title: Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components.
abstract: The highly conserved yeast R2TP complex, consisting of Rvb1, Rvb2, Pih1, and Tah1, participates in diverse cellular processes ranging from assembly of protein complexes to apoptosis. Rvb1 and Rvb2 are closely related proteins belonging to the AAA+ superfamily and are essential for cell survival. Although Rvbs have been shown to be associated with various protein complexes including the Ino80 and Swr1chromatin remodeling complexes, we performed a systematic quantitative proteomic analysis of their associated proteins and identified two additional complexes that associate with Rvb1 and Rvb2: the chaperonin-containing T-complex and the 19S regulatory particle of the proteasome complex. We also analyzed Rvb1 and Rvb2 purified from yeast strains devoid of PIH1 and TAH1. These analyses revealed that both Rvb1 and Rvb2 still associated with Hsp90 and were highly enriched with RNA polymerase II complex components. Our analyses also revealed that both Rvb1 and Rvb2 were recruited to the Ino80 and Swr1 chromatin remodeling complexes even in the absence of Pih1 and Tah1 proteins. Using further biochemical analysis, we showed that Rvb1 and Rvb2 directly interacted with Hsp90 as well as with the RNA polymerase II complex. RNA-Seq analysis of the deletion strains compared with the wild-type strains revealed an up-regulation of ribosome biogenesis and ribonucleoprotein complex biogenesis genes, down-regulation of response to abiotic stimulus genes, and down-regulation of response to temperature stimulus genes. A Gene Ontology analysis of the 80 proteins whose protein associations were altered in the PIH1 or TAH1 deletion strains found ribonucleoprotein complex proteins to be the most enriched category. This suggests an important function of the R2TP complex in ribonucleoprotein complex biogenesis at both the proteomic and genomic levels. Finally, these results demonstrate that deletion network analyses can provide novel insights into cellular systems.
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Mahadevan
authors.initials: M
authors.lastname: Lakshminarasimhan
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Gina
authors.initials: G
authors.lastname: Boanca
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Charles A S
authors.initials: CA
authors.lastname: Banks
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Gaye L
authors.initials: GL
authors.lastname: Hattem
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Ana E
authors.initials: AE
authors.lastname: Gabriel
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Brad D
authors.initials: BD
authors.lastname: Groppe
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Christine
authors.initials: C
authors.lastname: Smoyer
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Kate E
authors.initials: KE
authors.lastname: Malanowski
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Allison
authors.initials: A
authors.lastname: Peak
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and.
authors.forename: Laurence
authors.initials: L
authors.lastname: Florens
authors.affiliation: From the ‡Stowers Institute for Medical Research, Kansas City, Missouri 64110 and §Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160 mpw@stowers.org.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Washburn
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D004265:DNA Helicases / Q000378:metabolism*; D017353:Gene Deletion; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D018832:Molecular Chaperones / Q000235:genetics / Q000378:metabolism; D046912:Multiprotein Complexes / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D018832:Molecular Chaperones; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; C497702:PIH1 protein, S cerevisiae; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; C571197:Tah1 protein, S cerevisiae; D014157:Transcription Factors; D000251:Adenosine Triphosphatases; C428198:RVB1 protein, S cerevisiae; C428199:RVB2 protein, S cerevisiae; D004265:DNA Helicases
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