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Global analysis of protein localization in budding yeast

Author

Listed:
  • Won-Ki Huh

    (Department of Biochemistry and Biophysics)

  • James V. Falvo

    (Department of Biochemistry and Biophysics)

  • Luke C. Gerke

    (Department of Biochemistry and Biophysics)

  • Adam S. Carroll

    (Department of Biochemistry and Biophysics)

  • Russell W. Howson

    (Department of Biochemistry and Biophysics)

  • Jonathan S. Weissman

    (Department of Biochemistry and Biophysics
    Department of Cellular and Molecular Pharmacology)

  • Erin K. O'Shea

    (Department of Biochemistry and Biophysics)

Abstract

A fundamental goal of cell biology is to define the functions of proteins in the context of compartments that organize them in the cellular environment. Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously unlocalized proteins. Analysis of this high-resolution, high-coverage localization data set in the context of transcriptional, genetic, and protein–protein interaction data helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.

Suggested Citation

  • Won-Ki Huh & James V. Falvo & Luke C. Gerke & Adam S. Carroll & Russell W. Howson & Jonathan S. Weissman & Erin K. O'Shea, 2003. "Global analysis of protein localization in budding yeast," Nature, Nature, vol. 425(6959), pages 686-691, October.
    • Handle: RePEc:nat:nature:v:425:y:2003:i:6959:d:10.1038_nature02026
    DOI: 10.1038/nature02026
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    Cited by:

    1. Oliver M Crook & Aikaterini Geladaki & Daniel J H Nightingale & Owen L Vennard & Kathryn S Lilley & Laurent Gatto & Paul D W Kirk, 2020. "A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection," PLOS Computational Biology, Public Library of Science, vol. 16(11), pages 1-21, November.
    2. Stefan A. Hoffmann & Yizhi Cai, 2024. "Engineering stringent genetic biocontainment of yeast with a protein stability switch," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Xiaomei Wu & Erli Pang & Kui Lin & Zhen-Ming Pei, 2013. "Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
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    7. Julia P. Schessner & Vincent Albrecht & Alexandra K. Davies & Pavel Sinitcyn & Georg H. H. Borner, 2023. "Deep and fast label-free Dynamic Organellar Mapping," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    8. Yosuke Ito & Yuhei Chadani & Tatsuya Niwa & Ayako Yamakawa & Kodai Machida & Hiroaki Imataka & Hideki Taguchi, 2022. "Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    9. Louis-François Handfield & Yolanda T Chong & Jibril Simmons & Brenda J Andrews & Alan M Moses, 2013. "Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins," PLOS Computational Biology, Public Library of Science, vol. 9(6), pages 1-19, June.
    10. Nebojsa Jukic & Alma P. Perrino & Frédéric Humbert & Aurélien Roux & Simon Scheuring, 2022. "Snf7 spirals sense and alter membrane curvature," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Nicola M. Moloney & Konstantin Barylyuk & Eelco Tromer & Oliver M. Crook & Lisa M. Breckels & Kathryn S. Lilley & Ross F. Waller & Paula MacGregor, 2023. "Mapping diversity in African trypanosomes using high resolution spatial proteomics," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Michelle Lindström & Lihua Chen & Shan Jiang & Dan Zhang & Yuan Gao & Ju Zheng & Xinxin Hao & Xiaoxue Yang & Arpitha Kabbinale & Johannes Thoma & Lisa C. Metzger & Deyuan Y. Zhang & Xuefeng Zhu & Huis, 2022. "Lsm7 phase-separated condensates trigger stress granule formation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    13. Jian Cui & Jinghua Liu & Yuhua Li & Tieliu Shi, 2011. "Integrative Identification of Arabidopsis Mitochondrial Proteome and Its Function Exploitation through Protein Interaction Network," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-16, January.
    14. Alex N Nguyen Ba & Bob Strome & Jun Jie Hua & Jonathan Desmond & Isabelle Gagnon-Arsenault & Eric L Weiss & Christian R Landry & Alan M Moses, 2014. "Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-15, December.
    15. Arthur Fischbach & Angela Johns & Kara L. Schneider & Xinxin Hao & Peter Tessarz & Thomas Nyström, 2023. "Artificial Hsp104-mediated systems for re-localizing protein aggregates," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    16. Lit-Hsin Loo & Danai Laksameethanasan & Yi-Ling Tung, 2014. "Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-17, March.
    17. Md. Abdulla Al Mamun & Wei Cao & Shugo Nakamura & Jun-ichi Maruyama, 2023. "Large-scale identification of genes involved in septal pore plugging in multicellular fungi," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Rory M Donovan & Jose-Juan Tapia & Devin P Sullivan & James R Faeder & Robert F Murphy & Markus Dittrich & Daniel M Zuckerman, 2016. "Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories," PLOS Computational Biology, Public Library of Science, vol. 12(2), pages 1-25, February.
    19. Jian Qiu & William Stafford Noble, 2008. "Predicting Co-Complexed Protein Pairs from Heterogeneous Data," PLOS Computational Biology, Public Library of Science, vol. 4(4), pages 1-10, April.
    20. Sunny Sharma & Jun Yang & Ewa Grudzien-Nogalska & Jessica Shivas & Kelvin Y. Kwan & Megerditch Kiledjian, 2022. "Xrn1 is a deNADding enzyme modulating mitochondrial NAD-capped RNA," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    21. Joke J F A van Vugt & Martijn de Jager & Magdalena Murawska & Alexander Brehm & John van Noort & Colin Logie, 2009. "Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-14, July.
    22. Chung-Chi Liao & Yi-Sen Wang & Wen-Chieh Pi & Chun-Hsiung Wang & Yi-Min Wu & Wei-Yi Chen & Kuo-Chiang Hsia, 2023. "Structural convergence endows nuclear transport receptor Kap114p with a transcriptional repressor function toward TATA-binding protein," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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