The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome

Biochem J. 2020 Aug 28;477(16):3019-3032. doi: 10.1042/BCJ20200385.

Abstract

Cytosolic 80S ribosomes contain proteins of the mature cytosolic ribosome (r-proteins) as well as proteins with roles in ribosome biogenesis, protein folding or modification. Here, we refined the core r-protein composition in Arabidopsis thaliana by determining the abundance of different proteins during enrichment of ribosomes from cell cultures using peptide mass spectrometry. The turnover rates of 26 40S subunit r-proteins and 29 60S subunit r-proteins were also determined, showing that half of the ribosome population is replaced every 3-4 days. Three enriched proteins showed significantly shorter half-lives; a protein annotated as a ribosomal protein uL10 (RPP0D, At1g25260) with a half-life of 0.5 days and RACK1b and c with half-lives of 1-1.4 days. The At1g25260 protein is a homologue of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role in the 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins; 26 were enriched more than 10-fold during ribosome enrichment. Some of these enriched proteins have known roles in translation, while others are newly proposed ribosome-associated factors in plants. This analysis provides an improved understanding of A. thaliana ribosome protein content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and how protein turnover can help identify r-proteins involved in ribosome biogenesis or regulation in plants.

Keywords: Arabidopsis thaliana; proteomics; ribosomes.

Publication types

  • Letter
  • Comment

MeSH terms

  • Arabidopsis Proteins* / genetics
  • Arabidopsis* / genetics
  • Aspergillus fumigatus
  • Copper
  • Homeostasis
  • Humans
  • Iron
  • Receptors for Activated C Kinase / genetics
  • Ribosomal Proteins / genetics
  • Ribosomes / genetics
  • Transcription Factors

Substances

  • Arabidopsis Proteins
  • Mrt4 protein, human
  • RACK1 protein, Arabidopsis
  • Receptors for Activated C Kinase
  • Ribosomal Proteins
  • Transcription Factors
  • Copper
  • Iron