title: Systematic identification of tRNAome and its dynamics in Lactococcus lactis.
abstract: Transfer RNAs (tRNAs) through their abundance and modification pattern significantly influence protein translation. Here, we present a systematic analysis of the tRNAome of Lactococcus lactis. Using the next-generation sequencing approach, we identified 40 tRNAs 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 tRNAs. 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 tRNAs cognate to low abundance codons decrease, while the tRNAs 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.
authors.affiliation: Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
authors.forename: Pranav
authors.initials: P
authors.lastname: Puri
authors.forename: Collin
authors.initials: C
authors.lastname: Wetzel
authors.forename: Paul
authors.initials: P
authors.lastname: Saffert
authors.forename: Kirk W
authors.initials: KW
authors.lastname: Gaston
authors.forename: Susan P
authors.initials: SP
authors.lastname: Russell
authors.forename: Juan A
authors.initials: JA
authors.lastname: Cordero Varela
authors.forename: Pieter
authors.initials: P
authors.lastname: van der Vlies
authors.forename: Gong
authors.initials: G
authors.lastname: Zhang
authors.forename: Patrick A
authors.initials: PA
authors.lastname: Limbach
authors.forename: Zoya
authors.initials: Z
authors.lastname: Ignatova
authors.forename: Bert
authors.initials: B
authors.lastname: Poolman
mesh_terms: D000926:Anticodon; D003062:Codon; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D000926:Anticodon; D003062:Codon; D012343:RNA, Transfer