Premium
Systematic identification of tRNAome and its dynamics in L actococcus lactis
Author(s) -
Puri Pranav,
Wetzel Collin,
Saffert Paul,
Gaston Kirk W.,
Russell Susan P.,
Cordero Varela Juan A.,
Vlies Pieter,
Zhang Gong,
Limbach Patrick A.,
Ignatova Zoya,
Poolman Bert
Publication year - 2014
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.12710
Subject(s) - biology , transfer rna , codon usage bias , lactococcus lactis , gene , translation (biology) , housekeeping gene , genetics , dna microarray , rna , heterologous , messenger rna , translational regulation , gene expression , abundance (ecology) , start codon , computational biology , genome , lactic acid , fishery , bacteria
Summary Transfer RNAs ( tRNAs ) through their abundance and modification pattern significantly influence protein translation. Here, we present a systematic analysis of the tRNAome of L actococcus lactis . Using the next‐generation sequencing approach, we identified 40 tRNA s which carry 16 different post‐transcriptional modifications as revealed by mass spectrometry analysis. While small modifications are located in the tRNA body, hypermodified nucleotides are mainly present in the anticodon loop, which through wobbling expand the decoding potential of the tRNA s. Using tRNA ‐based microarrays, we also determined the dynamics in tRNA abundance upon changes in the growth rate and heterologous protein overexpression stress. With a fourfold increase in the growth rate, the relative abundance of tRNA s cognate to low abundance codons decrease, while the tRNA s cognate to major codons remain mostly unchanged. Significant changes in the tRNA abundances are observed upon protein overexpression stress, which does not correlate with the codon usage of the overexpressed gene but rather reflects the altered expression of housekeeping genes.