Decoding options and accuracy of translation of developmentally regulated UUA codon in Streptomyces: bioinformatic analysis

Abstract

BackgroundThe gene bldA for leucyl is known for almost 30 years as a key regulator of morphogenesis and secondary metabolism in genus Streptomyces. Codon UUA is the rarest one in Streptomyces genomes and is present exclusively in genes with auxiliary functions. Delayed accumulation of translation-competent is believed to confine the expression of UUA-containing transcripts to stationary phase. Implicit to the regulatory function of UUA codon is the assumption about high accuracy of its translation, e.g. the latter should not occur in the absence of cognate . However, a growing body of facts points to the possibility of mistranslation of UUA-containing transcripts in the bldA-deficient mutants. It is not known what type of near-cognate tRNA(s) may decode UUA in the absence of cognate tRNA in Streptomyces, and whether UUA possesses certain inherent properties (such as increased/decreased accuracy of decoding) that would favor its use for regulatory purposes.FindingsHere we took bioinformatic approach to address these questions. We catalogued the entire complement of tRNA genes from several relevant Streptomyces and identified genes for posttranscriptional modifications of tRNA that might be involved in UUA decoding by cognate and near-cognate tRNAs.ConclusionsBased on tRNA gene content in Streptomyces genomes, we propose possible scenarios of UUA codon mistranslation. UUA is not associated with an increased rate of missense errors as compared to other leucyl codons, contrasting general belief that low-abundant codons are more error-prone than the high-abundant ones.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-2683-6) contains supplementary material, which is available to authorized users.

Gene miaA for post‐transcriptional modification of tRNAXXA is important for morphological and metabolic differentiation in Streptomyces

“…Although hypotheses on the role of PTTMs in bldA ‐mediated regulation were proposed immediately after the discovery that bldA is a tRNA gene (Lawlor et al , ), no further studies in this direction have been undertaken. Recently, we have shown that several Streptomyces strains carry an extensive repertoire of PTTM genes, including those for A37 hypermodification (Rokytskyy et al , ); we also provided initial evidence that reduced level of MiaB‐mediated PTTM affects Streptomyces biology (Sehin et al , ). The latter work has been carried out on transposon mutant of Streptomyces ghanaensis ATCC14672 and left many questions unanswered because of low genetic tractability of ATCC14672.…”

“…Based on previous data (Rokytskyy et al , ) we focused on S. albus genes XNR_1074 and XNR_1078 (hereafter referred to as miaA and miaB respectively) that encode orthologs of the MiaA and MiaB proteins from proteobacteria. Location of miaA and miaB in S. albus genome is shown in Fig.…”

“…Disruption of miaA is expected to abolish all A37 PTTMs, as it is known (see Introduction) that MiaA‐catalyzed A37 isopentenylation is a prerequisite for MiaB‐dependent thiomethylation. It was not known at the beginning of our study as to whether S. albus possesses MiaE‐assisted modification of A37; no orthologs of proteobacterial MiaE protein were identified in BLASTP searches (Rokytskyy et al , ). HPLC analysis of tRNA hydrolysates from the parental SAM2 strain (derivative of J1074 carrying single attB φC31 , see Experimental procedures ) revealed the presence of two major fractions – ms 2 io 6 A and io 6 A (Fig.…”

Properties of Streptomyces albus J1074 mutant deficient in tRNALeu UAA gene bldA

“…We developed for S. albus J1074 a specialized codon reporter system based on S. coelicolor A number of recent studies suggest that it is not the delayed expression of bldA gene but formation of mature (translationally competent) tRNA holds the key to its regulatory function (Leskiw et al 1991;Xu et al 2008;Pettersson and Kirsebom 2011). Yet, besides initial in silico predictions (Rokytskyy et al 2016) nothing is known about genetics of tRNA maturation in Streptomyces. Likewise, there is growing body of data on crucial role of environmental factors in tRNA biology (Laxman et al 2013;Moukadiri et al 2014;Sakai et al 2016), although this area remains unexplored in case of bldA gene.…”

A Genetic Assay System to Study Mistranslation of Leucyl Codon Uua in Streptomyces

“…Mistranslation of UUA is usually invoked as the most plausible explanation of such observation. Our recent in silico study provided some support in favor of mistranslation hypothesis [15]. However, there is no model system for Streptomyces which would provide simple experimental framework to observe and probe mistranslation.…”