EcoliWiki - User contributions [en]

PMID:785220

2008-02-12T23:33:52Z

66.249.72.105: New PMID: Page!

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 '''Borck, K, Beggs, JD, Brammar, WJ, Hopkins, AS and Murray, NE''' (1976) The construction in vitro of transducing derivatives of phage lambda.''Mol. Gen. Genet.'' '''146''':199-207

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|{{TableHeadingColor}} |'''Abstract''' || Methods are described for the construction of plaque-forming, transducing derivatives of phage lambda, using appropirate receptor genomes and fragments of DNA generated by the restriction enzymes endo R.EcoRI and endo R.HindIII. The general properties of the transducing derivatives are described and discussed. Plaque-forming phages carrying the E. coli trp, his, cysB, thyA, supD, supE, sup F, hsd, tna and lig genes have been isolated.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=785220 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:16139196

2008-02-05T15:18:36Z

66.249.72.105: New PMID: Page!

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 '''Ellis, RJ''' (2005) Chaperomics: in vivo GroEL function defined.''Curr. Biol.'' '''15''':R661-3

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|{{TableHeadingColor}} |'''Abstract''' || A recent proteome analysis of protein folding inside cells of Escherichia coli predicts that only 84 of the approximately 2400 cytosolic proteins expressed in minimal media depend absolutely on the GroEL/GroES chaperone system to avoid aggregation. These proteins are enriched in alpha/beta domains and 13 are essential for growth.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16139196 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:6251457

2008-02-05T07:45:44Z

66.249.72.105: New PMID: Page!

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 '''Ogden, S, Haggerty, D, Stoner, CM, Kolodrubetz, D and Schleif, R''' (1980) The Escherichia coli L-arabinose operon: binding sites of the regulatory proteins and a mechanism of positive and negative regulation.''Proc. Natl. Acad. Sci. U.S.A.'' '''77''':3346-50

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|{{TableHeadingColor}} |'''Abstract''' || The locations of DNA binding by the proteins involved with positive and negative regulation of transcription initiation of the L-arabinose operon in Escherichia coli have been determined by the DNase I protection method. Two cyclic AMP receptor protein sites were found, at positions -78 to -107 and -121 to -146, an araC protein--arabinose binding site was found at position -40 to -78, and an araC protein-fucose binding site was found at position -106 to -144. These locations, combined with in vivo data on induction of the two divergently oriented arabinose promoters, suggest the following regulatory mechanism: induction of the araBAD operon occurs when cyclic AMP receptor protein, araC protein, and RNA polymerase are all present and able to bind to DNA. Negative regulation is accomplished by the repressing form of araC protein binding to a site in the regulatory region such that it stimultaneously blocks access of cyclic AMP receptor protein to two sites on the DNA, one site of which serves each of the two promoters. Thus, from a single operator site, the negative regulator represses the two outwardly oriented ara promoters. This regulatory mechanism explains the known positive and negative regulatory properties of the ara promoters.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6251457 PubMed]
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PMID:6457723

2008-02-05T07:34:38Z

66.249.72.105: New PMID: Page!

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 '''Sternberg, N, Hamilton, D, Austin, S, Yarmolinsky, M and Hoess, R''' (1981) Site-specific recombination and its role in the life cycle of bacteriophage P1.''Cold Spring Harb. Symp. Quant. Biol.'' '''45 Pt 1''':297-309

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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6457723 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11724532

2008-02-05T01:05:38Z

66.249.72.105: New PMID: Page!

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 '''Chen, S, Vojtechovsky, J, Parkinson, GN, Ebright, RH and Berman, HM''' (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.''J. Mol. Biol.'' '''314''':63-74

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|{{TableHeadingColor}} |'''Abstract''' || The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11724532 PubMed]
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PMID:794488

2008-01-31T16:03:00Z

66.249.72.105: New PMID: Page!

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 '''Hopkins, AS, Murray, NE and Brammar, WJ''' (1976) Characterization of lambdatrp-transducing bacteriophages made in vitro.''J. Mol. Biol.'' '''107''':549-69

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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:7608087

2008-01-31T16:01:16Z

66.249.72.105: New PMID: Page!

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 '''Guzman, LM, Belin, D, Carson, MJ and Beckwith, J''' (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter.''J. Bacteriol.'' '''177''':4121-30

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|{{TableHeadingColor}} |'''Abstract''' || We have constructed a series of plasmid vectors (pBAD vectors) containing the PBAD promoter of the araBAD (arabinose) operon and the gene encoding the positive and negative regulator of this promoter, araC. Using the phoA gene and phoA fusions to monitor expression in these vectors, we show that the ratio of induction/repression can be 1,200-fold, compared with 50-fold for PTAC-based vectors. phoA expression can be modulated over a wide range of inducer (arabinose) concentrations and reduced to extremely low levels by the presence of glucose, which represses expression. Also, the kinetics of induction and repression are very rapid and significantly affected by the ara allele in the host strain. Thus, the use of this system which can be efficiently and rapidly turned on and off allows the study of important aspects of bacterial physiology in a very simple manner and without changes of temperature. We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7608087 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:9202458

2008-01-31T04:25:55Z

66.249.72.105: New PMID: Page!

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 '''Gruer, MJ, Bradbury, AJ and Guest, JR''' (1997) Construction and properties of aconitase mutants of Escherichia coli.''Microbiology (Reading, Engl.)'' '''143 ( Pt 6)''':1837-46

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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli contains two genes (acnA and acnB) encoding aconitase activities. An acnB mutant was engineered by replacing the chromosomal acnB gene by an internally deleted derivative containing a tetR cassette. An acnB double mutant was then made by transducing a previously constructed acnA::kanR mutation into the acnB::tetR strain. Western blotting confirmed that the AcnA and AcnB proteins were no longer produced by the corresponding mutants and PCR analysis showed that the chromosomal acnB gene had been replaced by the disrupted gene. Aerobic and anaerobic growth in glucose minimal medium were impaired but not abolished by the acnB mutation, indicating that the lesion is partially complemented by the acnA+ gene, and growth was enhanced by glutamate. The acnAB double mutant would not grow on unsupplemented glucose minimal medium and although it responded to glutamate like a typical auxotroph under anaerobic conditions, under aerobic conditions no response to glutamate was observed before it was over-grown by 'revertants' lacking citrate synthase (acnAB gltA). The acnAB double mutant retained a low but significant aconitase activity (< or = 5% of wild-type), designated AcnC. Enzymological and regulatory studies with acn-lacZ fusions indicated that AcnB is the major aconitase, which is synthesized earlier in the growth cycle than AcnA, and subject to catabolite and anaerobic repression.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9202458 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:6102982

2008-01-31T03:47:30Z

66.249.72.105: New PMID: Page!

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 '''Humbert, R and Simoni, RD''' (1980) Genetic and biomedical studies demonstrating a second gene coding for asparagine synthetase in Escherichia coli.''J. Bacteriol.'' '''142''':212-20

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|{{TableHeadingColor}} |'''Abstract''' || Genetic experiments have indicated that asparagine auxotrophs of Escherichias coli K-12 can be made asparagine prototrophs at either of two sites on the chromosome and that wild-type strains require both sites to be mutated to produce asparagine auxotrophy. The former asn locus is now called asnA, and the new gene is designated asnB. The asnB gene is located near gal.AsnA+ asnB and asnA asnB+ strains were constructed, and the asparagine synthetic reaction was characterized in extracts. These studies revealed that the asnA gene codes for the enzyme previously described (H. Cedar and J.H. Schwartz, J. Biol. Chem. 244: 4112-4121, 1969), whereas the asnB gene is involved in the production of an enzyme which differs from the one previously described in its specific activity in extracts, its stability at low and high temperatures, and its apparent ability to use either glutamine or ammonia as amide nitrogen donor. Physiological studies showed that either enzyme alone is sufficient to allow a maximal growth rate under conditions of asparagine limitation.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6102982 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11722181

2008-01-29T15:30:09Z

66.249.72.105: New PMID: Page!

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 '''Keefe, AD, Wilson, DS, Seelig, B and Szostak, JW''' (2001) One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag.''Protein Expr. Purif.'' '''23''':440-6

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|{{TableHeadingColor}} |'''Abstract''' || We describe the use of the SBP-tag, a new streptavidin-binding peptide, for both the one-step purification and the detection of recombinant proteins. The SBP-tag sequence is 38 amino acids long and binds to streptavidin with an equilibrium dissociation constant of 2.5 nM. We demonstrate that a single-step purification of SBP-tagged proteins from bacterial extract yields samples that are more pure than those purified using maltose-binding protein or the His-tag. The capacity of the immobilized streptavidin used to purify SBP-tagged proteins is about 0.5 mg per milliliter of matrix, which is high enough to isolate large quantities of proteins for further study. Also, the elution conditions from the streptavidin column are very mild and specific, consisting of the wash buffer plus biotin. This combination of high-affinity, high-yield, mild elution conditions, and simplicity of use makes the SBP-tag suitable for high-throughput protein expression/purification procedures, including robotically manipulated protocols with microtiter plates. Additionally, the SBP-tag can be used for detection since a wide variety of streptavidin-conjugated fluorescent and enzymatic systems are commercially available. We also present a new, rapid, method for the measurement of protein-protein, protein-peptide, or protein-small molecule equilibrium dissociation constants that require as little as 1 fmol of labeled protein. We call this method the spin-filter binding inhibition assay.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11722181 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:15249042

2008-01-29T15:29:30Z

66.249.72.105: New PMID: Page!

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 '''Zhang, YB, Howitt, J, McCorkle, S, Lawrence, P, Springer, K and Freimuth, P''' (2004) Protein aggregation during overexpression limited by peptide extensions with large net negative charge.''Protein Expr. Purif.'' '''36''':207-16

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|{{TableHeadingColor}} |'''Abstract''' || Folding of the human coxsackie and adenovirus receptor immunoglobulin (Ig) variable-type domain (CAR D1) during overexpression in the Escherichia coli cytoplasm was shown previously to be partially rescued by fusion to a 22-residue C-terminal peptide. Here, peptide sequence features required for solubilization and folding of CAR D1 and similar Ig variable-type domains from two other human membrane proteins were investigated. Peptide extensions with net negative charge > -6 fully solubilized CAR D1, and approximately half of the peptide-solubilized protein was correctly folded. The Ig variable-type domains from human A33 antigen and myelin P-zero proteins were only partially solubilized by peptide extensions with net charge of -12, however, and only the solubilized P-zero domain appeared to fold correctly whereas the A33 domain formed soluble microaggregates of misfolded protein. Our results suggest a model where the large net charge of peptide extensions increases electrostatic repulsion between nascent polypeptides. The resulting decrease in aggregation rate can enable some polypeptides to fold spontaneously into their native protein conformations. Analysis of the solubility and folding status of sets of structurally homologous proteins, such as the Ig variable-type domains described here, during overexpression could provide insights into how amino acid and gene sequences influence the efficiency of spontaneous protein folding.
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:6330035

2008-01-29T15:27:25Z

66.249.72.105: New PMID: Page!

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 '''Phillips, TA, VanBogelen, RA and Neidhardt, FC''' (1984) lon gene product of Escherichia coli is a heat-shock protein.''J. Bacteriol.'' '''159''':283-7

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|{{TableHeadingColor}} |'''Abstract''' || The product of the pleiotropic gene lon is a protein with protease activity and has been tentatively identified as protein H94.0 on the reference two-dimensional gel of Escherichia coli proteins. Purified Lon protease migrated with the prominent cellular protein H94.0 in E. coli K-12 strains. Peptide map patterns of Lon protease and H94.0 were identical. A mutant form of the protease had altered mobility during gel electrophoresis. An E. coli B/r strain that is known to be defective in Lon function contained no detectable H94.0 protein under normal growth conditions. Upon a shift to 42 degrees C, however, the Lon protease was induced to high levels in K-12 strains and a small amount of protein became detectable at the H94.0 location in strain B/r. Heat induction of Lon protease was dependent on the normal allele of the regulatory gene, htpR, establishing lon as a member of the high-temperature-production regulon of E. coli.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6330035 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:3915782

2008-01-20T22:23:46Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''Evan, GI, Lewis, GK, Ramsay, G and Bishop, JM''' (1985) Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product.''Mol. Cell. Biol.'' '''5''':3610-6

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Six monoclonal antibodies have been isolated from mice immunized with synthetic peptide immunogens whose sequences are derived from that of the human c-myc gene product. Five of these antibodies precipitate p62c-myc from human cells, and three of these five also recognize the mouse c-myc gene product. None of the antibodies sees the chicken p110gag-myc protein. All six antibodies recognize immunoblotted p62c-myc. These reagents also provide the basis for an immunoblotting assay by which to quantitate p62c-myc in cells.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3915782 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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<protect>

{|class = 'sortable' {{Prettytable}} id='221972'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.W4793c9f220523&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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==References==
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<references/>

PMID:2896195

2008-01-20T22:23:22Z

66.249.72.105: New PMID: Page!

<protect>
{{RightTOC}}

 '''Samols, D, Thornton, CG, Murtif, VL, Kumar, GK, Haase, FC and Wood, HG''' (1988) Evolutionary conservation among biotin enzymes.''J. Biol. Chem.'' '''263''':6461-4

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2896195 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='221971'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.H4793c9d9d1f06&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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<references/>

PMID:2661528

2008-01-20T22:03:43Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''Russell, CB, Stewart, RC and Dahlquist, FW''' (1989) Control of transducer methylation levels in Escherichia coli: investigation of components essential for modulation of methylation and demethylation reactions.''J. Bacteriol.'' '''171''':3609-18

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || During bacterial chemotaxis in Escherichia coli, adaptation is accomplished by reversible methylation of the transmembrane signal transducers. Methyl groups are added by the CheR protein in a slow response to attractants and removed by the CheB protein in response to repellents. The methylesterase activity of the CheB protein is modulated by a factor that is controlled in a global fashion throughout the cell. By controlling the level of expression of the cheR, cheB, and transducer genes with exogenous promoters on multicopy plasmids, we demonstrate that the modulating factor exists in stoichiometric concentrations relative to CheB protein and that the generation or efficacy of this factor requires the cheA and/or cheW gene products, suggesting that phosphorylation of the methylesterase by CheA may be involved in its global activation. We show that in the absence of any modulation of the CheB activity, the CheR methyltransferase activity is modulated in a local fashion at the transducers, most likely as a result of a conformational change in the transducer protein brought about by the binding of ligand, and does not require CheA or CheW.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2661528 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='221970'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.S4793c53ee4829&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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<references/>

PMID:4563344

2008-01-18T19:51:28Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''Pauli, G and Overath, P''' (1972) ato Operon: a highly inducible system for acetoacetate and butyrate degradation in Escherichia coli.''Eur. J. Biochem.'' '''29''':553-62

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4563344 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='221969'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M4791034046a97&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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==References==
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<references/>

PMID:3025185

2008-01-18T19:51:21Z

66.249.72.105: New PMID: Page!

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 '''Jenkins, LS and Nunn, WD''' (1987) Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system.''J. Bacteriol.'' '''169''':42-52

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The structural organization and regulation of the genes involved in short-chain fatty acid degradation in Escherichia coli, referred to as the ato system, have been studied by a combination of classic genetic and recombinant DNA techniques. A plasmid containing a 6.2-kilobase region of the E. coli chromosome was able to complement mutations in the ato structural genes, atoA (acetyl-coenzyme A [CoA]:acetoacetyl [AA]-CoA transferase) and atoB (thiolase II), as well as mutations in the ato regulatory locus, atoC. Complementation studies performed with mutants defective in acetyl-CoA:AA-CoA transferase suggest that two loci, atoD and atoA, are required for the expression of functional AA-CoA transferase. The ato gene products were identified by in vitro transcription and translation and maxicell analysis as proteins of 48, 26.5, 26, and 42 kilodaltons for atoC, atoD, atoA, and atoB, respectively. In vitro and insertional mutagenesis of the ato hybrid plasmid indicated that the ato structural genes were arranged as an operon, with the order of transcription atoD-atoA-atoB. Although transcribed in the same direction as the atoDAB operon, the atoC gene appeared to use a promoter which was distinct from that used by the atoDAB operon. A delta atoC plasmid expressed the atoD, atoA, and atoB gene products only in strains containing a functional atoC gene. Although the exact mechanism of control was not evident from these studies, the data suggest that the atoC gene product is an activator which is required for the synthesis or activation of the atoDAB-encoded enzymes.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3025185 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='221968'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.C47910339669bb&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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PMID:8021189

2008-01-18T10:35:15Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''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

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{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.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8021189 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='221967'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M479080e35b462&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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<references/>

PMID:6291030

2008-01-18T06:13:21Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''Boeke, JD and Model, P''' (1982) A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.''Proc. Natl. Acad. Sci. U.S.A.'' '''79''':5200-4

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Gene III protein of bacteriophage f1 is inserted into the host cell membrane where it is assembled into phage particles. A truncated form of gene III protein, encoded by a recombinant plasmid and lacking the carboxyl terminus, does not remain in the membrane but instead appears to slip through it. Fusion of a hydrophobic "membrane anchor" from another membrane protein, the gene VIII protein, to the truncated gene III protein (by manipulation of the recombinant plasmid) restores membrane anchoring. A model for the relationship of gene III protein with the Escherichia coli membrane is discussed.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6291030 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='221966'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.F479043809ed01&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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<references/>

PMID:2551889

2008-01-18T05:31:55Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''San Millan, JL, Boyd, D, Dalbey, R, Wickner, W and Beckwith, J''' (1989) Use of phoA fusions to study the topology of the Escherichia coli inner membrane protein leader peptidase.''J. Bacteriol.'' '''171''':5536-41

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || A topology of the Escherichia coli leader peptidase has been previously proposed on the basis of proteolytic studies. Here, a collection of alkaline phosphatase fusions to leader peptidase is described. Fusions to the periplasmic domain of this protein exhibit high alkaline phosphatase activity, while fusions to the cytoplasmic domain exhibit low activity. Elements within the cytoplasmic domain are necessary to stably anchor alkaline phosphatase in the cytoplasm. The amino-terminal hydrophobic segment of leader peptidase acts as a weak export signal for alkaline phosphatase. However, when this segment is preceded by four lysines, it acts as a highly efficient export signal. The coherence of in vitro studies with alkaline phosphatase fusion analysis of the topology of leader peptidase further indicates the utility of this genetic approach to membrane protein structure and insertion.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2551889 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='221965'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.F479039cb20c49&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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<references/>

PMID:2962192

2008-01-16T20:09:43Z

66.249.72.105: New PMID: Page!

<protect>
{{RightTOC}}

 '''Lee, N, Francklyn, C and Hamilton, EP''' (1987) Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter.''Proc. Natl. Acad. Sci. U.S.A.'' '''84''':8814-8

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The state of Escherichia coli araI DNA occupancy by AraC protein has been found to change from a two-turn to a four-turn occupancy upon the addition of the inducer arabinose. The araI site is separable into two contiguous regions, araI1 and araI2. araI1 binds both ligand-bound and ligand-free AraC protein, whereas araI2 binds AraC protein in the presence of arabinose only. A mutation in araI and a known mutation in araC led to the loss of araI2 binding, while binding to araI1 was unaffected. Both mutants failed to activate the promoter of the araBAD operon. We propose that araI2 occupancy by AraC protein leads to RNA polymerase recognition of the araBAD promoter and that araI1 acts as a switch mechanism allowing both the repressor and the activator forms of AraC protein to regulate the araBAD promoter.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2962192 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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<protect>

{|class = 'sortable' {{Prettytable}} id='221964'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.J478e6486cb5bb&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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PMID:6377308

2008-01-16T19:56:54Z

66.249.72.105: New PMID: Page!

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{{RightTOC}}

 '''Miyada, CG, Stoltzfus, L and Wilcox, G''' (1984) Regulation of the araC gene of Escherichia coli: catabolite repression, autoregulation, and effect on araBAD expression.''Proc. Natl. Acad. Sci. U.S.A.'' '''81''':4120-4

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The araC gene encodes a positive regulatory protein required for L-arabinose utilization in Escherichia coli. Transcription from the araC promoter has been shown to be under positive control by cAMP receptor protein and under negative control by its protein product (autoregulation). This work describes the identification of the region of the araC promoter that interacts with the cAMP receptor protein to mediate catabolite repression. A 3-base-pair deletion centered 60 base pairs from the transcriptional initiation site results in a mutant araC promoter that, in the absence of araC protein, reduces transcriptional activity when compared with the wild-type promoter and is unresponsive to various concentrations of intracellular cAMP in vivo. The same deletion results in a lowered affinity of the araC promoter for cAMP receptor protein in vitro. However, this lowered affinity for the mutant araC promoter does not result in substantial reduction of intracellular araC protein because autoregulation of the araC gene dominates catabolite repression. The 3-base-pair deletion in the cAMP receptor protein binding site of the araC promoter does not affect catabolite repression of the adjacent araBAD operon. The implications of these results on current models for expression of the araBAD operon and the araC gene are discussed.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6377308 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='221963'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E478e6185a9e8f&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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