An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

PLoS Genet. 2021 Nov 29;17(11):e1009939. doi: 10.1371/journal.pgen.1009939. eCollection 2021 Nov.

Abstract

The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA gene dosage ratio based on chromosomal positions is almost identical to the observed and theoretically optimal tRNA/rRNA expression ratio, indicating that the chromosomal arrangement has evolved to favor maximal transcription of both types of genes at this condition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Bacterial / genetics
  • Escherichia coli / genetics*
  • Escherichia coli / growth & development
  • Gene Dosage / genetics
  • Genome, Bacterial / genetics*
  • RNA, Bacterial / genetics
  • RNA, Ribosomal / genetics
  • RNA, Transfer / genetics
  • Ribosomes / genetics*
  • Transcription, Genetic*

Substances

  • RNA, Bacterial
  • RNA, Ribosomal
  • RNA, Transfer

Grants and funding

This work was supported by grants to M.J.L. from the Volkswagen Foundation under the “Life?” initiative and from the German Research Foundation (DFG) through CRC 1310, and, under Germany’s Excellence Strategy, through EXC 2048/1 (Project ID: 390686111). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.