Quantitative analysis of protein interaction network dynamics in yeast.
Albi Celaj,Albi Celaj,Ulrich Schlecht,Justin D. Smith,Weihong Xu,Sundari Suresh,Molly Miranda,Ana Aparicio,Michael Proctor,Ronald W. Davis,Frederick P. Roth,Robert P. St.Onge +11 more
TLDR
A DNA‐barcode‐based multiplexed protein interaction assay in Saccharomyces cerevisiae is used to measure in vivo abundance of binary protein complexes under 14 environments and the value of this resource is illustrated in revealing mechanisms of network dynamics.Abstract:
Many cellular functions are mediated by protein–protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment‐dependent protein complex dynamics, we used a DNA‐barcode‐based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments. Many binary complexes (55%) were environment dependent, especially those involving transmembrane transporters. We observed many concerted changes around highly connected proteins, and overall network dynamics suggested that “concerted” protein‐centered changes are prevalent. Under a diauxic shift in carbon source from glucose to ethanol, a mass‐action‐based model using relative mRNA levels explained an estimated 47% of the observed variance in binary complex abundance and predicted the direction of concerted binary complex changes with 88% accuracy. Thus, we provide a resource of yeast protein interaction measurements across diverse environments and illustrate the value of this resource in revealing mechanisms of network dynamics.read more
Citations
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Mass-spectrometry-based draft of the Arabidopsis proteome.
Julia Mergner,Martin Frejno,Markus List,Michael Papacek,Xia Chen,Ajeet Chaudhary,Patroklos Samaras,Sandra Richter,Hiromasa Shikata,Hiromasa Shikata,Maxim Messerer,Daniel Lang,Stefan Altmann,Philipp Cyprys,Daniel P Zolg,Toby Mathieson,Marcus Bantscheff,Rashmi R. Hazarika,Tobias Schmidt,Corinna Dawid,Andreas Dunkel,Thomas Hofmann,Stefanie Sprunck,Pascal Falter-Braun,Frank Johannes,Klaus F. X. Mayer,Gerd Jürgens,Mathias Wilhelm,Jan Baumbach,Erwin Grill,Kay Schneitz,Claus Schwechheimer,Bernhard Kuster +32 more
TL;DR: A quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana provides a valuable resource for plant research.
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Molecular networks in Network Medicine: Development and applications.
Edwin K. Silverman,Harald H.H.W. Schmidt,Eleni Anastasiadou,Lucia Altucci,Marco Angelini,Lina Badimon,Jean-Luc Balligand,Giuditta Benincasa,Giovambattista Capasso,Federica Conte,Antonella Di Costanzo,Lorenzo Farina,Giulia Fiscon,Laurent Gatto,Michele Gentili,Joseph Loscalzo,Cinzia Marchese,Claudio Napoli,Paola Paci,Manuela Petti,John Quackenbush,John Quackenbush,Paolo Tieri,Davide Viggiano,Gemma Vilahur,Kimberly Glass,Kimberly Glass,Jan Baumbach,Jan Baumbach +28 more
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Doxorubicin induces an extensive transcriptional and metabolic rewiring in yeast cells
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Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks *
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Journal ArticleDOI
An atlas of protein-protein interactions across mouse tissues.
Michael A. Skinnider,Nichollas E. Scott,Nichollas E. Scott,Anna Prudova,Craig H. Kerr,Nikolay Stoynov,R. Greg Stacey,Queenie W.T. Chan,David G Rattray,Jörg Gsponer,Leonard J. Foster +10 more
TL;DR: The authors developed a quantitative proteomic approach combining protein correlation profiling with stable isotope labeling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues.
References
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TL;DR: T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
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