Translation initiation in <i>Escherichia coli</i>: sequences within the ribosome‐binding site

Ringquist, Steven; Shinedling, Sidney T.; Barrick, Doug; Green, Louis; Binkley, Jonathan; Stormo, Gary D.; Gold, Larry

doi:10.1111/j.1365-2958.1992.tb01561.x

Cited by 321 publications

(277 citation statements)

References 52 publications

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“…These mutant (SD UP ) ribosome-binding sites were then incorporated into congenic rncЈ-ЈlacZ protein (translational) fusions whose expression was subsequently examined in rnc þ and rnc14::Tn10 cells (note that the rnc14 mutation abolishes RNase III activity; Takiff et al, 1989). In the absence of RNase III (Table 1; rnc14), rnc Ј-ЈlacZ fusion expression increased with SD improvement as expected (Ringquist et al, 1992), but with two exceptions. First, expression from the GGAGG SD mutant was less than that from wild type (Table 1; cf.…”

Section: Increased Rnc Gene Translation Abrogates Rnase III Regulationmentioning

confidence: 84%

Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation

Matsunaga

Simons

1997

Molecular Microbiology

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SummaryControl of mRNA stability is an established means of regulating gene expression. However, the detailed mechanisms by which such control is achieved are only now emerging. In particular, there remains a question about the involvement of translation. Escherichia coli ribonuclease III (RNase III) negatively autoregulates expression of its own gene (rnc) approximately 10-fold, by cleaving the untranslated leader and initiating approximately 10-fold more rapid decay of the rnc mRNA, after which RNase III plays no further role. Here, we define the mechanism of this control further. Mutations that increase rnc gene translation abolish autoregulation by increasing the stability of the RNase III-cleaved transcript RNA approximately 10-fold, with no effect on the uncleaved species. Mutations that decrease translation destabilize the rnc mRNA in the presence or absence of RNase III. In so doing, they reveal a pathway of rnc transcript decay distinct from the RNase III-dependent pathway. Stability of a 'minirnc' transcript containing the rnc leader and only the first two codons of the rnc gene is unaffected by decreased translation, presumably because sequences required for this pathway were removed. Importantly, this mini-rnc transcript is regulated normally by RNase III. Moreover, rnc transcripts synthesized in vitro do not decay in cell-free extracts lacking ribosomes, unless they are first cleaved by RNase III. These two results show that RNase III cleavage can initiate rnc transcript decay independently of rnc gene translation, unambiguously establishing that control of mRNA decay need not involve changes in translation. How rnc gene translation is optimized for efficient autoregulation will also be discussed.

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Section: Increased Rnc Gene Translation Abrogates Rnase III Regulationmentioning

confidence: 84%

Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation

Matsunaga

Simons

1997

Molecular Microbiology

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“…Can pseudoknot dependence be overcome by improving the SD sequence of repA? A possible explanation for the absolute requirement of pseudoknot formation for repA translation is that since the predicted SD sequence of repA (UAAGCGA) has relatively weak homology with the consensus sequence (UAAGGAGG) (16), it may be poorly recognized by the ribosome. If so, mutations which strengthen the SD sequence should remove dependence on the pseudoknot.…”

Section: Resultsmentioning

confidence: 99%

Mutations affecting pseudoknot control of the replication of B group plasmids

1993

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The translational initiation region of the mRNA for the replication initiation protein (RepA) of pMU720 is predicted to be sequestered in an inhibitory secondary structure designated stem-loop III. Activation of repA translation requires both the disruption of stem-loop III by ribosomes involved in the translation and termination of the leader peptide RepB and the formation of a pseudoknot, a tertiary RNA structure.Disruption of stem-loop III by site-directed mutagenesis was found to be insufficient to allow high repA expression in the absence of pseudoknot formation, indicating that the pseudoknot acts as an enhancer of repA translation. Furthermore, extending the length of the leader peptide RepB and changing the distance between the pseudoknot and repA Shine-Dalgarno sequence were found to have major elfects on the translation of repA.Plasmid replication in prokaryotes is, in many cases, dependent on a replication initiation protein (Rep), whose expression determines a plasmid's copy number and stability. In the case of pT181 and IncFII plasmids, the regulators of Rep synthesis are small countertranscript RNAs which inhibit Rep expression by binding with their target RNAs. In pT181, binding of the countertranscript RNA to the mRNA for the Rep protein is proposed to cause premature transcriptional termination by altering the folding of the RNA (9, 13). The mechanism by which the countertranscript RNAs of the IncFII plasmids Rl and NR1 regulate Rep expression is not clear. However, it is thought that they indirectly regulate Rep expression by sterically inhibiting the translation of a leader peptide. Translation of the Rep protein is believed to be dependent on the translation of the leader peptide, and the two genes are said to be translationally coupled (4, 23).The replication frequency of the B group miniplasmid pMU720 is thought to be dependent on the expression of the repA gene, which is negatively regulated primarily at the posttranscriptional level by a small countertranscript RNA, RNAI (14,15). RNAI is transcribed from the opposite strand of, and is complementary to, the leader region of the mRNA coding for repA (RNAII) (see Fig. 1). Computer analysis of the folding of RNAII indicates that the translational initiation region (TIR) of repA is sequestered within a secondary structure designated stem-loop III (see Fig. 1 and Fig. 2). It is postulated that stem-loop III inhibits ribosome access to the repA TIR. Previous studies have revealed that for repA to be expressed, stem-loop III must be disrupted by the translation and termination of a small leader peptide RepB, and a pseudoknot has to form (15). Pseudoknot formation is essential for the translation of repA and involves pairing between complementary sequences in RNAII. One of these sequences lies in the loop of a large structure called stem-loop I (proximal pseudoknot sequence), which is complementary to RNAI (see Fig. 2), and the other involves bases adjacent to the ShineDalgarno (SD) sequence of repA (distal pseudoknot sequence). RNAI is thought to...

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“…The optimal spacing for an efficient interaction with the CCUCC core of the E. coli anti-SD region is approx. 7-9 nucleotides, which probably reflects an ideal distance for the subsequent positioning of the initiation codon in the core of the decoding region (Ringquist et al, 1992;La Teana et al, 1995). As most bacterial mRNAs possess an SD signal, it is therefore assumed that the favoured pathway that leads to translation initiation in prokaryotes first starts with SD base pairing ( Fig.…”

Section: Basic Mechanism Of Translation Initiation In Prokaryotesmentioning

confidence: 99%

Functional importance of RNA interactions in selection of translation initiation codons

Sprengart

Porter

1997

Molecular Microbiology

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SummaryRNA base pairing between the initiation codon and anticodon loop of initiator tRNA is essential but not sufficient for the selection of the 'correct' mRNA translational start site by ribosomes. In prokaryotes, additional RNA interactions between small ribosomal subunit RNA and mRNA sequences just upstream of the start codon can efficiently direct the ribosome to the initiation site. Although there is presently no proof for a similar important ribosomal RNA interaction in eukaryotes, the 5Ј non-coding regions of their mRNAs and 'consensus sequences' surrounding initiation codons have been shown to be strong determinants for initiation-site selection, but the exact mechanisms are not yet understood. Intramolecular base pairing in mRNA and participation of translation initiation factors can strongly influence the formation of mRNA-small ribosomal subunit-initiator tRNA complexes and modulate translational activities in both prokaryotes and eukaryotes. Only recently has it been appreciated that alternative mechanisms may also contribute to the selection of initiation codons in all organisms. Although direct proof is currently lacking, there is accumulating evidence that additional cis-acting mRNA elements and trans-acting proteins may form specific 'bridging' interactions with ribosomes during translation initiation.

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Translation initiation in Escherichia coli: sequences within the ribosome‐binding site

Cited by 321 publications

References 52 publications

Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation

Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation

Mutations affecting pseudoknot control of the replication of B group plasmids

Functional importance of RNA interactions in selection of translation initiation codons

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