Publication

Systematic identification of tRNAome and its dynamics in Lactococcus lactis

Puri, P., Wetzel, C., Saffert, P., Gaston, K. W., Russel, S. P., Cordero Varela, J. A., van der Vlies, P., Zhang, G., Limbach, P. A., Ignatova, Z. & Poolman, B. Sep-2014 In : Molecular Microbiology. 93, 5, p. 944-956 13 p.

Research output: Scientific - peer-reviewArticle

  • Pranav Puri
  • Collin Wetzel
  • Paul Saffert
  • Kirk W. Gaston
  • Susan P. Russel
  • Juan A. Cordero Varela
  • Pieter van der Vlies
  • Gong Zhang
  • Patrick A. Limbach
  • Zoya Ignatova
  • Bert Poolman

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.

Original languageEnglish
Pages (from-to)944-956
Number of pages13
JournalMolecular Microbiology
Volume93
Issue number5
Early online date6-Aug-2014
StatePublished - Sep-2014

    Keywords

  • TRANSFER-RNA ISOACCEPTORS, MASS-SPECTROMETRY, ESCHERICHIA-COLI, CODON USAGE, WOBBLE HYPOTHESIS, TRANSLATION, EXPRESSION, ANTICODON, PROTEIN, AVAILABILITY

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