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Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

Kenichiro Imai1, Naoya Fujita, M Michael Gromiha

  • 1AIST, Computational Biology Research Center, Tokyo, Aomi 135-0064, Japan.

BMC Genomics
|January 29, 2011
PubMed
Abstract

Insights

Few mitochondrial beta-barrel outer membrane proteins (MBOMPs) remain undiscovered. A new search, using beta-signals, suggests most MBOMPs are already known, especially in yeast.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genomics

Background:

  • Mitochondrial outer membranes resemble Gram-negative bacteria outer membranes, containing beta-barrel outer membrane proteins (BOMPs).
  • Only four families of mitochondrial BOMPs (MBOMPs) are currently identified, despite potential for many more.
  • The recent discovery of a beta-signal for MBOMP integration provides a new avenue for identifying undiscovered MBOMPs.

Purpose of the Study:

  • To conduct a comprehensive survey of eukaryotic protein sequences to identify novel MBOMPs.
  • To leverage recent findings on beta-signals, structural information, and a novel BOMP predictor for MBOMP identification.
  • To investigate the presence and characteristics of MBOMPs in yeast and Arabidopsis.

Main Methods:

  • Utilized a novel BOMP predictor trained on bacterial and mitochondrial BOMPs.
  • Employed beta-signal information and structural data in the protein sequence survey.
  • Performed a beta-signal independent search for MBOMPs in yeast and Arabidopsis proteomes.

Main Results:

  • Circumstantial evidence suggests few novel MBOMPs remain to be discovered, assuming they are monomeric and beta-signal dependent.
  • Analysis revealed exceptions to the current beta-signal model but confirmed its C-terminal presence in MBOMPs.
  • No strong MBOMP candidates were found in yeast, while Arabidopsis results were inconclusive.

Conclusions:

  • The study concludes that no remaining MBOMPs are likely to be discovered in yeast.
  • If all MBOMPs are beta-signal dependent, then few MBOMP families are likely undiscovered across all sequenced organisms.
  • The findings refine our understanding of MBOMP diversity and identification strategies.

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