Physiological significance of the two isoforms of initiator tRNAs in Escherichia coli

Abstract

ABSTRACT Escherichia coli possesses four initiator tRNA (i-tRNA) genes, three of which are present together as metZWV and the fourth one as metY . In E. coli B, all four genes ( metZWV and metY ) encode i-tRNA fMet1 , in which the G at position 46 is modified to m 7 G46 by TrmB (m 7 G methyltransferase). However, in E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNA fMet2 , having an A in place of m 7 G46. We generated E. coli strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on metY A46 ( metY of E. coli K origin encoding i-tRNA fMet2 ) or its derivative metY G46 (encoding i-tRNA fMet1 ) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNA fMet1 have a growth fitness advantage over those sustained on i-tRNA fMet2 . The growth fitness advantages are more pronounced for the strains sustained on i-tRNA fMet1 in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs in vivo . Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNA fMet1 than that of i-tRNA fMet2 . The stability of i-tRNA fMet1 remains unaffected upon the deletion of TrmB. These studies highlight how metY G46 and metY A46 alleles might influence the growth fitness of E. coli under certain nutrient-limiting conditions. IMPORTANCE Escherichia coli harbors four initiator tRNA (i-tRNA) genes: three of these at metZWV and the fourth one at metY loci. In E. coli B, all four genes encode i-tRNA fMet1 . In E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNA fMet2 , having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNA fMet1 . The strains sustained on i-tRNA fMet1 have a growth fitness advantage over those sustained on i-tRNA fMet2 . Strains harboring metY G46 (B mimic) or metY A46 (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.