Small membrane proteins found by comparative genomics and ribosome binding site models

Matthew R. Hemm, Brian J. Paul, Thomas D. Schneider, Gisela Storz, Kenneth E. Rudd

Research output: Contribution to journalArticle

118 Citations (Scopus)

Abstract

The correct annotation of genes encoding the smallest proteins is one of the biggest challenges of genome annotation, and perhaps more importantly, few annotated short open reading frames have been confirmed to correspond to synthesized proteins. We used sequence conservation and ribosome binding site models to predict genes encoding small proteins, defined as having 16-50 amino acids, in the intergenic regions of the Escherichia coli genome. We tested expression of these predicted as well as previously annotated genes by integrating the sequential peptide affinity tag directly upstream of the stop codon on the chromosome and assaying for synthesis using immunoblot assays. This approach confirmed that 20 previously annotated and 18 newly discovered proteins of 16-50 amino acids are synthesized. We summarize the properties of these small proteins; remarkably more than half of the proteins are predicted to be single-transmembrane proteins, nine of which we show co-fractionate with cell membranes.

Original languageEnglish
Pages (from-to)1487-1501
Number of pages15
JournalMolecular Microbiology
Volume70
Issue number6
DOIs
StatePublished - Dec 1 2008
Externally publishedYes

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Genomics
Ribosomes
Membrane Proteins
Binding Sites
Proteins
Genome
Molecular Sequence Annotation
Amino Acids
Intergenic DNA
Terminator Codon
Open Reading Frames
Genes
Chromosomes
Cell Membrane
Escherichia coli
Peptides

ASJC Scopus subject areas

  • Molecular Biology
  • Microbiology

Cite this

Small membrane proteins found by comparative genomics and ribosome binding site models. / Hemm, Matthew R.; Paul, Brian J.; Schneider, Thomas D.; Storz, Gisela; Rudd, Kenneth E.

In: Molecular Microbiology, Vol. 70, No. 6, 01.12.2008, p. 1487-1501.

Research output: Contribution to journalArticle

Hemm, Matthew R. ; Paul, Brian J. ; Schneider, Thomas D. ; Storz, Gisela ; Rudd, Kenneth E. / Small membrane proteins found by comparative genomics and ribosome binding site models. In: Molecular Microbiology. 2008 ; Vol. 70, No. 6. pp. 1487-1501.
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