Primary structure of the<i>ompF</i>gene that codes for a major outer membrane protein of<i>Escherichia coli</i>K-12

Inokuchi, Kaoru; Mutoh, Norihiro; Matsuyama, Shin-ichi; Mizushima, Shôji

doi:10.1093/nar/10.21.6957

Cited by 188 publications

(84 citation statements)

References 43 publications

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“…The primary sequences of all E. coli porins [90][91][92]21 I] including that of LamB [I 721 and Tsx (E. Bremer, J. Martinusson. and P. Valentin-Hansen, unpublished results) are known at present.…”

Section: Structure Of the Porin Poresmentioning

confidence: 99%

Permeation of hydrophilic molecules through the outer membrane of gram‐negativ bacteria

Benz

Bauer

1988

European Journal of Biochemistry

273

179

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Section: Structure Of the Porin Poresmentioning

confidence: 99%

Permeation of hydrophilic molecules through the outer membrane of gram‐negativ bacteria

Benz

Bauer

1988

European Journal of Biochemistry

273

179

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“…1B. In all cases, the promoter sequences were extended by 1 base (because of the distance between the -35 and the -10 regions) from the ompF promoter, which has a 17-bp spacer (7,9) and transcription is considered to initiate from the A residue immediately after the Sal I site (see Materials and Methods). Note that for the no.…”

Section: Resultsmentioning

confidence: 99%

“…Because the sequences of these promoters diverge from the consensus sequence, RNA polymerase is either unable to bind to the promoters or to isomerize the closed complex of the promoter and RNA polymerase to the open complex without the aid of transcriptional activators. In the case of ompC and ompF, RNA polymerase is unable to transcribe these genes without OmpR because the -35 and -10 regions of these genes are quite different from the consensus sequence (7,8). The OmpR binding sites for both genes have been shown to exist in the regions from -40 to -100 (9,10).…”

mentioning

confidence: 99%

Enhancement of RNA polymerase binding to promoters by a transcriptional activator, OmpR, in Escherichia coli: its positive and negative effects on transcription.

Tsung

Brissette

Inouye

1990

Proc. Natl. Acad. Sci. U.S.A.

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The OmpR binding sequence (OBS) in the upstream region of the ompF promoter of Escherichia coli was fused to 27 synthetic promoters. Transcription from a number of weak promoters, regardless of their sequences, was dramatically activated in the presence of OmpR, a transcriptional activator. In vivo DNA footprinting revealed that OmpR enhanced the binding of RNA polymerase to the promoters. This enhancement was essential for transcription of weak promoters, while OmpR binding to the OBS fused to a strong promoter was inhibitory for transcription. These results indicate that OmpR stabilizes the formation of an RNA polymerasepromoter complex, possibly a closed promoter complex, and that a transcription activator can serve not only as a positive but also as a negative regulator for gene expression. There are a number of E. coli genes whose transcription is activated by a protein factor binding to a specific sequence upstream of the RNA polymerase recognition site (3-5). The RNA polymerase recognition sites for genes requiring transcriptional activators for "7O RNA polymerase are considerably different from the consensus sequence consisting of the -35 region (TTGACA) and the -10 region (TATAAT) relative to +1, the transcription initiation site (6). Because the sequences of these promoters diverge from the consensus sequence, RNA polymerase is either unable to bind to the promoters or to isomerize the closed complex of the promoter and RNA polymerase to the open complex without the aid of transcriptional activators. In the case of ompC and ompF, RNA polymerase is unable to transcribe these genes without OmpR because the -35 and -10 regions of these genes are quite different from the consensus sequence (7,8 Fig. LA) as well as the -35 and -10 promoter sequence. The lacZ gene coding sequence starting from the eighth codon is fused in-frame to the above ompF sequence. By site-specific mutagenesis the 7-base-pair (bp) DNA sequence immediately after the Cd box (Fig. lA) of ompF, TCACGGf (asterisk indicates the first base in the -35 region of ompF), was replaced with the sequence AAGAEI to generate a unique Bgl II site (underlined). The DNA sequence between this Bgl II site and an original Pst I site at the + 1 position (transcription initiation site) of ompF was then replaced with synthetic oligonucleotides. For example, the sequence for promoter 1 consists of the consensus -35 sequence (TTGACA), an 18-bp spacer sequence (CTrTAAGCTTCCGGCTCG), the -10 sequence of the ompC promoter (GAGAAT), and a 9-bp sequence (GICGACAAT) after the -10 sequence to generate a unique Sal I site (underlined). The spacer sequence is identical to that of the lac promoter (6) except that the sixth T residue (indicated by an asterisk) was changed to A to create a unique HindIII site (underlined). The 9-bp sequence after the -10 sequence is from the lacZ promoter sequence, where the A residue with an asterisk indicates the transcription initiation site. Other synthetic promoters (from no. 2 to no. 27) were constructed by replacing DNA seque...

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“…For some E. coli proteins the synonymous codons are used in a non-random manner and the codons preferred are those recognised by the most abundant tRNA species in the cell; the concentration of each tRNA and the frequency of usage of the synonymous codons have been listed by Ikamura [22,231. Codons AGA, AGG and CGG for arginine, CCC for proline, GGA for glycine, CUA for leucine were considered to be rare codons (Table2) and are also not present in the mRNA of major outer membrane proteins: lipoprotein [24], OmpA [25], OmpF [26], OmpC [27], and LamB [28]. However, these codons and rare codons for other amino acids are present in relatively high proportions in minor proteins and regulatory proteins [15-201, which are maintained in the cell in low concentrations.…”

Section: Discussionmentioning

confidence: 99%

Intermediates in the synthesis of TolC protein include an incomplete peptide stalled at a rare Arg codon

Misra

Reeves

1985

Eur J Biochem

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TolC is a minor outer membrane protein of Escherichia coli K 12 and is initially synthesized as a precursor. A distinct intermediate polypeptide of Mr about 46000 was consistently observed at the initial stages of biosynthesis. The further elongation of this peptide can be blocked by chloramphenicol. We have investigated the cause of the temporary accumulation of the 46000‐Mr intermediate and we postulate that the presence of a rare codon AGA (Arg) at codon 402 of the tolC mRNA halts translating ribosomes owing to a limiting amount of the tRNAArg (AGA) species in the cell. The translation of tolC mRNA can be increased by providing T4 tRNAArg(AGA), encoded on a plasmid.

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Primary structure of theompFgene that codes for a major outer membrane protein ofEscherichia coliK-12

Cited by 188 publications

References 43 publications

Permeation of hydrophilic molecules through the outer membrane of gram‐negativ bacteria

Permeation of hydrophilic molecules through the outer membrane of gram‐negativ bacteria

Enhancement of RNA polymerase binding to promoters by a transcriptional activator, OmpR, in Escherichia coli: its positive and negative effects on transcription.

Intermediates in the synthesis of TolC protein include an incomplete peptide stalled at a rare Arg codon

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