Abstract
We provide computational protocols to identify chaperone interacting proteins using a combination of both physical (protein–protein) and genetic (gene–gene or epistatic) interaction data derived from the published large-scale proteomic and genomic studies for the budding yeast Saccharomyces cerevisiae. Using these datasets, we discuss bioinformatic analyses that can be employed to build comprehensive high-fidelity chaperone interaction networks. Given that many proteins typically function as complexes in the cell, we highlight various step-wise approaches for combining both the genetic and physical interaction datasets to decipher intra- and inter-connections for distinct chaperone- and non-chaperone-containing complexes in the network. Together, these informatics procedures will aid in identifying protein complexes with distinctive functional specializations in the cell that yield a very broad and diverse set of interactions. The described procedures can also be leveraged to datasets from other eukaryotes, including humans.
Key words
- Chaperone network
- Functional enrichment
- Genetic interactions
- Physical interactions
- Protein complexes
Ashwani Kumar and Kamran Rizzolo are Co-first authors.
Mohan Babu and Walid A. Houry are co-corresponding authors.
This is a preview of subscription content, access via your institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Saibil H (2013) Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 14:630–642
Balchin D, Hayer-Hartl M, Hartl FU (2016) In vivo aspects of protein folding and quality control. Science 353:aac4354
Finka A, Mattoo RU, Goloubinoff P (2016) Experimental milestones in the discovery of molecular chaperones as polypeptide unfolding enzymes. Annu Rev Biochem 85:715–742
Graves PR, Haystead TA (2002) Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 66:39–63
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA (2015) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 15:930–949
Martens L, Vizcaino JA (2017) A golden age for working with public proteomics data. Trends Biochem Sci 42:333–341
Aebersold R, Mann M (2016) Mass-spectrometric exploration of proteome structure and function. Nature 537:347–355
Boone C, Bussey H, Andrews BJ (2007) Exploring genetic interactions and networks with yeast. Nat Rev Genet 8:437–449
Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung YA, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A (2014) Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia Coli. PLoS Genet 10:e1004120
Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M (2016) Conditional epistatic interaction maps reveal global functional rewiring of genome integrity pathways in Escherichia Coli. Cell Rep 14:648–661
Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, CH L, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA (2016) A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165:1493–1506
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA (2017) Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst 4:291–305. e297
Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG (2006) Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet 38:896–903
Yu J, Pacifico S, Liu G, Finley RL Jr (2008) DroID: the drosophila interactions database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9:461
Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M (2015) A map of directional genetic interactions in a metazoan cell. eLife 4:e05464
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C (2004) Global mapping of the yeast genetic interaction network. Science 303:808–813
Zhao R, Davey M, Hsu YC, Kaplanek P, Tong A, Parsons AB, Krogan N, Cagney G, Mai D, Greenblatt J, Boone C, Emili A, Houry WA (2005) Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell 120:715–727
Zhao R, Houry WA (2007) Molecular interaction network of the Hsp90 chaperone system. Adv Exp Med Biol 594:27–36
Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA (2009) An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol 5:275
Larance M, Lamond AI (2015) Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 16:269–280
Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C (2016) A global genetic interaction network maps a wiring diagram of cellular function. Science 353:aaf1420
Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7:1017–1024
Oliver S (2000) Guilt-by-association goes global. Nature 403:601–603
Baryshnikova A (2016) Systematic functional annotation and visualization of biological networks. Cell Syst 2:412–421
Boucher B, Jenna S (2013) Genetic interaction networks: better understand to better predict. Front Genet 4:290
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–643
Wodak SJ, Pu S, Vlasblom J, Seraphin B (2009) Challenges and rewards of interaction proteomics. Mol Cell Proteomics 8:3–18
Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, Chandran S, Punna T, Christopolous C, Wong V, Yu A, Zhong G, Li J, Stagljar I, Conibear E, Wodak SJ, Emili A, Greenblatt JF (2012) Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489:585–589
Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF (2009) Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. Methods Mol Biol 548:187–207
Babu M, Kagan O, Guo H, Greenblatt J, Emili A (2012) Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J Vis Exp 69:e4057
Hart GT, Lee I, Marcotte ER (2007) A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 8:236
Zhang B, Park BH, Karpinets T, Samatova NF (2008) From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 24:979–986
Pu S, Wong J, Turner B, Cho E, Wodak SJ (2009) Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res 37:825–831
Wang J, Li M, Deng Y, Pan Y (2010) Recent advances in clustering methods for protein interaction networks. BMC Genomics 11(Suppl 3):S10
Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575–1584
Loganantharaj R, Cheepala S, Clifford J (2006) Metric for measuring the effectiveness of clustering of DNA microarray expression. BMC Bioinformatics 7(Suppl 2):S5
Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ (2007) Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics 7:944–960
Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806–810
Rutherford SL, Lindquist S (1998) Hsp90 as a capacitor for morphological evolution. Nature 396:336–342
Queitsch C, Sangster TA, Lindquist S (2002) Hsp90 as a capacitor of phenotypic variation. Nature 417:618–624
Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D’Andrea AD, Whitesell L, Lindquist S (2017) HSP90 shapes the consequences of human genetic variation. Cell 168:856–866
Rizzolo K, Huen J, Kumar A, Phanse S, Vlasblom J, Kakihara Y, Zeineddine HA, Minic Z, Snider J, Wang W, Pons C, Seraphim TV, Boczek EE, Alberti S, Costanzo M, Myers CL, Stagljar I, Boone C, Babu M, Houry WA (2017) Features of the chaperone cellular network revealed through systematic interaction mapping. Cell Rep 20:2735–2748
Acknowledgements
K.R. was supported by a Canadian Institutes of Health Research (CIHR) Training Program in Protein Folding and Interaction Dynamics: Principles and Diseases fellowship and by a University of Toronto Fellowship in the Department of Biochemistry. M.B. holds a CIHR New Investigator award (MSH-130178). This work was funded by CIHR grants MOP-125952, RSN- 124512, 132191, and FDN-154318 and MOP-132191 to M.B. and by MOP-93778, MOP-81256, and MOP-130374 to W.A.H.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kumar, A., Rizzolo, K., Zilles, S., Babu, M., Houry, W.A. (2018). Computational Analysis of the Chaperone Interaction Networks. In: Calderwood, S., Prince, T. (eds) Chaperones. Methods in Molecular Biology, vol 1709. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7477-1_20
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7477-1_20
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7476-4
Online ISBN: 978-1-4939-7477-1
eBook Packages: Springer Protocols