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PMID: 25040919 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Systematic identification of tRNAome and its dynamics in Lactococcus lactis.

Molecular microbiology ·Vol. 93 ·No. 5 ·2014-09-00 ·Pages 944-56

Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, Cordero Varela JA, van der Vlies P, Zhang G, Limbach PA, Ignatova Z, Poolman B

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.

MeSH Terms
Anticodon Codon Lactococcus lactis/genetics,metabolism RNA, Transfer/genetics,metabolism Transcription, Genetic
Chemicals
Anticodon Codon RNA, Transfer
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Puri Pranav
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.
Wetzel Collin
Saffert Paul
Gaston Kirk W
Russell Susan P
Cordero Varela Juan A
van der Vlies Pieter
Zhang Gong
Limbach Patrick A
Ignatova Zoya
Poolman Bert
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Article Info
Journal
Molecular microbiology
Abbr.
Mol Microbiol
ISSN
1365-2958
DOI
10.1111/mmi.12710
Published
2014-09-00
Epub
2014-00-06
Pages
944-56
Language
English
Region
England
NLM ID
8712028
PMCID
PMC4150846
Subset
IM
Grants
NIGMS NIH HHS · R01 GM058843 · United States
NIGMS NIH HHS · R56 GM058843 · United States
NIGMS NIH HHS · GM58843 · United States
External Links
PubMed source DOI: 10.1111/mmi.12710 PMC Full Text View journal details
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