Modulation of lambda integrase synthesis by rare arginine tRNA

Abstract

Lambda's int gene contains an anomalously high frequency of the rare arginine codons AGA and AGG when compared to genes of Escherichia coli or to the rest of phage lambda. These are the least frequent codons in genes of E. coli and are recognized by the rarest tRNAs. The presence of these codons reduces the translation rate and, depending on the context, this can strongly modulate translational efficiency by a variety of mechanisms. In this study, we show that expression of the natural int gene may also be modulated by rare arginine codon usage, and we explore this mechanism.

Sequence of the Genome of the Temperate, Serotype-Converting, Pseudomonas aeruginosa Bacteriophage D3

“…Two codons, AGA (Arg) and AUA (Ile), are rarely used in E. coli but employed more frequently in coliphage . It has been noted that the integrase has a higher proportion of the rare arginine codons AGA and AGG and that this influences expression of this gene (74). Taking two pairs of proteins which one would expect to be expressed at different levels, capsid (orf6) and major tail protein (orf16), compared with repressor (orf69) and integrase (orf35), it was noted that certain codons are favored in the highly expressed genes.…”

Depletion of Free 30S Ribosomal Subunits in Escherichia coli by Expression of RNA Containing Shine-Dalgarno-Like Sequences

“…Inhibition is most pronounced when the AGG cluster is in the AGG reading frame and near the 5Ј end of the coding sequence (23). Interestingly, this inhibitory effect is diminished or even abolished when the AGG codons are located in the middle of the gene (6) and is largely reversed by overexpression of tRNA Arg/UCU (7,35,36). These findings point to depletion of rare arginine-tRNAs by clusters of "hungry Arg codons" as the major cause of inhibition.…”

Messenger RNA release from ribosomes during 5′‐translational blockage by consecutive low‐usage arginine but not leucine codons in Escherichia coli

“…Furthermore, others have shown that overexpression of cognate tRNAArg eliminates 5Ј-translational blockage caused by AGG codons (Chen and Inouye, 1994;Zahn and Landy, 1996). If the AGGs were simply having a structural effect on the mRNA inhibiting initiation, expression of the cognate tRNA would not have been expected to reverse the effect.…”

“…It is known that inhibition of translation by AGG codons is a consequence of insufficient cognate tRNA, since supplying a plasmid expressing excess tRNA able to read these codons overcomes the inhibition (Brinkmann et al, 1989;Spanjaard et al, 1990;Chen and Inouye, 1994;Kane, 1995;Zahn and Landy, 1996). When ribosomes encounter a codon for which there is insufficient cognate tRNA (a 'hungry codon'), there are several alternative fates (reviewed in Parker, 1989), including mistranslation (reviewed in Kurland, 1992), frameshifting (Barak et al, 1996;also reviewed in Farabaugh, 1996) and probable stalling (for example, in attenuation mechanisms for amino acid biosynthetic operons; reviewed in Yanofsky, 1981).…”

“…In some experiments, there was no inhibition at all when the low-usage codons were in the middle of the gene (AGG Arg codons, Chen and Inouye, 1990; and CUA Leu codons, Goldman et al, 1995), while in others the inhibition was not as great (AGG codons, Rosenberg et al, 1993) and/or there were indications of translational frameshifting with lowusage codon insertions downstream (AGG codons, Spanjaard and van Duin, 1988;Rosenberg et al, 1993). As few as two consecutive AGG codons near the 5Ј end of the message confer significant inhibition of translation (Rosenberg et al, 1993;Zahn and Landy, 1996).…”