Integrated tRNA, transcript, and protein profiles in response to steroid hormone signaling

RNA. 2015 Oct;21(10):1807-17. doi: 10.1261/rna.052126.115. Epub 2015 Aug 19.

Abstract

The accurate and efficient transfer of genetic information into amino acid sequences is carried out through codon-anticodon interactions between mRNA and tRNA, respectively. In this way, tRNAs function at the interface between gene expression and protein synthesis. Whether tRNA levels are dynamically regulated and to what degree tRNA abundance influences the cellular proteome remains largely unexplored. Here we profile tRNA, transcript and protein levels in Drosophila Kc167 cells, a plasmatocyte cell line that, upon treatment with 20-hydroxyecdysone, differentiates into macrophages. We find that high abundance tRNAs associate with codons that are overrepresented in the Kc167 cell proteome, whereas tRNAs that are in low supply associate with codons that are underrepresented. Ecdysone-induced differentiation of Kc167 cells leads to changes in mRNA codon usage in a manner consistent with the developmental progression of the cell. At both early and late time points, ecdysone treatment concomitantly increases the abundance of tRNAThr(CGU), which decodes a differentiation-associated codon that becomes enriched in the macrophage proteome. These results together suggest that tRNA levels may provide a meaningful regulatory mechanism for defining the cellular proteomic landscape.

Keywords: Drosophila; codon usage bias; ecdysone; proteomics; small RNA.

MeSH terms

  • Animals
  • Cell Differentiation
  • Cell Line
  • Codon
  • Drosophila
  • Ecdysone / physiology*
  • Humans
  • Proteins / physiology*
  • Proteomics
  • RNA, Messenger / genetics*
  • RNA, Transfer / genetics*
  • Signal Transduction*
  • Transcription, Genetic

Substances

  • Codon
  • Proteins
  • RNA, Messenger
  • Ecdysone
  • RNA, Transfer

Associated data

  • GEO/GSE69934