Messenger RNA recognition in Escherichia coli: a possible second site of interaction with 16S ribosomal RNA.

Abstract

Examination of the nucleotides following the ATG or GTG initiation codons of a file of 251 genes from Escherichia coli has shown that 247 (98.4%) of them contain a sequence of at least three and 168 (66.9%) of them a sequence of at least four consecutive nucleotides that is complementary to some part of the 16 nt at the 5' terminus of the bacterial 16S rRNA. It is proposed that this sequence, which falls within the first 24 nt coding for the genetic message, might be involved in mRNA recognition through a mechanism analogous to the wellestablished 'Shine-Dalgarno' interaction with the 3' terminus of the 16S rRNA. Comparison of these data with data derived from a file of 117 'false' gene starts that have a Shine-Dalgarno-like sequence followed by a suitably spaced ATG or GTG triplet but which are believed not to lie at the beginnings of genetic messages shows the association that we have found to be statistically significant at the 99.9% level.

Characterization of repetitive sequences controlling phase variation of Haemophilus influenzae lipopolysaccharide

“…None of the loci had identifiable Shine-Dalgarno sequences upstream from their initiation codons. However, the sequence (CAAT)n provides a significant 5-base-pair match with a downstream 16S rRNA-binding consensus sequence in E. coli (20). Following the last tetrapeptide (SINQ), there is no similarity in the deduced amino acid sequences for licl, lic2, and lic3 for those portions of the proteins whose sequences were established (Fig.…”

Overproduction and localization of components of the polyketide synthase of Streptomyces glaucescens involved in the production of the antibiotic tetracenomycin C

“…Rather than reflecting differences in codon usage, the increases may reflect compositional changes in the nucleotide sequence downstream of the translational start codon, which can affect the efficiency of translational initiation. In this context it was interesting to assess whether complementarity between these sequences and the 5' segment of 16S rRNA might be important, as suggested by Petersen et al (33). Regions of complementarity of three nucleotides or more were created in each of the constructs that gave increased levels of expression, except for pIJ2242 (Fig.…”

“…In these studies we set out to overproduce the ORF 1, 2, and 3 components of the tetracenomycin C polyketide synthase. Following the success of Leadlay and co-workers in expressing streptomycete genes to high levels in E. coli (10,34,44), we concentrated on the pT7 system of Tabor and Richardson (46 (33) and may play a role in ribosome recognition and hence influence the efficiency of translational initiation.…”

Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit

“…Suggestive support for a neighbourhood of 5'-and 3'-terminal sequences comes from the proposal of Peterson et al (37), that in addition to the 3'-terminal region, sequence positions 1 to 18 of the 5' end of bacterial 16S rRNA may also be involved in mRNA recognition. This extended type of mRNA recognition with 3' and 5'-terminal sequences of 16S rRNA pairing on adjacent regions of mRNA would imply neighbourhood of the two termini, but in contrast to our model would also imply melting of helices 1 (positions 9-13) and 2 (positions [18][19][20] during mRNA recognition.…”