MITOP: database for mitochondria-related proteins, genes and diseases

Scharfe, Curt; Zaccaria, Paolo; Hoertnagel, Konstanze; Jaksch, Michaela; Klopstock, Thomas; Lill, Roland; Prokisch, Holger; Gerbitz, Klaus-Dieter; Mewes, Hans‐Werner; Meitinger, Thomas

doi:10.1093/nar/27.1.153

Cited by 33 publications

(33 citation statements)

References 13 publications

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“…The molecular weight distribution of all identified proteins correlated well with that of the YPD database for mitochondrial proteins and the overall molecular weight distribution of the predicted proteins from the whole yeast genome (36) (data not shown). The proteins identified by us cover 92% of the known mitochondrial proteins listed in the MITOP yeast database (43). Taylor et al (13) identified 35 subunits (45%) of the known 77 subunits of the human heart mitochondrial ribosome; this value is in good agreement with the assessed overall coverage of the mitochondrial proteome by this study (13,14).…”

Section: Vs Lane 4)supporting

confidence: 81%

The proteome of Saccharomyces cerevisiae mitochondria

Sickmann

Reinders²,

Wagner³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

815

666

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We performed a comprehensive approach to determine the proteome of Saccharomyces cerevisiae mitochondria. The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. From >20 million MS spectra, 750 different proteins were identified, indicating an involvement of mitochondria in numerous cellular processes. All known components of the oxidative phosphorylation machinery, the tricarboxylic acid cycle, and the stable mitochondria-encoded proteins were found. Based on the mitochondrial proteins described in the literature so far, we calculate that the identified proteins represent Ϸ90% of all mitochondrial proteins. The function of a quarter of the identified proteins is unknown. The mitochondrial proteome will provide an important database for the analysis of new mitochondrial and mitochondria-associated functions and the characterization of mitochondrial diseases.

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Section: Vs Lane 4)supporting

confidence: 81%

The proteome of Saccharomyces cerevisiae mitochondria

Sickmann

Reinders²,

Wagner³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

815

666

View full text Add to dashboard Cite

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“…Most mitochondrial proteins are synthesized as larger precursors containing N-terminal cleavable extension peptides called presequences (34). However, MitoP, a commonly used computer program predicting mitochondrial presequences (35), predicted that spinach Protox IIS has no typical cleavable mitochondrial presequence. This prediction is in agreement with our experimental data that the molecular size of mature Protox IIS in leaves is identical with that of an in vitro synthesized product (Figs.…”

Section: Discussionmentioning

confidence: 99%

Dual Targeting of Spinach Protoporphyrinogen Oxidase II to Mitochondria and Chloroplasts by Alternative Use of Two In-frame Initiation Codons

Watanabe

Che

Iwano

et al. 2001

Journal of Biological Chemistry

148

117

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Protoporphyrinogen oxidase (Protox) is the final enzyme in the common pathway of chlorophyll and heme biosynthesis. Two Protox isoenzymes have been described in tobacco, a plastidic and a mitochondrial form. We isolated and sequenced spinach Protox cDNA, which encodes a homolog of tobacco mitochondrial Protox (Protox II). Alignment of the deduced amino acid sequence between Protox II and other tobacco mitochondrial Protox homologs revealed a 26-amino acid N-terminal extension unique to the spinach enzyme. Immunoblot analysis of spinach leaf extract detected two proteins with apparent molecular masses of 57 and 55 kDa in chloroplasts and mitochondria, respectively. In vitro translation experiments indicated that two translation products (59 and 55 kDa) are produced from Protox II mRNA, using two in-frame initiation codons. Transport experiments using green fluorescent proteinfused Protox II suggested that the larger and smaller translation products (Protox IIL and IIS) target exclusively to chloroplasts and mitochondria, respectively.

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“…To identify oligonucleotide and cDNA sequences represented on the expression chips that correspond to known mitochondrial genes, we performed a BLASTX search of probe-set consensus sequences against the entries in MITOP (12). A human or mouse probe meeting…”

Section: Methodsmentioning

confidence: 99%

“…We began by examining a set of Ϸ300 well studied, nuclear-encoded genes known to encode proteins localized to the mitochondrion (12). These genes, particularly those involved in oxidative phosphorylation, tend to be coregulated in yeast, as shown by microarray experiments (16).…”

Section: Neighborhood Analysis Of Large-scale Mrna Expression Data Setsmentioning

confidence: 99%

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

Mootha

Lepage

Miller

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

532

394

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Identifying the genes responsible for human diseases requires combining information about gene position with clues about biological function. The recent availability of whole-genome data sets of RNA and protein expression provides powerful new sources of functional insight. Here we illustrate how such data sets can expedite disease-gene discovery, by using them to identify the gene causing Leigh syndrome, French-Canadian type (LSFC, Online Mendelian Inheritance in Man no. 220111), a human cytochrome c oxidase deficiency that maps to chromosome 2p16-21. Using four public RNA expression data sets, we assigned to all human genes a ''score'' reflecting their similarity in RNA-expression profiles to known mitochondrial genes. Using a large survey of organellar proteomics, we similarly classified human genes according to the likelihood of their protein product being associated with the mitochondrion. By intersecting this information with the relevant genomic region, we identified a single clear candidate gene, LRPPRC. Resequencing identified two mutations on two independent haplotypes, providing definitive genetic proof that LRPPRC indeed causes LSFC. LRPPRC encodes an mRNA-binding protein likely involved with mtDNA transcript processing, suggesting an additional mechanism of mitochondrial pathophysiology. Similar strategies to integrate diverse genomic information can be applied likewise to other disease pathways and will become increasingly powerful with the growing wealth of diverse, functional genomics data.

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MITOP: database for mitochondria-related proteins, genes and diseases

Cited by 33 publications

References 13 publications

The proteome of Saccharomyces cerevisiae mitochondria

The proteome of Saccharomyces cerevisiae mitochondria

Dual Targeting of Spinach Protoporphyrinogen Oxidase II to Mitochondria and Chloroplasts by Alternative Use of Two In-frame Initiation Codons

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

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