Sequence-based discovery of the human and rodent peroxisomal proteome

Igor V. Kurochkin, Takeshi Nagashima, Akihiko Konagaya, Christian Schönbach

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Background: Peroxisomes are metabolic organelles present in virtually all eukaryotic cells. They contain enzymes involved in hydrogen peroxide-based respiration and lipid metabolism. At present, only a small number of peroxisomal enzymes that are associated with oxidative stress response and metabolic disorders have been characterised biochemically. Therefore, we devised a sequence-based, multistep knowledge discovery strategy to identify potential novel peroxisomal protein candidates in small rodent model organisms and human. Methods: Screening of 130 629 putative translations of GenBank® rodent and primate mRNA sequences was limited to the classical type-1 peroxisomal targeting signal [SA]-K-L. This motif is over-represented among peroxisomal proteins and has a high targeting efficiency. Subsequent steps of identifying co-occurring motifs, secondary structure properties, orthologues and variants, in combination with literature searching and visual inspection by domain experts, aimed at reduction of both false positive and negative validation targets. Results: Our method yielded 117 known peroxisome-targeted proteins and 29 novel candidate proteins. Of special interest were the mouse C530046K17Rik and 1300019N10Rik protein sequences that contain domains associated with enzymatic functions. C530046K17Rik showed no similarity to any known sequence of the animal kingdom, but weak similarity to the possible Leishmania quinone oxidoreductase and a putative cyanobacterium nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidoreductase. 1300019N10Rik contains two protease-related domains, glutamyl endopeptidase I and trypsin-like serine and cysteine proteases, which may have unique specificities to achieve efficient breakdown of proteins in the peroxisomes. Conclusion: One mouse C57BL/6J strain-specific isocitrate dehydrogenase 1 isoform might be suitable to investigate potential phenotypes associated with the deficit of the intraperoxisomal reduced form of NADP (NADPH) and 2-oxoglutarate. Our biological knowledge discovery strategy enabled not only the identification of peroxisomal enzymes already described in the literature, but also the prediction of several novel proteins with possible roles in peroxisomal biochemistry and metabolism that are currently under experimental validation.

Original languageEnglish
Pages (from-to)93-104
Number of pages12
JournalApplied Bioinformatics
Volume4
Issue number2
DOIs
Publication statusPublished - 2005
Externally publishedYes

Fingerprint

Proteome
proteome
Rodentia
rodents
Proteins
peroxisomes
Peroxisomes
NADP (coenzyme)
NADP
proteins
oxidoreductases
Enzymes
proteinases
enzymes
Data mining
Oxidoreductases
Phosphates
isocitrate dehydrogenase
cysteine proteinases
Leishmania

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems
  • Agricultural and Biological Sciences(all)

Cite this

Sequence-based discovery of the human and rodent peroxisomal proteome. / Kurochkin, Igor V.; Nagashima, Takeshi; Konagaya, Akihiko; Schönbach, Christian.

In: Applied Bioinformatics, Vol. 4, No. 2, 2005, p. 93-104.

Research output: Contribution to journalArticle

Kurochkin, Igor V. ; Nagashima, Takeshi ; Konagaya, Akihiko ; Schönbach, Christian. / Sequence-based discovery of the human and rodent peroxisomal proteome. In: Applied Bioinformatics. 2005 ; Vol. 4, No. 2. pp. 93-104.
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