Organelle DB: an updated resource of eukaryotic protein localization and function

Wiwatwattana, Nuwee; Landau, Christopher M.; Cope, Greg; Harp, Gabriel; Kumar, Anuj

doi:10.1093/nar/gkl1000

Cited by 31 publications

(23 citation statements)

References 14 publications

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“…Gene ontology (GO) analysis of the associated proteins in the Saccharomyces Genome Database suggested a relative enrichment in cytoplasmic-and plasma membrane-resident proteins across all the conditions (Fig. 2B) (49). We also noted a number of mitochondrial proteins, consistent with an emerging role for that organelle in polyQ-associated processes (50).…”

Section: Identification Of Polyq-interacting Proteins By Lc-ms/msmentioning

confidence: 57%

Ordered Assembly of Heat Shock Proteins, Hsp26, Hsp70, Hsp90, and Hsp104, on Expanded Polyglutamine Fragments Revealed by Chemical Probes

Walter

Smith

Wisén

et al. 2011

Journal of Biological Chemistry

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In Saccharomyces cerevisae, expanded polyglutamine (polyQ) fragments are assembled into discrete cytosolic aggregates in a process regulated by the molecular chaperones Hsp26, Hsp70, Hsp90, and Hsp104. To better understand how the different chaperones might cooperate during polyQ aggregation, we used sequential immunoprecipitations and mass spectrometry to identify proteins associated with either soluble (Q25) or aggregation-prone (Q103) fragments at both early and later times after induction of their expression. We found that Hsp26, Hsp70, Hsp90, and other chaperones interact with Q103, but not Q25, within the first 2 h. Further, Hsp70 and Hsp90 appear to be partially released from Q103 prior to the maturation of the aggregates and before the recruitment of Hsp104. To test the importance of this seemingly ordered process, we used a chemical probe to artificially enhance Hsp70 binding to Q103. This treatment retained both Hsp70 and Hsp90 on the polyQ fragment and, interestingly, limited subsequent exchange for Hsp26 and Hsp104, resulting in incomplete aggregation. Together, these results suggest that partial release of Hsp70 may be an essential step in the continued processing of expanded polyQ fragments in yeast.The heat shock proteins (HSPs) 3 are abundant molecular chaperones that have been shown to be important for maintaining proteostasis under both normal conditions and during times of cellular stress (1-3). Together, these factors play multiple roles in quality control, especially related to polypeptide synthesis, folding, and turnover (4 -7). Moreover, HSPs are emerging as drug targets in cancer, neurodegenerative disorders and other diseases (8, 9). Thus, there is interest in better understanding how they coordinate protein quality control decisions.The major families of HSPs are named based on their approximate kDa molecular weights, including Hsp60, Hsp70, Hsp90,

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Section: Identification Of Polyq-interacting Proteins By Lc-ms/msmentioning

confidence: 57%

Ordered Assembly of Heat Shock Proteins, Hsp26, Hsp70, Hsp90, and Hsp104, on Expanded Polyglutamine Fragments Revealed by Chemical Probes

Walter

Smith

Wisén

et al. 2011

Journal of Biological Chemistry

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“…Several subcellular localization databases focused on proteins have been previously constructed, such as DBSubLoc, Organelle DB, eSLDB, LOCATE, SUBA, LocDB and PSORTdb databases (3,16–21). They had led to a more comprehensive understanding of the biological functions in proteins.…”

Section: Discussion and Future Prospectsmentioning

confidence: 99%

RNALocate: a resource for RNA subcellular localizations

Zhang

Tan

Wang

et al. 2016

Nucleic Acids Research

134

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Increasing evidence has revealed that RNA subcellular localization is a very important feature for deeply understanding RNA's biological functions after being transported into intra- or extra-cellular regions. RNALocate is a web-accessible database that aims to provide a high-quality RNA subcellular localization resource and facilitate future researches on RNA function or structure. The current version of RNALocate documents more than 37 700 manually curated RNA subcellular localization entries with experimental evidence, involving more than 21 800 RNAs with 42 subcellular localizations in 65 species, mainly including Homo sapiens, Mus musculus and Saccharomyces cerevisiae etc. Besides, RNA homology, sequence and interaction data have also been integrated into RNALocate. Users can access these data through online search, browse, blast and visualization tools. In conclusion, RNALocate will be of help in elucidating the entirety of RNA subcellular localization, and developing new prediction methods. The database is available at http://www.rna-society.org/rnalocate/.

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“…5H). Previous studies with GFP-tagged Erg11 derivatives localized Erg11 to the endoplasmic reticulum (38), cytoplasm (35), or granular sites (39).…”

Section: Strains Lacking Dap1mentioning

confidence: 99%

Regulation of Iron Homeostasis Mediated by the Heme-binding Protein Dap1 (Damage Resistance Protein 1) via the P450 Protein Erg11/Cyp51

Craven

Mallory

Hand

2007

Journal of Biological Chemistry

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Fungal infections arise frequently in immunocompromised patients, and sterol synthesis is a primary pathway targeted by antifungal drugs. In particular, the P450 protein Erg11/Cyp51 catalyzes a critical step in ergosterol synthesis, and the azole class of antifungal drugs inhibits Erg11. Dap1 is a heme-binding protein related to cytochrome b 5 that activates Erg11, so that cells lacking Dap1 accumulate the Erg11 substrate and are hypersensitive to Erg11 inhibitors. Heme binding by Dap1 is crucial for its function, and point mutants in its heme-binding domain render Dap1 inactive for sterol biosynthesis and DNA damage resistance. Like Dap1, the human homologue, PGRMC1/Hpr6, also regulates sterol synthesis and DNA damage resistance. In the present study, we demonstrate that the Dap1 heme-1 domain is required for growth under conditions of low iron availability. Loss of Dap1 is suppressed by elevated levels of Erg11 but not by increased heme biosynthesis. Dap1 localizes to punctate cytoplasmic structures that co-fractionate with endosomes, and Dap1 contributes to the integrity of the vacuole. The results suggest that Saccharomyces cerevisiae Dap1 stimulates a P450-catalyzed step in sterol synthesis via a distinct localization from its homologues in Schizosaccharomyces pombe and mammals and that this function regulates iron metabolism.

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Organelle DB: an updated resource of eukaryotic protein localization and function

Cited by 31 publications

References 14 publications

Ordered Assembly of Heat Shock Proteins, Hsp26, Hsp70, Hsp90, and Hsp104, on Expanded Polyglutamine Fragments Revealed by Chemical Probes

Ordered Assembly of Heat Shock Proteins, Hsp26, Hsp70, Hsp90, and Hsp104, on Expanded Polyglutamine Fragments Revealed by Chemical Probes

RNALocate: a resource for RNA subcellular localizations

Regulation of Iron Homeostasis Mediated by the Heme-binding Protein Dap1 (Damage Resistance Protein 1) via the P450 Protein Erg11/Cyp51

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