Evolutionary flux of potentially bldA-dependent Streptomyces genes containing the rare leucine codon TTA

Abstract

Previous studies have shown that one of the six leucine codons, UUA, is rare in Streptomyces, and that, while the gene for the UUA-specific tRNA, bldA, can generally be inactivated in diverse streptomycetes without impairing vegetative growth, bldA mutants are typically defective in reproductive aerial growth and in antibiotic production. Here, four complete genome sequences and 143 gene clusters for antibiotic biosynthesis from diverse streptomycetes were analysed in order to evaluate the evolution and function of genes whose possession of TTA codons makes them dependent on bldA. It was deduced that the last common ancestor of the four sequenced genomes, possibly 220 million years ago, already possessed the bldA system, together with perhaps 200 TTA-containing target genes. Some 33 of these genes are retained by the modern descendants, though only three of them retain a TTA in all occurrences. Nearly all of these 33, as well as many of the TTA-containing genes with orthologues in two or three of the four genomes, have the same location on the chromosomes as in their common ancestor. However, the majority of TTA-containing genes (61% overall in the four genomes) are species-specific, and were probably acquired by comparatively recent horizontal gene transfer. Most of these genes are of unknown function, and it is likely that many of them confer specialised ecological benefits. On the other hand, one class of species-specific, functionally recognisable, horizontally acquired genes--the gene clusters for antibiotic production--very often contain TTA codons; and nearly half of them have TTA codons in their pathway-specific regulatory genes.

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

“…Changing the TTA codon of actII-ORF4, or of mmyB and mmfL, to an alternative leucine codon caused the specific restoration of production of the relevant antibiotic in a bldA mutant (39,57), providing a potentially useful route to the elimination of competing bldA-dependent pathways. It is very common for a TTA codon to be present in cluster-situated regulatory genes: among 143 secondary metabolic biosynthetic gene clusters, 109 included TTA-containing genes, most of which encoded regulators (159). This, and the TTA codon in adpA (see below), explains why disruption of bldA eliminates biosynthesis of a variety of secondary metabolites in diverse streptomycetes.…”

Growth-Regulated Expression of a Bacteriocin, Produced by the Sweet Potato Pathogen Streptomyces ipomoeae , That Exhibits Interstrain Inhibition

“…TTA-containing Streptomyces genes are typically species specific and apparently nonessential in function and often show evidence of relatively recent lateral transmission (3,16). The possible origin of the ipomicin structural gene ipoA in S. ipomoeae and the mechanism of action of ipomicin currently remain unknown, and no homologs exist for either in the databases.…”

pSLA2-M ofStreptomyces rocheiIs a Composite Linear Plasmid Characterized by Self-Defense Genes and Homology with pSLA2-L

“…The TTA codon was found in 10 orfs (orf3, orf8, orf20, orf28, orf45, orf63, orf94, orf104, orf116, and orf117), making their translation dependent on the leucyl-tRNA coded by bldA. 20) Although TTA codons are present in 2-3% of the whole genome of Streptomyces, 21) they are more abundant (8%, 10/121) in pSLA2-M. In this respect, five TTA-containing orfs were found in pSLA2-L (3.5%, 5/143).…”