Escherichia coli translation protein factors

Relatively recently Fe/S proteins have been found to function in the regulation of biosynthesis. This can be by promoting deoxyribonucleic acid (DNA) transcription, e.g. the [2Fe-2S] containing Escherichia coli superoxide-activated (SoxR) transcription activator [10-12], or the presumably [4Fe-4S]-containing E. coli transcription factor fumarate nitrate reduction (FNR) [13,14], Alternatively, the Fe/S protein can act by interference with messenger ribonucleic acid (mRNA) translation, i.e., the iron regulatory proteins (IRPs) [15,16], These interactions are stoichiometric, therefore not catalytic. Presumably, they are also a form of sensoring, namely, of oxidants and/or iron [17],... 

Although the mechanism whereby proteins are synthesized is the same in all living forms, classical distinctions exist between eucaryal (post-transcriptional) and bacterial (co-transcriptional) translation. In-frame read-out of (usually polycistronic) bacterial mRNAs is established via Shine-Dalgarno mRNA 16S-rRNA recognition mechanisms polypeptide synthesis is initiated by a formylated methionine and the initiation reactions are assisted by a limited number of protein factors (three in Escherichia coli) that primarily influence kinetic parameters [3],... 

Several fluorescence and biochemical experiments reveal the detailed mechanism of translation and the contribution of KPR towards the fidelity of protein synthesis. The incorporation of an amino acid into the peptide is composed of two consecutive processes initial selection of tRNA at the A site of the ribosome followed by KPR [23]. Various factors affect the initial selection of tRNA such as the HB energy between the codon-anticodon base pairs, the specific interactions between the large subunit of the ribosome and aa-tRNA, etc. The contribution of the initial selection step to the overall error fraction for Escherichia coli is observed to be -1/6, compared to the overall error fraction -7 x 10 for cognate and near-cognate anticodons. As a consequence the contribution of KPR is expected to be 1/24 i.e. -80% of the observed fidelity comes from the KPR. The translation process occurs through the following mechanism (see Figure 13.2). 

The mechanism whereby RNA is translated into protein is complex, and the cell devotes considerable resources to the translational machinery. The components include 20 different amino acids, transfer RNAs, aminoacyl-tRNA synthetases, ribosomes, and a number of protein factors which cycle on and off the ribosomes and facilitate various steps in initiation of translation, elongation of the nascent polypeptide chain, and termination of synthesis with release of the completed polypeptide from the ribosome. The process depends on a supply of energy provided by ATP and GTP. The rate of protein synthesis is typically in the range of 6 (immature red blood cells of the rabbit) to 20 Escherichia coli growing optimally) peptide bonds per sec. at 37°C. 

Although AUG is the initiation codon normally used in bacteria, studies of binding of fMet-tRNAf to ribosomes (Clarck and Marcher, 1966) or translation of synthetic polynucleotides (Thach et ai, 1966) have revealed that GUG and, to a lesser extent, UUG are also functional initiation codons. A single case of initiation at an AUU codon is also known for the Escherichia coli initiation factor IF-3 protein (Sacerdot et ai, 1982). By contrast, a compilation of over 200 ribosome binding site sequences in eukaryotic mRNA (Kozak, 1981a, 1983) has yielded only AUG as initiation codon. It appears, therefore, that initiation of eukaryotic translation occurs exclusively at AUG codons. 

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