Download In Silico Prediction of Peroxisomal Proteins in Mouse

Genome Informatics 14: 539–540 (2003)
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In Silico Prediction of Peroxisomal Proteins in Mouse
Igor V. Kurochkin
Christian Schönbach
[email protected]
[email protected]
Akihiko Konagaya
[email protected]
Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
Keywords: peroxisome, prediction, protein sorting, subcellular location
1
Introduction
Peroxisomes are small vesicle-like subcellular respiratory organelles present in virtually all eukaryotic
cells. Peroxisomes are involved in lipid metabolism, such as β-oxidation of fatty acids, synthesis of
sterols and bile acids and also in glyoxylate metabolism and gluconeogenesis [3]. The importance
of peroxisomes is underscored by the existence in human of a group of serious metabolic disorders
caused either by impairment of peroxisome biogenesis or by defects of individual peroxisomal enzymes.
Despite the fact that peroxisomes were first discovered in the 1960s, the functions performed by these
organelles are still not fully understood. Identification of all peroxisome components will aid in our
understanding of peroxisome biology and discovery of molecular targets to treat disorders associated
with this organelle.
2
Method and Results
The import of most proteins into the peroxisomal matrix is signal mediated. Almost all peroxisomal
matrix proteins carry the type 1 (PTS1) signal at the extreme C-terminus, consisting of three amino
acids, S/AKL. A few peroxisomal proteins contain type 2 (PTS2) targeting signal located near the
N-terminus of proteins. A conceptually translated protein database (RTPS) derived from RIKEN
FANTOM2 collection of transcripts (60,770 cDNA sequences) [2] was scanned for PTS1. Only ORFs
with more than 100 codons in length were considered.
The search identified 23 known peroxisomal matrix proteins including coenzyme A diphosphotase,
phosphomevalonate kinase, glyceronephosphate O-acyltransferase, acyl-coenzyme A oxidase 1, and
sterol carrier protein 2. A number of identified PTS1-containing proteins were highly similar to
known nuclear, mitochondrial or plasma membrane proteins indicating that the signaling system for
peroxisomal localization is not limited to the three residues at the C-terminus but may also include
the region adjacent to PTS1.
2.1
New PTS1-Containing Proteins
The analysis also identified 5 new PTS1-containing proteins. Search for known motifs suggests that two
of them may perform catalytic functions, those encoded by clones C530046K17 and 1300019N10. Clone
C530046K17 predicts a protein of 377 amino acid residues. It contains NAD(P)-binding Rossmannfold and is weakly similar to Arabidopsis thaliana and Cicer arietinum probable NADP-dependent
oxidoreductases. Clone 1300019N10 predicts a protein of 568 amino acids and contains trypsin-like
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serine protease domain. It is weakly homologous to trypsin-like serine protease from Clostridium thermocellum though the latter protein does not contain PTS1. Interestingly, hypothetical protein F3H9.3
from Arabidopsis thaliana, which shares weak homology with 1300019N10 protein, also contains SKL
at its C-terminus. It should be noted that the members of trypsin family are inherently secreted,
being synthesized with a signal peptide that targets them to the secretory pathway. However, a protein encoded by clone 1300019N10 does not contain a signal peptide and thus represents an unusual
trypsin-like protease with a potential to be targeted to a subcellular compartment. The presence of
proteases in peroxisomes is intriguing. So far, only one protease, insulin-degrading enzyme (IDE), has
been shown to be present in peroxisomes. It was suggested that IDE might be involved in degradation
of oxidatively damaged proteins in the organelle [1].
Three other identified clones, 9530079E12, D130032J17 and 3830406C13, encode proteins of 114,
103 and 127 amino acids, respectively. They lack known protein motifs and have no homologues in
protein databases.
2.2
Analysis of Pex Proteins
In addition to peroxisomal matrix proteins, we searched FANTOM2 cDNA collection for the presence of
peroxins (Pex), proteins involved in peroxisome biogenesis. To date 24 PEX genes have been described
in yeast [4]. Using sequence of yeast PEXs as queries, BLAST analysis of FANTOM2 dataset revealed
13 PEX genes conserved in mouse (PEX1, PEX2, PEX3, PEX5, PEX6, PEX7, PEX10, PEX11,
PEX12, PEX13, PEX14, PEX16, and PEX19). Interestingly, human homologs have been found so far
for the same set of 13 PEX genes.
3
Discussion
In an attempt to discover novel peroxisomal proteins, we utilized RIKEN FANTOM2 cDNA collection,
which represents the most comprehensive survey of a mammalian transcriptome so far. Analysis of the
conceptually translated protein database revealed 5 novel previously unrecognized protein components
of the peroxisome. Two of the proteins might perform enzymatic functions. Further experiments have
to establish whether or not proteins identified here are actually targeted to peroxisomes and elucidate
their role in this organelle.
We realize that the approach used in current study provides a lower limit of detection of peroxisomal
proteins as proteins may enter the organelle by some unknown yet mechanisms others than PTS1
pathway. Comprehensive proteomics analysis of peroxisome represents an ultimate approach required
to define all protein components of this organelle.
References
[1] Morita, M., Kurochkin, I.V., Motojima, K., Goto, S., Takano, T., Okamura, S., Sato, R., Yokota,
S., and Imanaka, T., Insulin-degrading enzyme exists inside of rat liver peroxisomes and degrades
oxidized proteins, Cell Struct. Funct., 25(5):309–315, 2000.
[2] The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II
Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length
cDNAs, Nature, 420(6915):563–573, 2002.
[3] Titorenko, V.I. and Rachubinski, R.A., Dynamics of peroxisome assembly and function, Trends
Cell Biol., 11(1):22–29, 2001.
[4] Purdue, P.E. and Lazarow, P.B., Peroxisome biogenesis, Annu. Rev. Cell Dev. Biol., 17:701–752,
2001.