb</term><term>Nagb promoter</term><term>Nagb promoters</term><term>Nagc</term><term>Nagc operator</term><term>Nagc operator mutagenesis</term><term>Nagc operators</term><term>Nagc repressor</term><term>Nagc strain</term><term>Nage</term><term>Nage operator</term><term>Native acrylamide</term><term>Natl acad</term><term>Nucleotide sequence</term><term>Operator mutations</term><term>Operon</term><term>Plumbridge</term><term>Plumbridge kolb</term><term>Polynucleotide kinase</term><term>Prokaryotic</term><term>Promoter</term><term>Repressor</term><term>Repressor binding</term><term>Retardation analysis</term><term>Weickert adhya</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: The NagC repressor binds to two sites in the intergenicnagE-Bregion overlapping the divergently expressednagEandnagBpromoters. In addition the NagC repressor binds to two sites upstream of themanXYZoperon. Although basically palindromic, there is little sequence consensus between the four operators. To identify the DNA sequence important for NagC recognition, we have taken advantage of the fact that repression of thenagEandnagBgenes requires the formation of a loop of DNA between molecules of the repressor bound to thenagEandnagBoperators. ThenagEoperator was systematically mutagenised and the effect of the mutations measured on the level of expression from anagB-lacZfusion. These experiments showed that the most important positions for recognition are the two A·T base-pairs at positions −5 and −6 from the centre of symmetry. These are the only absolutely conserved bases in the four operators. Certain changes of residues at position −3 and −4 have fairly strong effects while changes at −7 to −10 have only minor effects. However the presence of a G or C base at positions +11 or −11 produces a NagC binding site with considerably higher affinity than the wild-typenagEoperator bothin vitroandin vivo, a “super-operator”. The presence of a super-operator considerably increased the stability of the binary looped NagC-DNA complexin vitro. However in the presence of cAMP/CAP, NagC showed the same apparent binding affinity to wild-type and super-operators indicating that one role of cAMP/CAP in the repression complex is to reduce the need for high affinity sites. These super-operators allow a higher level of repression of thenagEpromoter compared to thenagB, presumably due to the existence of linear complexes of NagC bound to BoxE.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Plumbridge, Jacqueline" sort="Plumbridge, Jacqueline" uniqKey="Plumbridge J" first="Jacqueline" last="Plumbridge">Jacqueline Plumbridge</name></region><name sortKey="Kolb, Annie" sort="Kolb, Annie" uniqKey="Kolb A" first="Annie" last="Kolb">Annie Kolb</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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