The LIFEdb database in 2006

Mehrle, Alexander; Rosenfelder, Heiko; Schupp, Ingo; Val, Coral del; Arlt, Dorit; Hahne, Florian; Bechtel, Stephanie; Simpson, Jeremy C.; Hofmann, Oliver; Hide, Winston; Glatting, Karl-Heinz; Huber, Wolfgang; Pepperkok, Rainer; Poustka, Annemarie; Wiemann, Stefan

doi:10.1093/nar/gkj139

Cited by 36 publications

(29 citation statements)

References 14 publications

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“…Tagging of endogenous proteins, which has been applied successfully to the yeast proteome ( 46, 57 ), has been extended to mouse but is not yet a high-throughput method ( 82 ). Large-scale efforts to visualize tagged exogenous proteins in mammals include the ongoing lifeDB project (http://www.lifedb.de) ( 66 ) and the completed MitoCarta project (http://www.broadinstitute.org/pubs/MitoCarta) ( 83 ). Currently, there are a total of 321 human proteins and 166 mouse mitochondrial proteins evidenced through microscopy, according to the MitoMiner database ( 97 ).…”

Section: Defining the Mitochondrial Proteomementioning

confidence: 99%

The Mitochondrial Proteome and Human Disease

Calvo

Mootha

2010

Annu. Rev. Genom. Hum. Genet.

524

404

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For nearly three decades, the sequence of the human mitochondrial genome (mtDNA) has provided a molecular framework for understanding maternally inherited diseases. However, the vast majority of human mitochondrial disorders are caused by nuclear defects, which is not surprising since the mtDNA encodes only 13 proteins. Advances in genomics, mass spectrometry, and computation have only recently made it possible to systematically identify the complement of over 1,000 proteins that comprise the mammalian mitochondrial proteome. Here, we review recent progress in characterizing the mitochondrial proteome and highlight insights into its complexity, tissue heterogeneity, evolutionary origins, and biochemical versatility. We then discuss how this proteome is being used to discover the genetic basis of respiratory chain disorders as well as to expand our definition of mitochondrial disease. Finally, we explore future prospects and challenges for using the mitochondrial proteome as a foundation for systems analysis of the organelle.

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Section: Defining the Mitochondrial Proteomementioning

confidence: 99%

The Mitochondrial Proteome and Human Disease

Calvo

Mootha

2010

Annu. Rev. Genom. Hum. Genet.

524

404

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“…So far systematic studies of subcellular localization of proteins have been performed either with cellular fractionation (2) or fluorescence microscopy (3,4). The most commonly used approach in the latter case is based on transfection of cells with cDNA clones fused to a fluorescent reporter protein, like green fluorescent protein.…”

Section: Molecular and Cellular Proteomics 7:499 -508 2008mentioning

confidence: 99%

“…Although numerous experiments have shown the usefulness of this approach (3,4), recent studies have indicated that green fluorescent protein can induce translocation to the nucleus causing artifactual localization results (5).…”

Section: Molecular and Cellular Proteomics 7:499 -508 2008mentioning

confidence: 99%

Toward a Confocal Subcellular Atlas of the Human Proteome

Barbe

Lundberg

Oksvold

et al. 2008

Molecular & Cellular Proteomics

130

112

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Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.

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“…Vacuole membrane protein 1 has been predicted to be a seven transmembrane protein (Hirokawa et al, 1998;Figure 2a) and the overexpressed human protein was reported to localize to the ER and Golgi apparatus (Starkuviene et al, 2004;Mehrle et al, 2006). The overexpressed rat protein was shown to induce intracellular vacuole formation with Vmp1 integrated into the membrane of these vacuoles (Dusetti et al, 2002).…”

mentioning

confidence: 99%

Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells

et al. 2007

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Vacuole membrane protein 1 (Vmp1) is described as a cancer-relevant cell cycle modulator, but the function of this protein and its mode of action in tumor progression are still unknown. In this study, we show that the VMP1 mRNA level is significantly reduced in kidney cancer metastases as compared to primary tumors. Further, VMP1 expression is also decreased in the invasive breast cancer cell lines HCC1954 and MDA-MB-231 as compared to the non-invasive cell lines MCF-12A, T-47D and MCF-7. We show for the first time that Vmp1 is a plasma membrane protein and an essential component of initial cell-cell contacts and tight junction formation. It interacts with the tight junction protein Zonula Occludens-1 and colocalizes in spots between neighboring HEK293 cells. Downregulation of VMP1 by RNAi results in loss of cell adherence, and increases the invasion capacity of the non-invasive kidney cancer cell line Caki-2. In conclusion, our findings establish Vmp1 to be a novel cell-cell adhesion protein and that its expression level determines the invasion and metastatic potential of cancer cells.

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The LIFEdb database in 2006

Cited by 36 publications

References 14 publications

The Mitochondrial Proteome and Human Disease

The Mitochondrial Proteome and Human Disease

Toward a Confocal Subcellular Atlas of the Human Proteome

Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells

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