https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=PeiEcoliWiki - User contributions [en]2026-11-04T00:29:11ZUser contributionsMediaWiki 1.43.11https://ecoliwiki.org/colipedia/index.php?title=EcoliWiki:Literature_Team_Comments&diff=431118EcoliWiki:Literature Team Comments2008-05-20T18:32:14Z<p>Pei: /* Pei Yap, Spring 2008 */</p>
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<div>Below are comments provided by the first team of students to add reference articles to the EcoliWiki related to the linkage map of E.coli K-12. Since April of 2007 they have added ___ articles. <br />
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== Miriam Garcia, Lab Curator Fall 2007/Spring 2008 ==<br />
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== Matthew Lakich, Fall 2007/Spring 2008 ==<br />
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== Aaron Hopkins, Spring 2008 ==<br />
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== Joseph Kim, Spring 2008 ==<br />
Besides some Internet connection hardships I experienced on my end, the literature pages and reference articles were fairly easy to get through once I got the hang of it. The use of Google Docs worked well here and I was able to get done fairly quickly and leave time for other work. Ordering pdf's of articles not available was a breeze also. Overall it was an enjoyable experience.<br />
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== Katrina Trapp, Spring 2008 ==<br />
This task I found much easier than editing the wiki pages. It only took a few trys for me to get the hang of it. Everything went pretty smoothly and I thought that use of the Googledocs was a fantastic idea. It was easy to organize and to see the work that we had already accomplished. Overall this was a smooth and easy experience.<br />
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== Pei Yap, Spring 2008 ==<br />
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[[Category:Public Team Pages]]<br />
I thought it much easier to do the literatures because it was the same thing for each of them and I got through it quicker once I learnt how to multi-task. However, this task was more tedious and not as exciting as the wiki pages. <br />
The Google docs were really helpful because it was easy to put in the details and organize things.</div>Peihttps://ecoliwiki.org/colipedia/index.php?title=EcoliWiki:Literature_Team_Comments&diff=431117EcoliWiki:Literature Team Comments2008-05-20T18:30:33Z<p>Pei: /* Pei Yap, Spring 2008 */</p>
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<div>Below are comments provided by the first team of students to add reference articles to the EcoliWiki related to the linkage map of E.coli K-12. Since April of 2007 they have added ___ articles. <br />
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== Miriam Garcia, Lab Curator Fall 2007/Spring 2008 ==<br />
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== Matthew Lakich, Fall 2007/Spring 2008 ==<br />
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<br />
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== Aaron Hopkins, Spring 2008 ==<br />
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<br />
<br />
== Joseph Kim, Spring 2008 ==<br />
Besides some Internet connection hardships I experienced on my end, the literature pages and reference articles were fairly easy to get through once I got the hang of it. The use of Google Docs worked well here and I was able to get done fairly quickly and leave time for other work. Ordering pdf's of articles not available was a breeze also. Overall it was an enjoyable experience.<br />
<br />
== Katrina Trapp, Spring 2008 ==<br />
This task I found much easier than editing the wiki pages. It only took a few trys for me to get the hang of it. Everything went pretty smoothly and I thought that use of the Googledocs was a fantastic idea. It was easy to organize and to see the work that we had already accomplished. Overall this was a smooth and easy experience.<br />
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== Pei Yap, Spring 2008 ==<br />
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<br />
[[Category:Public Team Pages]]<br />
I thought it much easier to do the literatures because it was the same thing for each of them and I got through it quicker once I learnt how to multi-task. However, this task was more tedious and not as exciting as the wiki pages.</div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3040739&diff=403704PMID:30407392008-04-30T10:17:37Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Bognar, AL, Osborne, C and Shane, B''' (1987) Primary structure of the Escherichia coli folC gene and its folylpolyglutamate synthetase-dihydrofolate synthetase product and regulation of expression by an upstream gene.''J. Biol. Chem.'' '''262''':12337-43</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The nucleotide sequence of the gene for folylpoly-gamma-glutamate synthetase-dihydrofolate synthetase (folC) has been determined. The deduced amino acid sequence codes for a protein of Mr 45,380 and contains regions with homology to the A and B regions of ATP-binding sites. The folC gene is adjacent to a gene located 70 base pairs upstream of the initiation codon for folC. The nucleotide sequence of this upstream gene was also determined. Deletion of the upstream gene sequences from recombinant plasmids containing the folC gene results in about a 100-fold decrease in plasmid-dependent folylpolyglutamate synthetase activity, suggesting that the major promoter for folC is 5' to the upstream gene. The upstream gene codes for a protein of Mr 33,346, which is expressed in maxicells and amplified in cells containing the upstream gene in recombinant pUC8 plasmids. Expression of the upstream gene in maxicells was greater than that of folC, as determined by the intensity of 35S-labeled proteins after sodium dodecyl sulfate-gel electrophoresis. A region of dyad symmetry exists between the coding sequences of the two genes which may code for a transcription termination signal and be responsible for the attenuation of the expression of the folC gene relative to the upstream gene. The folC gene is located about 1 kilobase upstream of the purF gene region at 50 min on the Escherichia coli map. The function of the upstream gene product is unknown. It contains sequences with homology to metal-binding domains in nucleic acid-binding proteins. A new purification procedure for obtaining large quantities of folylpolyglutamate synthetase-dihydrofolate synthetase is described.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8655499&diff=403614PMID:86554992008-04-30T10:17:09Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Bogan, JA and Helmstetter, CE''' (1996) mioC transcription, initiation of replication, and the eclipse in Escherichia coli.''J. Bacteriol.'' '''178''':3201-6</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The potential role of mioC transcription as a negative regulator of initiation of chromosome replication in Escherichia coli was evaluated. When initiation was aligned by a shift of dnaC2(Ts) mutants to nonpermissive temperature (40 degrees C), mioC transcript levels measured at the 5' end or reading through oriC disappeared within one mass doubling. Upon return to permissive temperature (30 degrees C), the transcripts reappeared coordinately about 15 min after the first synchronized initiation and then declined sharply again 10 min later, just before the second initiation. Although these observations were consistent with the idea that mioC transcription might have to be terminated prior to initiation, it was found that the interval between initiations at permissive temperature, i.e., the eclipse period, was not influenced by the time required to shut down mioC transcription, since the eclipse was the same for chromosomes and minichromosomes which lacked mioC transcription. This finding did not, in itself, rule out the possibility that mioC transcription must be terminated prior to initiation of replication, since it might normally be shut off before initiation, and never be limiting, even during the eclipse. Therefore, experiments were performed to determine whether the continued presence of mioC transcription during the process of initiation altered the timing of initiation. It was found that minichromosomes possessing a deletion in the DnaA box upstream of the promoter transcribed mioC continuously and replicated with the same timing as those that either shut down expression prior to initiation or lacked expression entirely. It was further shown that mioC transcription was present throughout the induction of initiation by addition of chloramphenicol to a dnaA5(Ts) mutant growing at a semipermissive temperature. Thus, transcription through oriC emanating from the mioC gene promoter is normally inhibited prior to initiation of replication by the binding of DnaA protein, but replication can initiate with the proper timing even when transcription is not shut down; i.e., mioC does not serve as a negative regulator of initiation. It is proposed, however, that the reappearance and subsequent disappearance of mioC transcription during a 10-min interval at the end of the eclipse serves as an index of the minimum time required for the establishment of active protein-DNA complexes at the DnaA boxes in the fully methylated origin region of the chromosome. On this basis, the eclipse constitutes the time for methylation of the newly formed DNA strands (15 to 20 min at 30 degrees C) followed by the time for DnaA protein to bind and activate oriC for replication (10 min).<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6394957&diff=403546PMID:63949572008-04-30T10:16:47Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Boeke, JD, LaCroute, F and Fink, GR''' (1984) A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance.''Mol. Gen. Genet.'' '''197''':345-6</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Mutations at the URA3 locus of Saccharomyces cerevisiae can be obtained by a positive selection. Wild-type strains of yeast (or ura3 mutant strains containing a plasmid-borne URA3+ gene) are unable to grow on medium containing the pyrimidine analog 5-fluoro-orotic acid, whereas ura3- mutants grow normally. This selection, based on the loss of orotidine-5'-phosphate decarboxylase activity seems applicable to a variety of eucaryotic and procaryotic cells.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:1311326&diff=403511PMID:13113262008-04-30T10:16:37Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Boehmer, PE and Emmerson, PT''' (1992) The RecB subunit of the Escherichia coli RecBCD enzyme couples ATP hydrolysis to DNA unwinding.''J. Biol. Chem.'' '''267''':4981-7</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The RecB subunit of the Escherichia coli RecBCD enzyme has previously been reported to possess DNA-dependent ATPase activity (Hickson, I. D., Robson, C. N., Atkinson, K. E., Hutton, L., and Emmerson, P. T. (1985) J. Biol. Chem. 260, 1224-1229). Here we demonstrate that a specific interaction between RecB protein and ATP can also be shown by photoaffinity labeling with the ATP analogue 8-azido-ATP. Furthermore, the capacity of the RecB protein to support ATP hydrolysis varies with the structure and length of the DNA cofactor. Single-stranded linear and circular DNA are markedly better in promoting ATP hydrolysis than duplex DNA. The purified RecB protein can function as a DNA helicase, displacing oligonucleotides annealed to viral M13 DNA in an ATP-dependent and orientation-specific manner.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:1838215&diff=403481PMID:18382152008-04-30T10:16:27Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Böck, A, Forchhammer, K, Heider, J and Baron, C''' (1991) Selenoprotein synthesis: an expansion of the genetic code.''Trends Biochem. Sci.'' '''16''':463-7</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || A number of enzymes employ the unusual amino acid selenocysteine as part of their active site because of its high chemical reactivity. Selenocysteine is incorporated into these proteins co-translationally: biosynthesis occurs on a specific tRNA and insertion into a growing polypeptide is directed by a UGA codon in the mRNA. In E. coli, this requires a specific translation factor. Selenocysteine thus represents a unique expansion of the genetic code.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2060797&diff=403472PMID:20607972008-04-30T10:16:23Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Bockamp, EO, Blasco, R and Viñuela, E''' (1991) Escherichia coli thymidine kinase: nucleotide sequence of the gene and relationships to other thymidine kinases.''Gene'' '''101''':9-14</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The thymidine kinase (TK)-encoding gene (tdk) of Escherichia coli is located at min 27 of the E. coli genetic map. Sequence analysis of this region revealed an open reading frame of 205 codons. Identification of this region as the E. coli tdk gene was confirmed by its similarity to other TK-encoding genes. The E. coli amino acid (aa) sequence showed significant similarity to the corresponding TK polypeptides of vertebrates and large DNA viruses, but showed no similarity to known herpes virus TK enzymes. Mapping of highly conserved positions among all sequences indicates the importance of these residues for catalytic activity and may facilitate further functional studies. Using a distance matrix method, the evolutionary relationships among the TK aa sequence of poxviruses, eukaryotes and prokaryotes were analyzed and a potential phylogenetic tree was established.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8787606&diff=403437PMID:87876062008-04-30T10:16:10Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blumenthal, RM, Borst, DW and Matthews, RG''' (1996) Experimental analysis of global gene regulation in Escherichia coli.''Prog. Nucleic Acid Res. Mol. Biol.'' '''55''':1-86</span><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2163388&diff=403407PMID:21633882008-04-30T10:15:58Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blum, PH, Jovanovich, SB, McCann, MP, Schultz, JE, Lesley, SA, Burgess, RR and Matin, A''' (1990) Cloning and in vivo and in vitro regulation of cyclic AMP-dependent carbon starvation genes from Escherichia coli.''J. Bacteriol.'' '''172''':3813-20</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The regulation of three Escherichia coli carbon starvation (cst) genes fused to lacZ was examined. Expression of these genes is induced by starvation for a carbon source. The role of carbon and cyclic AMP (cAMP) availability and of an altered-function crp mutation were investigated for their effect on cst expression in vivo. The experiments indicated that cAMP concentrations controlled the absolute expression of one cst fusion, but the other two cst fusions were dependent upon some component not present in exponentially growing cells under conditions of glucose excess, even when cAMP was added. To examine the regulation of these genes in further detail, the three cst::lacZ fusions were cloned on multicopy plasmids. All three cst::lacZ fusions retained their inducible regulatory phenotype in the multicopy state. Analysis of the expression of the cloned cst::lacZ fusions in an in vitro-coupled transcription-translation cell-free system demonstrated that the predominant promoter(s) present on each cloned DNA was dependent on sigma 70 for expression. In vitro cAMP titration curves indicated that this molecule was necessary and sufficient for the expression of one fusion but not sufficient for the second fusion, while the third fusion exhibited constitutive levels of expression in vitro. The results are discussed in the context of the E. coli carbon starvation response.</protect><br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2163388 PubMed]<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8890153&diff=403373PMID:88901532008-04-30T10:15:45Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blount, P, Sukharev, SI, Moe, PC, Schroeder, MJ, Guy, HR and Kung, C''' (1996) Membrane topology and multimeric structure of a mechanosensitive channel protein of Escherichia coli.''EMBO J.'' '''15''':4798-805</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || We have studied the membrane topology and multimeric structure of a mechanosensitive channel, MscL, which we previously isolated and cloned from Escherichia coli. We have localized this 15-kDa protein to the inner membrane and, by PhoA fusion, have shown that it contains two transmembrane domains with both the amino and carboxyl termini on the cytoplasmic side. Mutation of the glutamate at position 56 to histidine led to changes in channel kinetics which were dependent upon the pH on the periplasmic, but not cytoplasmic side of the membrane, providing additional evidence for the periplasmic positioning of this part of the molecule. Tandems of two MscL subunits expressed as a single polypeptide formed functional channels, suggesting an even number of transmembrane domains per subunit (amino and carboxyl termini on the same side of the membrane), and an even number of subunits per functional complex. Finally, cross-linking studies suggest that the functional MscL complex is a homohexamer. In summary, these data are all consistent with a protein domain assignment and topological model which we propose and discuss.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8890153 PubMed]<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6355771&diff=403364PMID:63557712008-04-30T10:15:41Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Bloxham, DP, Herbert, CJ, Giles, IG and Ner, SS''' (1983) The use of bacteriophage M13 carrying defined fragments of the Escherichia coli gltA gene to determine the location and structure of the citrate synthase promoter region.''Mol. Gen. Genet.'' '''191''':499-506</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The gltA gene from Escherichia coli, which encodes citrate synthase, has been located on a 3.24 Kb HindIII/EcoRl restriction fragment. This region contains one restriction site for BamHl and two for BglII. Defined restriction fragments from this region were cloned into suitably cleaved replicative form M13mp8 and M13mp9. The recombinants (M13gtlA1 leads to 10) were isolated as single stranded DNA and characterised on the basis of molecular weight and DNA sequence. The single stranded DNA was converted to the double stranded replicative form and used to transform E. coli strain JM103 from which bacteriophage were isolated. Infection of JM103 with different bacteriophage followed by measurement of expressed citrate synthase activity showed that the complete gltA gene must span the BamHl restriction site, that the control region was on the 5'-terminal side of this restriction site and that the coding region for citrate synthase protein commenced on the 3'-terminal side. Analysis of the DNA sequence of this region allowed us to confirm this model, to identify the start sequence for translation of the structural gene and a number of sequences controlling the initiation of transcription. Of special interest is the fact that there must be an extensive leader sequence (305 nucleotides) separating the predicted sites for initiation of transcription and translation.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8876191&diff=403298PMID:88761912008-04-30T10:15:20Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blount, P, Sukharev, SI, Schroeder, MJ, Nagle, SK, Kung, C and Sukharev, SI''' (1996) Single residue substitutions that change the gating properties of a mechanosensitive channel in Escherichia coli.''Proc. Natl. Acad. Sci. U.S.A.'' '''93''':11652-7</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || MscL is a channel that opens a large pore in the Escherichia coli cytoplasmic membrane in response to mechanical stress. Previously, we highly enriched the MscL protein by using patch clamp as a functional assay and cloned the corresponding gene. The predicted protein contains a largely hydrophobic core spanning two-thirds of the molecule and a more hydrophilic carboxyl terminal tail. Because MscL had no homology to characterized proteins, it was impossible to predict functional regions of the protein by simple inspection. Here, by mutagenesis, we have searched for functionally important regions of this molecule. We show that a short deletion from the amino terminus (3 amino acids), and a larger deletion of 27 amino acids from the carboxyl terminus of this protein, had little if any effect in channel properties. We have thus narrowed the search of the core mechanosensitive mechanism to 106 residues of this 136-amino acid protein. In contrast, single residue substitutions of a lysine in the putative first transmembrane domain or a glutamine in the periplasmic loop caused pronounced shifts in the mechano-sensitivity curves and/or large changes in the kinetics of channel gating, suggesting that the conformational structure in these regions is critical for normal mechanosensitive channel gating.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6184364&diff=403249PMID:61843642008-04-30T10:14:56Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blinkowa, A, Haldenwang, WG, Ramsey, JA, Henson, JM, Mullin, DA and Walker, JR''' (1983) Physiological properties of cold-sensitive suppressor mutations of a temperature-sensitive dnaZ mutant of Escherichia coli.''J. Bacteriol.'' '''153''':66-75</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Suppressors of a temperature-sensitive dnaZ polymerization mutant of Escherichia coli have been identified by selecting temperature-insensitive revertants. Those suppressed strains which concomitantly became cold sensitive were chosen for further study. Intragenic suppressor mutations, which caused cold-sensitive defects in DNA polymerization, were located in dnaZ by transduction with lambda dnaZ+ phages. Extragenic suppressor mutations were mapped within the initiation gene dnaA. These suppressor-containing strains were defective in initiation at low temperature as determined by measurements of DNA synthesis in vivo and in toluene-treated cells. The occurrence of suppressor mutations of dnaZ(Ts) within the dnaA gene is considered evidence that the dnaA and dnaZ products interact in vivo. A second indication of a dnaA-dnaZ protein-protein interaction was provided by the observation that the introduction of additional copies of the dnaZ+ gene into a strain carrying the dnaA suppressor mutation was lethal [whether the strain was dnaZ+ or dnaZ(Ts)].</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8550429&diff=403228PMID:85504292008-04-30T10:14:46Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Bledig, SA, Ramseier, TM and Saier, MH''' (1996) Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli.''J. Bacteriol.'' '''178''':280-3</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || Expression of a pykF-lacZ fusion was studied as a function of the carbon source in wild-type strains and strains lacking or overproducing the FruR protein of Escherichia coli. FruR controls the response to the carbon source by repressing pykF expression more strongly under gluconeogenic than under glycolytic conditions, a phenomenon we term catabolite activation.<br />
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{|class = 'sortable' {{Prettytable}} id='232695' <br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2668268&diff=403212PMID:26682682008-04-30T10:14:35Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blaut, M, Whittaker, K, Valdovinos, A, Ackrell, BA, Gunsalus, RP and Cecchini, G''' (1989) Fumarate reductase mutants of Escherichia coli that lack covalently bound flavin.''J. Biol. Chem.'' '''264''':13599-604</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Menaquinol-fumarate oxidoreductase of Escherichia coli is a four-subunit membrane-bound complex that catalyzes the final step in anaerobic respiration when fumarate is the terminal electron acceptor. The catalytic domain of fumarate reductase consists of the FrdA subunit, which contains the active site, and a FAD prosthetic group covalently attached to His44, plus the FrdB subunit which contains at least two of the three nonidentical iron-sulfur clusters of the enzyme. To examine the role of covalently bound FAD in enzyme activity and electron transfer during anaerobic cell growth, site-directed mutagenesis was used to alter His44 of the FrdA subunit to a Ser, Cys, or Tyr residue. The resulting mutant enzyme complexes that were synthesized associated normally with the cytoplasmic membrane, but had decreased ability (greater than 70%) to reduce fumarate with reduced benzyl viologen, an artificial electron donor of low redox potential (Em = -359 mV; Clark, W. M. (1972) Oxidation-Reduction Potentials of Organic Systems, Robert E. Kreiger Publishing Co., Melbourne, FL). Even lower activities were measured when the higher potential, natural electron donor menaquinol was used, which, however, correlated with the slower growth rates of the different mutant complexes. In contrast to the normal enzyme, the mutant enzyme complexes were unable to oxidize succinate. Substitution of Arg for His44 produced a totally inactive enzyme complex that permitted no cell growth on nonfermentable substrates with fumarate as electron acceptor. All four mutant complexes contained noncovalently bound FAD in stoichiometric amounts. These data indicate a unique role of the 8 alpha-[N(3)-histidyl] FAD linkage in enzyme activity, by raising the redox potential of free FAD to permit reduction by both menaquinol and succinate.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8265357&diff=403192PMID:82653572008-04-30T10:14:24Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blattner, FR, Burland, V, Plunkett, G, Sofia, HJ and Daniels, DL''' (1993) Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes.''Nucleic Acids Res.'' '''21''':5408-17</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || We present the sequence of 176 kilobases of the Escherichia coli K-12 genome, from katG at 89.2 to an open reading frame (ORF) of unknown function at 92.8 minutes on the genetic map. This brings the total of contiguous sequence from the E. coli genome project to 500 kb (81.5 to 92.8 minutes). This segment contains 134 putative coding genes (ORFs) of which 66 genes were previously identified. Eight new genes--acs, pepE, and nrfB-G--were identified as well as the previously mapped gldA and alr genes. Still, 58 ORFs remain unidentified despite literature and similarity searches. The arrangement of proposed genes relative to possible promoters and terminators suggests 55 potential transcription units. Other features include 13 REP elements, one IRU (ERIC) repeat, 59 computer-predicted bends, 42 Chi sites and one new grey hole. Sixteen signal peptides were found, including those of lamB, btuB, and malE. Two ribosomal RNA loci, rrnB and rrnE, are located in this segment, so we have now sequenced four of the seven E. coli rRNA loci. Comparison of the rRNA loci reveals some differences in the ribosomal structural RNAs which are generally compatible with the proposed secondary structures.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:9278503&diff=403187PMID:92785032008-04-30T10:14:22Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V, Riley, M, Collado-Vides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B and Shao, Y''' (1997) The complete genome sequence of Escherichia coli K-12.''Science'' '''277''':1453-74</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9278503 PubMed]<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:1545706&diff=403140PMID:15457062008-04-30T10:13:57Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blasco, F, Pommier, J, Augier, V, Chippaux, M and Giordano, G''' (1992) Involvement of the narJ or narW gene product in the formation of active nitrate reductase in Escherichia coli.''Mol. Microbiol.'' '''6''':221-30</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || Two membrane-bound nitrate reductases, NRA and NRZ, exist in Escherichia coli. Both isoenzymes are composed of three structural subunits, alpha, beta, and gamma encoded by narG/narZ, narH/narY and narI/narV, respectively. The genes are in transcription units which also contain a fourth gene encoding a polypeptide, delta, which is not part of the final enzyme. A strain which is devoid of, or does not express, the nar genes, was used to investigate the role of the delta and gamma polypeptides in the formation and/or processing of the nitrate reductase. When only the alpha and beta polypeptides are produced, an (alpha beta) complex exists which is inactive and soluble. When the alpha, beta and delta polypeptides are produced, the (alpha beta) complex is active with artificial donors such as benzyl viologen but is soluble. When the alpha, beta and gamma polypeptides are produced, the (alpha beta) complex is inactive but partially binds the membrane. It was concluded that the gamma polypeptide is involved in the binding of the (alpha beta) complex to the membrane while the delta polypeptide is indispensable for the (alpha beta) nitrate reductase activity. The activation by the delta polypeptide does not seem to involve the insertion of the redox centres of the enzyme since the purified inactive (alpha beta) complex was shown to contain the four iron-sulphur centres and the molybdenum cofactor, which are normally present in the native purified enzyme. The extreme sensitivity of this inactive complex to thermal denaturation or tryptic treatment favours the idea that the delta polypeptide promotes the correct assembly of the alpha and beta subunits. Although this corresponds to the definition of a chaperone protein this possibility has been rejected. In this study we have also demonstrated that the delta or gamma polypeptide encoded by one nar operon can be substituted successfully for by its respective counterpart from the other nar operon to give an active membrane bound heterologous nitrate reductase enzyme.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2674654&diff=403132PMID:26746542008-04-30T10:13:54Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blasco, F, Iobbi, C, Giordano, G, Chippaux, M and Bonnefoy, V''' (1989) Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer.''Mol. Gen. Genet.'' '''218''':249-56</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The nucleotide sequence of the narGHJI operon that encodes the nitrate reductase of Escherichia coli was completed. It encodes four polypeptides NarG, NarH, NarJ and NarI of molecular weight 138.7, 57.7, 26.5 and 25.5 kDa, respectively. The analysis of deduced amino acid sequence failed to reveal any structure capable of binding iron within the NarG polypeptide. In contrast, cysteine arrangements typical of iron-sulfur centers were found in the NarH polypeptide. This suggested that the latter is an electron transfer unit of the nitrate reductase complex. Such a view is opposite to the current description of the nitrate reductase. The findings allowed us to propose a model for the electron transfer steps that occur during nitrate reduction. The NarG polypeptide was found to display a high degree of homology with numerous E. coli molybdoproteins. Moreover, the same genetic and functional organizations as well as the presence of highly conserved stretches of amino acids were noted between both NarG/NarH and DmsA/DmsB (encoding the dimethyl sulfoxide reductase) pairs.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2233673&diff=403091PMID:22336732008-04-30T10:13:34Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blasco, F, Iobbi, C, Ratouchniak, J, Bonnefoy, V and Chippaux, M''' (1990) Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon.''Mol. Gen. Genet.'' '''222''':104-11</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The structural genes for NRZ, the second nitrate reductase of Escherichia coli, have been sequenced. They are organized in a transcription unit, narZYWV, encoding four subunits, NarZ, NarY, NarW and NarV. The transcription unit is homologous (73% identity) to the narGHJI operon which encodes the genes for NRA, the better characterized nitrate reductase of this organism. The level of homology between the corresponding polypeptides ranges from 69% for the NarW/NarJ pair to 86% for the NarV/NarI pair. The NarZ polypeptide contains the five conserved regions present in all other known molybdoproteins of E. coli and their relative order is the same. The NarY polypeptide, which contains the same four cysteine clusters in the same order as NarH, is probably an electron transfer unit of the complex. Upstream of narZ, an open reading frame, ORFA, is present which could encode a product which has homology (73% identity) with the COOH-terminal end of NarK. The ORFA-narZ intergenic region, however, is about 80 nucleotides long and does not contain the cis-acting elements, NarL and Fnr boxes, nor the terC4 terminator sequence present in the 500 nucleotide narK-narG intergenic region. This might explain why the narZYWV and the narGHJI operons are regulated differently. Our results tend to support the hypothesis that a DNA fragment larger than that encompassing the narGHJI genes has been duplicated.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3017988&diff=403083PMID:30179882008-04-30T10:13:31Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blasband, AJ, Marcotte, WR and Schnaitman, CA''' (1986) Structure of the lc and nmpC outer membrane porin protein genes of lambdoid bacteriophage.''J. Biol. Chem.'' '''261''':12723-32</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The lc gene of the lambdoid bacteriophage PA-2 and the nmpC gene located on a defective lambdoid prophage in the 12-min region of the Escherichia coli K12 chromosome have been sequenced. The porin proteins encoded by these two genes were almost identical, with only 4 of the 365 residues of the precursor forms of the proteins being different. The Lc and NmpC proteins were strongly homologous to the OmpC, ompF, and PhoE proteins, with greater than 56% of the residues identical in each case. Sequencing of the region flanking the lc gene allowed precise positioning of this gene with respect to the rightward cos site of the phage and to sequences which are homologous between PA-2 and lambda. In wild-type strains of E. coli K12, the nmpC gene is not expressed and contains an IS5 insertion near the 3' end of the coding region. This insertion deletes 18 residues from the COOH terminus of NmpC protein and adds 8 residues from an open reading frame extending into IS5 sequence. Expression of this form of the gene in an expression vector plasmid demonstrated that this altered protein is still capable of being translocated to the outer membrane. Plasmid expression experiments using lc-nmpC hybrid genes show that it is the presence of the IS5 insertion which prevents expression of the porin in wild-type E. coli K12. In the nmpC mutant which expresses the protein, there has been a precise excision of the IS5 which regenerates a COOH terminus of NmpC protein which is identical to that of the Lc protein. Blot hybridization detected no mRNA transcripts from the wild-type nmpC gene, although transcripts were readily detected from the lc gene in PA-2 lysogens and from the nmpC mutant which has excised the IS5. This indicates that IS5 affects the production or stability of transcripts from the adjacent nmpC gene.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3032909&diff=403051PMID:30329092008-04-30T10:13:12Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blasband, AJ and Schnaitman, CA''' (1987) Regulation in Escherichia coli of the porin protein gene encoded by lambdoid bacteriophages.''J. Bacteriol.'' '''169''':2171-6</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Specialized lambda transducing phages carrying the cloned lc porin gene from the lambdoid bacteriophage PA-2, including various amounts of a sequence 5' to the start of transcription, were used to study the regulation of the porin gene. It was found that a cyclic AMP receptor protein consensus binding site 65 base pairs 5' to the start of transcription was required for catabolite repression of lc but was not sufficient for maximum expression under derepressing conditions. A sequence located more than 209 base pairs 5' to the start of transcription was necessary for maximum expression. By manipulating the copy number of the lc gene and the temperature and by measuring both the rate of synthesis of mRNA and the amount of Lc protein in the outer membrane, it was determined that the expression of lc is regulated primarily at the level of transcription and that expression is not autoregulated. Evidence is also presented that the silent phage porin gene nmpC of Escherichia coli K-12 is transcribed to the same extent as lc even though it does not give rise to a stable pool of mRNA. The structure of the 5' end of lc and nmpC is similar to that of ompF, and a model for transcriptional regulation is presented which may apply to all of these porin genes.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3079718&diff=403034PMID:30797182008-04-30T10:13:02Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanco, C, Ritzenthaler, P and Mata-Gilsinger, M''' (1986) Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression.''Genetics'' '''112''':173-82</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The uidA gene is the first gene involved in the hexuronide-hexuronate pathway in Escherichia coli K-12 and is under the dual control of the uidR and uxuR encoded repressors. Point mutations affecting the uidR regulatory gene were sought to investigate the regulation of uidA. When the uidR mutant allele was on a multicopy plasmid and the wild-type allele was on the chromosome, some of the mutant phenotypes were dominant to the wild-type phenotype, indicating that the active form of the UidR repressor is multimeric. We have demonstrated that expression of the mutant phenotype is dependent on gene dosage. The dominance of the uidR allele was also sensitive to the presence of the wild-type uxuR allele in the cell. This behavior probably results from UidR-UxuR repressor interactions. A mechanism is proposed: we suggest that the UidR and UxuR repressors interact after their binding to the operator site of uidA; the binding of one regulatory molecule may facilitate the binding of the other one in a cooperative process.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3889544&diff=403021PMID:38895442008-04-30T10:12:55Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanco, C, Ritzenthaler, P and Mata-Gilsinger, M''' (1985) Nucleotide sequence of a regulatory region of the uidA gene in Escherichia coli K12.''Mol. Gen. Genet.'' '''199''':101-5</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Multiple regulatory events are involved in the expression of the uidA gene. A regulatory region of this gene has been located on a 460 base pair Sau3A-EcoRI fragment and its nucleotide sequence was determined by the dideoxy method using pEMBL plasmids. A preliminary analysis of this sequence revealed the presence of numerous palindromic structures with some overlaps.</protect><br />
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<span style = 'font-size: large'> '''Blanco, C, Ritzenthaler, P and Kolb, A''' (1986) The regulatory region of the uxuAB operon in Escherichia coli K12.''Mol. Gen. Genet.'' '''202''':112-9</span><br />
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{|{{Prettytable}} align = 'center' width= '70%'<br />
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|{{TableHeadingColor}} |'''Abstract''' || The uxuAB operon is composed of two genes coding for enzymes involved in hexuronate degradation. This operon is negatively controlled by the uxuR and exuR regulatory gene products. Starting from uxu hybrid plasmids, a 300 bp Sau3A restriction fragment was isolated and shown to contain the entire uxu regulatory region using in vitro gene fusions that brought lac gene expression under the control of the transcriptional and translational signals of the uxuA gene. The nucleotide sequence of this fragment was established. The start of the uxu mRNA was localized by S1 mapping experiments (the presence of a CAP binding site upstream of the promoter was shown by DNAse I footprinting and in vitro titration). The N-terminal amino acid sequence of the purified uxuA-lacZ gene product allowed the mapping of the uxuA initiation codon at 115 bp from the start of transcription.<br />
</noinclude><br />
|-<br />
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3083215 PubMed]<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6276362&diff=402993PMID:62763622008-04-30T10:12:35Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanco, C, Ritzenthaler, P and Mata-Gilsinger, M''' (1982) Cloning and endonuclease restriction analysis of uidA and uidR genes in Escherichia coli K-12: determination of transcription direction for the uidA gene.''J. Bacteriol.'' '''149''':587-94</span><br />
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{|{{Prettytable}} align = 'center' width= '70%'<br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The two genes of the Escherichia coli K-12 uid region (the structural gene uidA and the regulatory gene uidR) were isolated on a ColE1-uid hybrid plasmid from the bank of Clarke and Carbon. We made a restriction map of this region and correlated it with the genetic map by subcloning the uid restriction fragments into plasmids pBR322, pBR325, and pACYC177. In these plasmids, amplification of the products of the uidA and uidR genes occurred. The enzyme coded for by uidA was identified by polyacrylamide gel electrophoresis of crude extracts from strains containing the uidA plasmid. A 1-megadalton EcoRI-BamHI segment contained the uidAo operator, and the direction of transcription of the uidA gene was determined. The restriction analysis also suggested that the order of the loci in this region is manA, uidA, uidAo, uidR.</protect><br />
|-<br />
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|}<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3934044&diff=402960PMID:39340442008-04-30T10:12:16Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanco, C, Mata-Gilsinger, M and Ritzenthaler, P''' (1985) The use of gene fusions to study the expression of uidR, a negative regulatory gene of Escherichia coli K-12.''Gene'' '''36''':159-67</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The uidR regulatory gene of Escherichia coli codes for a repressor molecule that negatively controls the expression of the uidA gene. The uidR gene was fused in front of the lacZ gene in vitro on plasmid cloning vectors developed by Casadaban et al. [J. Bacteriol. 143 (1980) 971-980. The transcriptional direction of uidR was deduced from the restriction pattern and the phenotypic properties of the uidR-lacZ fusion plasmids. The gene is transcribed counterclockwise on the standard E. coli map, as is the uidA gene. The uidR-lacZ fusions were also used to examine the regulation of expression from the uidR promoter. It was observed that the uidR gene expression is repressed by its own product and is sensitive to catabolite control. The uidR-lacZ-encoded proteins of various sizes were isolated but attempts to obtain hybrid molecules possessing, in a single polypeptide, both the beta-galactosidase and UidR repressor activities were unsuccessful.</protect><br />
|-<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6296052&diff=402940PMID:62960522008-04-30T10:12:05Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanco, C, Mata-Gilsinger, M and Ritzenthaler, P''' (1983) Construction of hybrid plasmids containing the Escherichia coli uxaB gene: analysis of its regulation and direction of transcription.''J. Bacteriol.'' '''153''':747-55</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The uxaB gene of Escherichia coli, encoding for altronate oxidoreductase involved in the hexuronate degradative pathway, was isolated on a ColE1-uxaB hybrid plasmid from the Clarke and Carbon bank. The restriction map of this plasmid was established. The uxaB gene was mapped on a 1.5-megadalton HindIII-KpnI DNA fragment. Use of an in vitro gene fusion between uxaB and lacZ genes led to the determination that uxaB is transcribed from the KpnI towards the HindIII restriction sites. Gene amplification in cells containing various uxaB hybrid plasmids allowed us to show a gradation in the level of repression of exu operator sites by the exuR regulatory gene product.</protect><br />
|-<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3525742&diff=402924PMID:35257422008-04-30T10:11:55Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blanco, C and Mata-Gilsinger, M''' (1986) A DNA sequence containing the control sites for the uxaB gene of Escherichia coli.''J. Gen. Microbiol.'' '''132''':697-705</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The nucleotide sequence of a 286 bp fragment containing the uxaB control region of Escherichia coli has been determined. The transcriptional start of the uxaB gene has been located and the promoter signals identified. Various fragments of the uxaB promoter-proximal region were fused in vitro with the lacZ gene. Results obtained with these fusions indicate that the operator-promoter sites are located on a 110 bp restriction fragment. The determination of the amino acid sequence of the NH2-terminus of the uxaB gene product revealed that the uxaB gene is not initiated with the AUG codon but with the unusual GTG codon. CRP, the cyclic AMP receptor protein, does not bind to the uxaB control region DNA even though expression of the uxaB gene is sensitive to catabolite repression.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3031429&diff=402904PMID:30314292008-04-30T10:11:45Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanchin-Roland, S, Blanquet, S, Schmitter, JM and Fayat, G''' (1986) The gene for Escherichia coli diadenosine tetraphosphatase is located immediately clockwise to folA and forms an operon with ksgA.''Mol. Gen. Genet.'' '''205''':515-22</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The DNA sequences of the diadenosine tetraphosphatase gene (apaH) and of the flanking regions were determined. Three other genes were identified in the flanking regions: ksgA, apaG and folA encoding, respectively, a 16 S rRNA methyltransferase, an unidentified protein of Mr 13,826 and dihydrofolate reductase, with the order folA-apaH-apaG-ksgA. The apaH gene is thus located between folA and ksgA at 1 min on the Escherichia coli chromosome linkage map and folA is transcribed clockwise, whereas ksgA, apaG and apaH are transcribed in the opposite direction. It was shown that ksgA, apaG and apaH can be expressed from a polycistronic mRNA originating from a promoter (p1) located upstream of ksgA. However, another promoter (p2) was found within the ksgA structural gene. This promoter, active in vivo, can account for p1-independent expression of the two distal cistrons, apaG and apaH. Finally, the effect on diadenosine tetraphosphatase over-production of a frameshift mutation causing premature translational termination of apaG suggests that expression of apaG and apaH is coupled at the translational level.</protect><br />
|-<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:6379647&diff=402884PMID:63796472008-04-30T10:11:34Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blanar, MA, Sandler, SJ, Armengod, ME, Ream, LW and Clark, AJ''' (1984) Molecular analysis of the recF gene of Escherichia coli.''Proc. Natl. Acad. Sci. U.S.A.'' '''81''':4622-6</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>We analyzed the nucleotide sequence of a 1.325-kilobase region of wild-type Escherichia coli containing a functional recF gene and six Tn3 mutations that inactivate recF. The analysis shows a potentially translatable reading frame of 1071 nucleotides, which is interrupted by all six insertions. A protein of 40.5 kilodaltons would result from translation of the open reading frame, and a radioactive band of protein of an apparent molecular weight of approximately 40 kilodaltons was seen by the maxicell method using a recF+ plasmid. Putative truncated peptides were seen when two recF::Tn3 mutant plasmids were used. Differential expression of dnaN and recF from a common promoter was noted. recF332::Tn3 was transferred to the chromosome where, in hemizygous condition, it produced UV sensitivity indistinguishable from that produced by two presumed recF point mutations.</protect><br />
|-<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:1931824&diff=402866PMID:19318242008-04-30T10:11:26Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blakely, G, Colloms, S, May, G, Burke, M and Sherratt, D''' (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division.''New Biol.'' '''3''':789-98</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || XerC is a site-specific recombinase of the bacteriophage lambda integrase family that is encoded by xerC at 3700 kbp on the genetic map of Escherichia coli. The protein was originally identified through its role in converting multimers of plasmid ColE1 to monomers; only monomers are stably inherited. Here we demonstrate that XerC also has a role in the segregation of replicated chromosomes at cell division. xerC mutants form filaments with aberrant nucleotides that appear unable to partition correctly. A DNA segment (dif) from the replication terminus region of the E. coli chromosome binds XerC and acts as a substrate for XerC-mediated site-specific recombination when inserted into multicopy plasmids. This dif segment contains a region of 28 bp with sequence similarity to the crossover region of ColE1 cer. The cell division phenotype of xerC mutants is suppressed in strains deficient in homologous recombination, suggesting that the role of XerC/dif in chromosomal metabolism is to convert any chromosomal multimers (arising through homologous recombination) to monomers.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8402918&diff=402833PMID:84029182008-04-30T10:11:09Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blakely, G, May, G, McCulloch, R, Arciszewska, LK, Burke, M, Lovett, ST and Sherratt, DJ''' (1993) Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12.''Cell'' '''75''':351-61</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The stable inheritance of ColE1-related plasmids and the normal partition of the E. coli chromosome require the function of the Xer site-specific recombination system. We show that in addition to the XerC recombinase, whose function has already been implicated in this system, a second chromosomally encoded recombinase, XerD, is required. The XerC and XerD proteins show 37% identity and bind to separate halves of the recombination site. Both proteins act catalytically in the recombination reaction. Recombination site asymmetry and the requirement of two recombinases ensure that only correctly aligned sites are recombined. We predict that normal partition of most circular chromosomes requires the participation of site-specific recombination to convert any multimers (arising by homologous recombination) to monomers.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8402918 PubMed]<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8598302&diff=402817PMID:85983022008-04-30T10:10:59Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Blakely, G and Sherratt, D''' (1996) Determinants of selectivity in Xer site-specific recombination.''Genes Dev.'' '''10''':762-73</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>A remarkable property of some DNA-binding proteins that can interact with and pair distant DNA segments is that they mediate their biological function only when their binding sites are arranged in a specific configuration. Xer site-specific recombination at natural plasmid recombination sites (e.g., cer in ColE1) is preferentially intramolecular, converting dimers to monomers. In contrast, Xer recombination at the Escherichia coli chromosomal site dif can occur intermolecularly and intramolecularly. Recombination at both types of site requires the cooperative interactions of two related recombinases, XerC and XerD, with a 30-bp recombination core site. The dif core site is sufficient for recombination when XerC and XerD are present, whereas recombination at plasmid sites requires approximately 200 bp of adjacent accessory sequences and accessory proteins. These accessory factors ensure that recombination is intramolecular. Here we use a model system to show that selectivity for intramolecular recombination, and the consequent requirement for accessory factors, can arise by increasing the spacing between XerC- and XerD-binding sites from 6 to 8 bp. This reduces the affinity of the recombinases for the core site and changes the geometry of the recombinase/DNA complex. These changes are correlated with altered interactions of the recombinases with the core site and a reduced efficiency of XerC-mediated cleavage. We propose that the accessory sequences and proteins compensate for these changes and provide a nucleoprotein structure of fixed geometry that can only form and function effectively on circular molecules containing directly repeated sites.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2154333&diff=402782PMID:21543332008-04-30T10:10:42Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blair, DF and Berg, HC''' (1990) The MotA protein of E. coli is a proton-conducting component of the flagellar motor.''Cell'' '''60''':439-49</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || A number of mutants of motA, a gene necessary for flagellar rotation in E. coli, were isolated and characterized. Many mutations were dominant, owing to competition between functional and nonfunctional MotA for a limited number of sites on the flagellar motor. A new class of mutant was discovered in which flagellar torque is normal at low speeds but reduced at high speeds. Hydrogen isotope effects on these mutants indicate that MotA catalyzes proton transfer. We confirmed an earlier observation that overproduction of MotA leads to accumulation of the protein in the cytoplasmic membrane and to significant decreases in growth rate. When nonfunctional mutant variants of MotA were overproduced instead, they accumulated in the cytoplasmic membrane, but growth was not impaired. These results also suggest that MotA conducts protons. This was confirmed by measuring the proton permeabilities of vesicles containing wild-type or mutant MotA proteins.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2061285&diff=402718PMID:20612852008-04-30T10:10:12Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Blair, DF, Kim, DY and Berg, HC''' (1991) Mutant MotB proteins in Escherichia coli.''J. Bacteriol.'' '''173''':4049-55</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The MotB protein of Escherichia coli is an essential component in each of eight torque generators in the flagellar rotary motor. Based on its membrane topology, it has been suggested that MotB might be a linker that fastens the torque-generating machinery to the cell wall. Here, we report the isolation and characterization of a number of motB mutants. As found previously for motA, many alleles of motB were dominant, as expected if MotB is a component of the motor. In other respects, however, the motB mutants differed from the motA mutants. Most of the mutations mapped to a hydrophilic, periplasmic domain of the protein, and nothing comparable to the slow-swimming alleles of motA, which show normal torque when tethered, was found. Some motB mutants retained partial function, but when tethered they produced subnormal torque, indicating that their motors contained only one or two functional torque generators. These results support the hypothesis that MotB is a linker.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2061285 PubMed]<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3881440&diff=402702PMID:38814402008-04-30T10:10:02Z<p>Pei: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Black, PN, Kianian, SF, DiRusso, CC and Nunn, WD''' (1985) Long-chain fatty acid transport in Escherichia coli. Cloning, mapping, and expression of the fadL gene.''J. Biol. Chem.'' '''260''':1780-9</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Transport of long-chain fatty acids across the inner membrane of Escherichia coli K-12 requires a functional fadL gene (Maloy, S. R., Ginsburgh, C. L., Simons, R. W., and Nunn, W. D. (1981) J. Biol. Chem. 256, 3735-3742). Mutants defective in the fadL gene lack a 33,000-dalton inner membrane protein as evaluated using two-dimensional pI/sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (Ginsburgh, C. L., Black, P. N., and Nunn, W. D. (1984) J. Biol. Chem. 259, 8437-8443). In an effort to determine whether the fadL gene is the structural gene for this 33,000-dalton protein, we have cloned, mapped, and analyzed the expression of the fadL gene. The fadL gene has been localized on a 2.8-kilobase EcoRV fragment of E. coli genomic DNA. Plasmids containing this gene (i) complement all fadL mutants, (ii) increase the long-chain fatty acid transport activity of fadL strains harboring them by 2- to 3-fold, and (iii) direct the synthesis of a membrane protein which has the same molecular weight and isoelectric point as that described by Ginsburgh et al. This is a heat-modifiable protein which has an apparent molecular weight of 43,000 daltons when solubilized at 100 degrees C in the presence of SDS and 33,000 daltons when solubilized at 50 degrees C in the presence of SDS.</protect><br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:1460045&diff=402662PMID:14600452008-04-30T10:09:43Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Black, PN, DiRusso, CC, Metzger, AK and Heimert, TL''' (1992) Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase.''J. Biol. Chem.'' '''267''':25513-20</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || In the enteric bacterium, Escherichia coli, acyl coenzyme A synthetase (fatty acid:CoA ligase (AMP-forming) EC 6.2.1.3) activates exogenous long-chain fatty acids concomitant with their transport across the inner membrane into metabolically active CoA thioesters. These compounds serve as substrates for acyl-CoA dehydrogenase in the first step in the process of beta-oxidation. The acyl-CoA synthetase structural gene, fadD, has been identified on clone 6D1 of the Kohara E. coli gene library and by a process of subcloning and complementation analyses shown to be contained on a 2.2-kilobase NcoI-ClaI fragment of genomic DNA. The polypeptide encoded within this DNA fragment was identified following T7 RNA polymerase-dependent induction and estimated to be M(r) = 62,000 using SDS-polyacrylamide gel electrophoresis. The N-terminal amino acid sequence of acyl-CoA synthetase was determined by automated sequencing to be Met-Lys-Lys-Val-Trp-Leu-Asn-Arg-Tyr-Pro. Sequence analysis of the 2.2-kilobase NcoI-ClaI fragment revealed a single open reading frame encoding these amino acids as the first 10 residues of a protein with a molecular weight of 62,028. The initiation codon for methionine was TTG. Primer extension of total in vivo mRNA from two fadD-specific oligonucleotides defined the transcriptional start at an adenine residue 60 base pairs upstream from the predicted translational start site. Two FadR operator sites of the fadD gene were identified at positions -13 to -29 (OD1) and positions -99 to -115 (OD2) by DNase I footprinting. Comparisons of the predicted amino acid sequence of the E. coli acyl-CoA synthetase to the deduced amino acid sequences of the rat and yeast acyl-CoA synthetases and the firefly luciferase demonstrated that these enzymes shared a significant degree of similarity. Based on the similar reaction mechanisms of these four enzymes, this similarity may define a region required for the same function.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:3286621&diff=402655PMID:32866212008-04-30T10:09:38Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Black, PN''' (1988) The fadL gene product of Escherichia coli is an outer membrane protein required for uptake of long-chain fatty acids and involved in sensitivity to bacteriophage T2.''J. Bacteriol.'' '''170''':2850-4</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The fadL+ gene of Escherichia coli encodes an outer membrane protein (FadL) essential for the uptake of long-chain fatty acids (C12 to C18). The present study shows that in addition to being required for uptake of and growth on the long-chain fatty acid oleate (C18:1), FadL acts as a receptor of bacteriophage T2. Bacteriophage T2-resistant (T2r) strains lacked FadL and were unable to take up and grow on long-chain fatty acids. Upon transformation with the fadL+ clone pN103, T2r strains became sensitive to bacteriophage T2 (T2s), became able to take up long-chain fatty acids at wild-type levels, and contained FadL in the outer membrane.<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:2041474&diff=402594PMID:20414742008-04-30T10:09:09Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Black, ME and Hruby, DE''' (1991) Nucleotide sequence of the Escherichia coli thymidine kinase gene provides evidence for conservation of functional domains and quaternary structure.''Mol. Microbiol.'' '''5''':373-9</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || Using lambda bacteriophage clones from the Kohara Escherichia coli library spanning minutes 25.5 to 28.5 on the E. coli chromosome (strain W3110), two overlapping DNA fragments were identified which were able to confer thymidine kinase (TK) enzyme activity to a TK- strain of E. coli (KY895). This genetic complementation assay was used in concert with subcloning procedures to identify the minimal region (a 900 bp EcoRI-SalI fragment) which contained the E. coli thymidine kinase gene (tdk). The nucleotide sequence of the EcoRI-SalI fragment and a small portion of the adjoining downstream fragment was determined. Computer analysis of the derived sequence indicated the presence of a rightward-reading open reading frame of 615 bp which was capable of encoding a 205-amino-acid polypeptide with a predicted Mr of 23458 daltons. The in vivo transcriptional activity of this locus was confirmed by Northern blot hybridization analysis of RNA isolated from E. coli JM101 or KY895 which detected a 650-nucleotide RNA transcribed from this region. This places the tdk gene at approximately minute 27.35 on the E. coli W3110 chromosome, about 15 kb downstream from the narG locus and approximately 25 kb upstream of the trp operon. Although the predicted Mr of the E. coli TK protein was 23.5 kDa, gel-filtration analyses suggested that, like eukaryotic thymidine kinases, the active form of this enzyme is a multimeric complex.(ABSTRACT TRUNCATED AT 250 WORDS)<br />
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<references/></div>Peihttps://ecoliwiki.org/colipedia/index.php?title=PMID:8021189&diff=402589PMID:80211892008-04-30T10:09:06Z<p>Pei: </p>
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<span style = 'font-size: large'> '''Black, DS, Irwin, B and Moyed, HS''' (1994) Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis.''J. Bacteriol.'' '''176''':4081-91</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The hip locus of Escherichia coli affects the frequency of persistence to the lethal consequences of selective inhibition of either DNA or peptidoglycan synthesis. Regulation of the hip operon, which consists of a regulatory region and two genes, hipB and hipA, was examined with strains containing a hip-lac transcriptional fusion placed in single copy at the lambda att site. Disruption of the hip locus increased activity from the fusion 16-fold. Repression was restored by supplying HipB in trans. HipB was overexpressed and purified. On the basis of gel filtration and cross-linking studies, HipB is a dimer in solution. Sequence analysis revealed that HipB is a Cro-like DNA-binding protein. The interaction of HipB with the hip regulatory region was examined by gel retardation, DNase I protection, and methylation protection studies. HipB binds with a Kapp (K apparent) of 40 pM to four operator sites with the conserved sequence TATCCN8GGATA (N represents any nucleotide). Binding to the operators is nearly simultaneous and appears to be cooperative. Analysis of the role of HipA in the regulation of the hip operon is complicated by the toxicity of HipA in the absence of HipB. Strains disrupted in hipB but not in hipA could not be recovered. Moreover, hipA-containing plasmids cannot be replicated in strains defective in or lacking hipB. HipA is found exclusively in a tight complex with HipB. Although disruption of hipA slightly increased expression from the hip-lac fusion, in vitro studies suggest that HipA does not bind to the hip regulatory region directly but indirectly via HipB.<br />
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<span style = 'font-size: large'> '''Black, DS, Kelly, AJ, Mardis, MJ and Moyed, HS''' (1991) Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis.''J. Bacteriol.'' '''173''':5732-9</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>High-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis, the Hip phenotype, results from mutations at the hip locus of Escherichia coli K-12. The nucleotide sequence of DNA fragments which complement these mutations revealed an operon consisting of a possible regulatory region, including sequences with modest homology to an E. coli promoter, and two open reading frames which are translated both in vitro and in vivo. The stop codon of a 264-bp open reading frame, hipB, and the start codon of a 1,320-bp open reading frame, hipA, share an adenine residue. Assays of promoter strength, the location of the probable promoter with respect to the start of transcription, and codon usage all indicate that hipB and hipA are weakly expressed genes. The activity of the promoter is impaired by an adjacent downstream sequence which includes the coding region of hipB. The impairment is partially relieved by insertion of a premature translation termination signal within the coding region of hipB, suggesting involvement of the HipB protein in the regulation of this promoter. The arrangement of hipB and hipA within the operon and the toxicity of hipA for strains defective in or lacking hipB suggest an important interaction between the products of these genes.</protect><br />
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<span style = 'font-size: large'> '''Björk, GR and Kjellin-Stråby, K''' (1978) Escherichia coli mutants with defects in the biosynthesis of 5-methylaminomethyl-2-thio-uridine or 1-methylguanosine in their tRNA.''J. Bacteriol.'' '''133''':508-17</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>Two tRNA methyltransferase mutants, isolated as described in the accompanying paper (G.R. Björk and K. Kjellin-Stråby, J. Bacteriol. 133:499-207, 1978), are biochemicaaly and genetically characterized. tRNA from mutant IB13 lacks 5-methylaminomethyl-2-thio-uridine in vivo due to a permanently nonfunctional methyltransferase. Thus tRNA from this mutant is a specific substrate for the corresponding tRNA methyltransferase in vitro. In spite of this defect in tRNA, such a mutant is viable. Mutant IB11 is conditionally defective in the biosynthesis of 1-methylguanosine in tRNA due to a temperature-sensitive tRNA (1-methyl-guanosine) methyltransferase. In mutant cells grown at a high temperature, the level of 1-methylguanosine in bulk tRNA is 20% of that of the wild type, demonstrating that in this mutant an 80% deficiency of 1-methylguanosine in tRNA is not lethal. Genetically these two distinct lesions, trmC2, causing 5=methylaminomethyl-2-thio-uridine deficiency, and trmD1, giving a temperature-sensitive tRNA (1-methylguanosine)methyltransferase, are both located between 50 and 61 min on the Escherichia coli chromosome.</protect><br />
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<span style = 'font-size: large'> '''Bjelland, S and Seeberg, E''' (1996) Different efficiencies of the Tag and AlkA DNA glycosylases from Escherichia coli in the removal of 3-methyladenine from single-stranded DNA.''FEBS Lett.'' '''397''':127-9</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli possesses two different DNA repair glycosylases, Tag and AlkA, which have similar ability to remove the alkylation product 3-methyladenine from double-stranded DNA. In this study we show that these enzymes have quite different activities for the excision of 3-methyladenine from single-stranded DNA, AlkA being 10-20 times more efficient than Tag. We propose that AlkA and perhaps other glycosylases as well may have an important role in the excision of base damage from single-stranded regions transiently formed in DNA during transcription and replication.<br />
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<span style = 'font-size: large'> '''Biville, F, Turlin, E and Gasser, F''' (1991) Mutants of Escherichia coli producing pyrroloquinoline quinone.''J. Gen. Microbiol.'' '''137''':1775-82</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || In glucose minimal medium a PTS- strain of Escherichia coli [delta (ptsH ptsI crr)] could grow slowly (doubling time, d = 10 h). When the population reached 5 x 10(6) to 2 x 10(7) cells ml-1, mutants growing rapidly (d = 1.5 h) appeared and rapidly outgrew the initial population. These mutants (EF mutants) do not use a constitutive galactose permease for glucose translocation. They synthesize sufficient pyrroloquinoline quinone (PQQ) to yield a specific activity of glucose dehydrogenase (GDH) equivalent to that found in the parent strain grown in glucose minimal medium supplemented with 1 nM-PQQ. Membrane preparations containing an active GDH oxidized glucose to gluconic acid, which was also present in the culture supernatant of EF strains in glucose minimal medium. Glucose utilization is the only phenotypic trait distinguishing EF mutants from the parent strain. Glucose utilization by EF mutants was strictly aerobic as expected from a PQQ-dependent catabolism. The regulation of PQQ production by E. coli is discussed.<br />
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<span style = 'font-size: large'> '''Bitner, RM and Kuempel, PL''' (1982) P1 transduction mapping of the trg locus in rac+ and rac strains of Escherichia coli K-12.''J. Bacteriol.'' '''149''':529-33</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The trg locus, which had been located at min 31 in the cotransduction gap in the terminus region of the chromosome of Escherichia coli, has been mapped by transduction with bacteriophage P1. This locus exhibited no cotransduction with fnr when rac+ strains were used. If rac strains were used, which removed approximately 27 kilobase pairs of DNA, trg and fnr exhibited 8.2% cotransduction. Although this mapping of trg at min 31.1 considerably reduces the size of the cotransduction gap, trg exhibited no cotransduction with a Tn10 insertion located on the other side of the gap at min 34.2.</protect><br />
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<span style = 'font-size: large'> '''Bishop, RE, Penfold, SS, Frost, LS, Höltje, JV and Weiner, JH''' (1995) Stationary phase expression of a novel Escherichia coli outer membrane lipoprotein and its relationship with mammalian apolipoprotein D. Implications for the origin of lipocalins.''J. Biol. Chem.'' '''270''':23097-103</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || We report a novel outer membrane lipoprotein of Escherichia coli. DNA sequencing between ampC and sugE at the 94.5 min region of the E. coli chromosome revealed an open reading frame specifying 177 amino acid residues. Primer extension analysis demonstrated that the promoter is activated at the transition between exponential and stationary growth phases under control of the rpoS sigma factor gene, and this was confirmed in vivo by monitoring expression of beta-galactosidase activity from a lacZ translational fusion. The amino acid sequence exhibited 31% identity with human apolipoprotein D (apoD), which is a component of plasma high density lipoprotein and belongs to the eukaryotic family of lipocalins. The bacterial lipocalin (Blc) contained a short deletion of 7 amino acid residues corresponding to a hydrophobic surface loop that is thought to facilitate the physical interaction between apoD and high density lipoprotein. However, Blc exhibited a typical prokaryotic lipoprotein signal peptide at its amino terminus. Overexpression, membrane fractionation, and metabolic labeling with [3H]palmitate demonstrated that Blc is indeed a globomycin-sensitive outer membrane lipoprotein. Blc represents the first bacterial member of the family of lipocalins and may serve a starvation response function in E. coli.<br />
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<span style = 'font-size: large'> '''Bitner, RM and Kuempel, PL''' (1981) P1 transduction map spanning the replication terminus of Escherichia coli K12.''Mol. Gen. Genet.'' '''184''':208-12</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The region of the E. coli chromosome that contains the replication terminus has not previously been spanned by P1 cotransduction. We have used Tn5, Tn9 and Tn10 transposons inserted in this region as genetic markers, and have constructed a genetic map that extends from fnr (min 29.3) to manA (min 35.7). The relevant transposons that have been mapped in this region and which are described in this report are trg-1::Tn5 (min 31.1), zdc-235::Tn10 (min 32.3), zdd-230::Tn9 (min 33.3), and zde-234::Tn10 (min 34.2). The size of this region as determined by P1 cotransduction is very similar to previous estimates obtained by bacterial conjugation.</protect><br />
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<span style = 'font-size: large'> '''Birkmann, A, Zinoni, F, Sawers, G and Böck, A''' (1987) Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli.''Arch. Microbiol.'' '''148''':44-51</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || <protect>The regulatory elements involved in expression of the gene (fdhF) for the selenopolypeptide of formate dehydrogenase and of a gene (or transcriptional unit) (hyd) specifically responsible for the formation of the gas-evolving hydrogenase (hydrogenase 3) in Escherichia coli were investigated. Formate (or a product of it) is required for expression of both systems since in a pyruvate-formate-lyase deficient mutant induction occurs only when formate is supplemented externally. Under this condition, formate can partially overcome repression by nitrate. The transcription of both the fdhF gene and the hydrogenase-3-encoding systems is independent of the presence of a wild-type fnr gene when formate is present, supporting the view that the Fnr effect on the formation of the formate-hydrogen-lyase pathway is indirect. Mutations blocking the synthesis of a functional molybdenum cofactor also had no major affect on fdhF and hyd expression. The nucleotide sequence of the 5' flanking region of the fdhF gene was determined and the transcription start point of the fdhF gene was localized by nuclease S1 mapping. Nuclease Bal31 generated deletion clones were constructed and the regulation of their expression was studied. Anaerobic expression and induction by formate depended on the presence of a stretch of approximately 185 nucleotides upstream of the translation start. Elements mediating formate induction and oxygen or nitrate repression could not be separated physically. The regulatory features of the fdhF upstream region bear striking resemblance to systems whose expression are dependent upon upstream activating elements.</protect><br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2443100 PubMed]<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br />
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==See also==<br />
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==References==<br />
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<references/></div>Pei