MitoP2, an integrated database on mitochondrial proteins in yeast and man

Andréoli, Christophe; Prokisch, Holger; Hörtnagel, Konstanze; Mueller, Jakob C.; Münsterkötter, Martin; Scharfe, Curt; Meitinger, Thomas

doi:10.1093/nar/gkh137

Cited by 75 publications

(52 citation statements)

References 30 publications

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“…Protein sequence analyses were done using PSORTII (http://psort.nibb.ac.jp) and MitoP2 ( [42] . The MTS was further analyzed by wheel plots using a program by Webgenetics (http://webgenetics.com/ cgibin/wg?form=wheel&ID=0).…”

Section: Computational Sequence Analysesmentioning

confidence: 99%

Two small enzyme isoforms mediate mammalian mitochondrial poly(ADP-ribose) glycohydrolase (PARG) activity

Meyer

Meyer-Ficca

Whatcott

et al. 2007

Experimental Cell Research

101

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Poly(ADP-ribose)glycohydrolase (PARG) is the major enzyme capable of rapidly hydrolyzing poly (ADP-ribose)(PAR) formed by the diverse members of the PARP enzyme family. This study presents an alternative splice mechanism by which two novel PARG protein isoforms of 60 kDa and 55 kDa are expressed from the human PARG gene, termed hPARG60 and hPARG55, respectively. Homologous forms were found in the mouse (mPARG63 and mPARG58) supporting the hypothesis that expression of small PARG isoforms is conserved among mammals. A PARG protein of ∼60kDa has been described for decades but with its genetic basis unknown, it was hypothesized to be a product of posttranslational cleavage of larger PARG isoforms. While this is not excluded entirely, isolation and expression of cDNA clones from different sources of RNA indicate that alternative splicing leads to expression of a catalytically active hPARG60 in multiple cell compartments. A second enzyme, hPARG55 that can be expressed through alternative translation initiation from hPARG60 transcripts is strictly targeted to the mitochondria. Functional studies of a mitochondrial targeting signal (MTS) in PARG exon IV suggest that hPARG60 may be capable of shuttling between nucleus and mitochondria, which would be in line with a proposed function of PAR in genotoxic stress-dependent, nuclear-mitochondrial crosstalk.

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Section: Computational Sequence Analysesmentioning

confidence: 99%

Two small enzyme isoforms mediate mammalian mitochondrial poly(ADP-ribose) glycohydrolase (PARG) activity

Meyer

Meyer-Ficca

Whatcott

et al. 2007

Experimental Cell Research

101

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“…A one-to-one orthologous matrix with 2603 rows (genes) and nine columns (species) was created. The mitochondrial genes were downloaded from the manually curated MitoP2 database (Andreoli et al 2004; http://www.mitop.de:8080/mitop2/). In the database, 528 S. cerevisiae genes are annotated as mitochondrial genes based on published literature.…”

Section: Orthologous Gene Definition and Evolutionary Distance Estimamentioning

confidence: 99%

Relaxation of yeast mitochondrial functions after whole-genome duplication

Jiang¹,

Guan²,

Pinney³

et al. 2008

Genome Res.

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Mitochondria are essential for cellular energy production in most eukaryotic organisms. However, when glucose is abundant, yeast species that underwent whole-genome duplication (WGD) mostly conduct fermentation even under aerobic conditions, and most can survive without a functional mitochondrial genome. In this study, we show that the rate of evolution for the nuclear-encoded mitochondrial genes was greater in post-WGD species than pre-WGD species. Furthermore, codon usage bias was relaxed for these genes in post-WGD yeast species. The codon usage pattern and the distribution of a particular transcription regulatory element suggest that the change to an efficient aerobic fermentation lifestyle in this lineage might have emerged after WGD between the divergence of Kluyveromyces polysporus and Saccharomyces castellii from their common ancestor. This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species.

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“…Analysis of markers of subcellular compartments by Western blotting is used for determination of purity of isolated mitochondrial fractions. Further, subcellular localization of identified proteins can be checked in databases of mitochondrial proteins 34 or by systems that predict subcellular localization 35 . Commercially available kits based on differential centrifugation can simplify and speed up the separation and could be an alternative approach when limited amounts of sample are available or for processing large numbers of samples 36 .…”

Section: Sample Preparationmentioning

confidence: 99%

Proteomic approaches to the study of renal mitochondria

Tůma¹,

Kuncová²,

Mareš³

et al. 2016

Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

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Background and Aims. Dysfunction of kidney mitochondria plays a critical role in the pathogenesis of a number of renal diseases. Proteomics represents an untargeted attempt to reveal the remodeling of mitochondrial proteins during disease. Combination of separation methods and mass spectrometry allows identification and quantitative analysis of mitochondrial proteins including protein complexes. The aim of this review is to summarize the methods and applications of proteomics to renal mitochondria. Methods. Using keywords "mitochondria", "kidney", "proteomics", scientific databases (PubMed and Web of knowledge) were searched from 2000 to August 2015 for articles describing methods and applications of proteomics to analysis of mitochondrial proteins in kidney. Included were publications on mitochondrial proteins in kidneys of humans and animal model in health and disease. Results and Conclusion. Proteomics of renal mitochondria has been/is mostly used in diabetes, hypertension, acidosis, nephrotoxicity and renal cancer. Integration of proteomics with other methods for examining protein activity is promising for insight into the role of renal mitochondria in pathological states. Several challenges were identified: selection of appropriate model organism, sensitivity of analytical methods and analysis of mitochondrial proteome in different renal zones/biopsies in the course of various kidney disorders.

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MitoP2, an integrated database on mitochondrial proteins in yeast and man

Cited by 75 publications

References 30 publications

Two small enzyme isoforms mediate mammalian mitochondrial poly(ADP-ribose) glycohydrolase (PARG) activity

Two small enzyme isoforms mediate mammalian mitochondrial poly(ADP-ribose) glycohydrolase (PARG) activity

Relaxation of yeast mitochondrial functions after whole-genome duplication

Proteomic approaches to the study of renal mitochondria

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