Defining a Minimal Cell: Essentiality of Small ORFs and ncRNAs in a Genome-Reduced Bacterium

Mol Syst Biol. 2015 Jan 21;11(1):780. doi: 10.15252/msb.20145558.

Abstract

Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome.

Keywords: minimal genome; non‐coding RNAs; small proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / genetics*
  • Genes, Essential
  • Genome, Bacterial*
  • Mycoplasma pneumoniae / genetics*
  • Open Reading Frames*
  • Protein Conformation
  • RNA, Untranslated / genetics*
  • Sequence Analysis, DNA
  • Transcription, Genetic

Substances

  • DNA, Bacterial
  • RNA, Untranslated