How bacterial ribosomes select translation initiation sites

Minimal energy foldings of eukaryotic mRNAs form a separate leader domain

We have investigated the minimal energy foldings of 38 mature mRNAs, including the globin family, the insulins, the growth hormones and interleukin-2, and have compared these foldings with those of fully and partly randomised sequences. The mRNAs differ from the random sequences in that they form a separate leader hairpin of 40-60 nucleotides, with the initiation codon typically located downstream of this hairpin, followed by a main fold in which a region flanking the initiation codon is basepaired with the trailer: resulting in a close proximity of the 5' and 3' end of the mRNA. The formation of this conformation depends not only--or primarily--on the structure of the leader, but on both the leader and trailer sequence and their interaction with the coding sequence. Thus if, as the frequent occurrence of this pattern suggests, the secondary structure of the leader regions plays a role in the initiation of translation, possibly accounting for the specificity of initiation and the different translational efficiencies of various mRNAs, we expect that these features may be influenced both by leader and trailer mutants.

Potential secondary structure at translation-initiation sites

Since translational start codons also occur internally, more-complex features within mRNA must determine initiation. We compare the potential secondary structure of 123 prokaryotic mRNA start regions to that of regions coding for internal methionines. The latter display an unexpectedly-uniform, almost-periodic pattern of pairing potential. In contrast, sequences 5' to start codons have little self-pairing, and do not pair extensively with the proximal coding region. Pairing potential surrounding start codons was found to be less than half of that found near internal AUGs. In groups of random sequences where the distribution of nucleotides at each position, or of trinucleotides at each in-frame codon position, matched the observed natural distribution, there was no periodicity in the pairing potential of the internal sequences. Randomized internal sequences had less pairing: the ratio of pairing intensity between internals and starts was reduced from 2.0 to 1.6 by randomization. We propose that the transition from the relatively-unstructured start domains to the highly-structured internal sequences may be an important determinant of translational start-site recognition.

Eukaryotic mRNA 5'-leader sequences have dual regions of complementarity to the 3'-terminus of 18s rRNA

We have used a microcomputer program to test eukaryotic mRNA 5'-leader sequences for complementarity to the 3'-terminus of 18S rRNA. No mismatched bases, bulge loops, or viral mRNA's were utilized. At least one-fourth of the more than 200 mRNA's studied were found to have two distinct regions of complementarity which resulted in an ability to bind to two separate rRNA regions (GAAGG and UUUGG). The analysis of 60 mRNAs with these dual sites resulted in a consensus structure that was a mean distance of 11.75 bases 5' from the initiator AUG and had an average predicted interstrand binding strength of delta G = -13.40 kcal. These characteristics compare favorably to those observed for the prokaryotic 16S rRNA-mRNA Shine and Dalgarno bond.

Localization of the initiation of translation in messenger RNAs of prokaryotes by learning techniques

Learning processes are applied to the recognition of protein coding regions in prokaryotes. Non-contradictory, statistical and logical rules are deduced from a set of known examples of coding sequences. These rules enable to build characteristic patterns on the m-RNA upstream of the initiating codon. These rules are applied with success to recognize more than 180 coding sequences and to detect and/or eliminate hypothetical reading frames or unknown genes.

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.

The nucleotide sequence of the dnaA gene and the first part of the dnaN gene of Escherichia coli K-12

The nucleotide sequence of the dnaA gene and the first 10% of the dnaN gene was determined. From the nucleotide sequence the amino acid sequence of the dnaA gene product was derived. It is a basic protein of 467 amino acid residues with a molecular weight of 52.5 kD. The expression of the dnaA gene is in the counterclockwise direction like the one of the dnaN gene, for which potential startsites were found.

Efficient translation of the coat protein cistron of tobacco mosaic virus in a cell-free system from Escherichia coli

Translation of tobacco mosaic virus (TMV) RNA in a cell-free system derived from Escherichia coli (MRE 600) reveals several discrete polypeptides in the Mr range of 10,000-50,000. The major product is a polypeptide of Mr 17,500 which comigrates with authentic TMV coat protein on sodium dodecyl sulphate/polyacrylamide gel electrophoresis. Structural investigations by peptide-mapping techniques and differential radiolabelling confirm that the major product is TMV coat protein with an N-terminal methionine. The major polypeptide product can be assembled in vitro into virus-like ribonucleoprotein particles. The structural and evolutionary implications of this observation, and the values of TMV in elucidating eukaryotic mRNA interactions with the prokaryotic protein-synthesizing machinery, are discussed.