Systematic analysis of bypass suppression of essential genes

• DOI: 10.15252/msb.20209828
• Publication Date: 2020-09-17T08:20:36Z
• Authors: Jolanda van Leeuwen; Carles Pons; Guihong Tan; Zi Yang Wang; Jing Hou; Jochen Weile; Marinella Gebbia; Wendy Liang; Ermira Shuteriqi; Zhijian Li; Maykel Lopes; Matej Ušaj; Andreia Dos Santo...; Natascha van Lies...; Chad L Myers; Frederick P Roth; Patrick Aloy; Brenda J Andrews; Charles Boone
• Keywords: genetic interactions; 0301 basic medicine; Medicine (General); 0303 health sciences; Genes, Essential; QH301-705.5; compensatory evolution; Genes, Fungal; Articles; Saccharomyces cerevisiae; Aneuploidy; Aneuploidy; Evolution, Molecular; Gene Deletion; Gene Duplication; Gene Regulatory Networks; Genes, Essential; Genes, Fungal; Genes, Suppressor; Multiprotein Complexes/metabolism; Saccharomyces cerevisiae/genetics; Suppression, Genetic; compensatory evolution; gene essentiality; genetic interactions; genetic networks; genetic suppression; Evolution, Molecular; 03 medical and health sciences; R5-920; Suppression, Genetic; gene essentiality; genetic networks; Gene Duplication; Multiprotein Complexes; genetic suppression; Gene Regulatory Networks; Biology (General); Genes, Suppressor; Gene Deletion

Article17 September 2020Open Access Transparent process Systematic analysis of bypass suppression essential genes Jolanda van Leeuwen Corresponding Author [email protected] orcid.org/0000-0003-3991-518X Center for Integrative Genomics, Bâtiment Génopode, University Lausanne, Switzerland Donnelly Centre Cellular and Biomolecular Research, Toronto, ON, Canada Search more papers by this author Carles Pons Institute Research in Biomedicine (IRB Barcelona), The Barcelona Science Technology, Barcelona, Spain Guihong Tan Jason Zi Wang Department Molecular Genetics, Jing Hou Jochen Weile orcid.org/0000-0003-1628-9390 Lunenfeld-Tanenbaum Institute, Sinai Health System, Marinella Gebbia Wendy Liang Ermira Shuteriqi Zhijian Li Maykel Lopes Matej Ušaj Andreia Dos Santos Natascha Lieshout Chad L Myers Computer Engineering, Minnesota-Twin Cities, Minneapolis, MN, USA Frederick P Roth orcid.org/0000-0002-6628-649X Science, Patrick Aloy Institució Catalana de Recerca i Estudis Avançats (ICREA), Brenda J Andrews orcid.org/0000-0001-6427-6493 Charles Boone orcid.org/0000-0002-3542-6760 Information *,1,2,‡, Pons3,‡, Tan2, Wang2,4, Hou2, Weile2,4,5, Gebbia2,5, Liang2, Shuteriqi2, Li2, Lopes1, Ušaj2, Lieshout2,5, Myers6, Roth2,4,5,7, Aloy3,8, *,2,4 1Center 2Donnelly 3Institute 4Department 5Lunenfeld-Tanenbaum 6Department 7Department 8Institució ‡These authors contributed equally to work *Corresponding author. Tel: [phone]; E-mail: [phone]; Systems Biology (2020)16:e9828https://doi.org/10.15252/msb.20209828 PDFDownload PDF article text main figures. Peer ReviewDownload a summary the editorial decision including letters, reviewer comments responses feedback. ToolsAdd favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract Essential tend be highly conserved across eukaryotes, but, some cases, their critical roles can bypassed through genetic rewiring. From systematic 728 different yeast genes, we discovered that 124 (17%) were dispensable genes. Through whole-genome sequencing detailed analysis, investigated interactions genome alterations underlying suppression. Dispensable often had paralogs, enriched encoding membrane-associated proteins, depleted members protein complexes. Functionally related frequently drove interactions. These gene properties predictive dispensability specific suppressors among hundreds on aneuploid chromosomes. Our findings identify yeast's core set reveal are from human cells, correlating with display cell line-specific essentiality Cancer Dependency Map (DepMap) project. Synopsis A identifies Whole-genome is used show distinct predict cells. Bypass strong functional connection gene, which suppressor generally only suppressed single mechanism, aneuploidies mutations involve both loss-of-function gain-of-function alleles. list 805 defined either absolutely required viability or complex mechanisms. Introduction Genetic suppression, its simplest form, occurs when mutation one overcomes mutant phenotype associated another (Botstein, 2015). general principles type interaction key our understanding genotype-to-phenotype relationship. Frequently, effect dependent background it occurs, complicates identification complete sets causal variants phenotypes, many common diseases (Nadeau, 2001; Harper et al, In particular, mechanisms driving relevant architecture evolution. also resilience healthy people carrying penetrant disease may novel strategies therapeutic intervention (Riazuddin 2000; Chen 2016b). Mapping interactions, model organisms provides powerful approach dissecting function pathway connectivity defining elucidate relationships (Costanzo 2016; 2017; Fang 2019). High-throughput studies derived synthetic array (SGA) budding yeast, Saccharomyces cerevisiae, have identified thousands negative positive fitness defect double less severe, respectively, than expected combining mutants 2010, 2016). SGA mutations, deletion alleles nonessential temperature-sensitive (TS) reduced function. general, rich information, identifying together control functions, whereas indirect connections However, most extreme form within same (Baryshnikova 2010b; Van provide queries analysis. S. was deleting copy each ~ 6,000 individually diploid then testing haploid offspring (Giaever 2002). total, 18% (~ 1,100) under standard, nutrient-rich growth conditions. Although play 2002; Costanzo 2016), sometimes lead rewiring cellular processes fundamental requirement otherwise (Dowell 2010; Sanchez Spontaneous isolated selecting faster growing large populations cells compromised an (Van 2016) (Liu 2015; 2016a). Here, describe construction collection strains, allele gene. We use test 70% revealing rendered rewiring, discover Results Global context-dependent To systematically developed generating This method relied "query" deleted but viable because presence TS carried plasmid (Appendix Fig S1A, Materials Methods). construct these PCR-amplified available strains cotransformed PCR product linearized selection cassette into strain heterozygous corresponding resulting assembled sporulated, progeny selected using present contained 1,179 query unique all genes), 329 represented multiple (Dataset EV1). For strain, 100–150 million incubated at range temperatures close restrictive temperature allele, 4–6 independent experiments case. While divide slowly expand population, majority will not able grow rapidly conditions, apart those acquire spontaneous mutation, colony. isolation ensures relatively few genomic facilitates nucleotide polymorphisms (SNPs) sequencing. Cells subsequently transferred medium against assess absence (Fig 1A). Loss confirmed several secondary assays (see Ultimately, total 380 could EV2). Figure 1. Properties A. Strategy isolating B. number newly plotted (1 experiment = ˜ 25 cells). Shown 1,000 random permutations experimental results computational fit data. Note four per permutations, while median five performed. C, D. Enrichment tested (C) annotation biological class (D) various gene- protein-level properties. Fisher's exact Mann–Whitney U-tests performed determine statistical significance results. E. Dispensability complex, subunits encoded shown, subdivided dispensability. F. nuclear pore chromatin remodeling RSC (Hodges shown. Subunits color-coded according dispensability, color scheme as (E). SEC13 encodes subunit included figure Sec13's role coat II (Copic 2012). Download PowerPoint context previous work, 60 (48%) been described previously, 36 (29%) previously interaction, additional 28 known remains unknown EV3). Thirty literature, assay eight published study differing S288c system; 18 screen characterized detail; clearly missed due differences environmental conditions slight changes between laboratories. whether larger numbers would allowed us rare potentially compared experiments, 1B). showed unlikely substantial note cannot easily achieved mutation. conclude minimum, 17% such translation degradation rarely found set, involved nuclear–cytoplasmic transport, signaling, cycle progression, polarity morphogenesis, secretory sorting 1C). Previous analyses revealed distinguish them relative depletion enrichment members, tendency strongly expressed higher coexpression degree (i.e., share similar expression patterns other genes) (Jeong Giaever Carlson 2006; Michaut 2011; Woods 2013; Qin 2018). agreement survey 2015), tended behave like they (i) paralogs; lower degree; (iii) components complexes 1D). proteins. Thus, possess properties, Most belong well-defined (Michaut 2011), allowing investigate modules. Of 149 least two 105 70%) composed exclusively indispensable none tolerated EV4, 1E). part machinery, proteasome, exosome, initiation factors, consistent degradation, RNA processing, 1C E). contrast, 11 complexes, bypassed. subunits, spanned variety mRNA transport (signal recognition particle TREX complex), signaling (TOR 2), transcriptional regulation (RNA polymerase I upstream activating cofactor 2 RENT complex). Notably, subset partially (15 subunits) U4/U6.U5 triple small ribonucleoprotein (25 subunits). displayed complex. example, cytoplasmic ribosomal paralogs submodule dispensable. instance, lining inside pore, mainly specificity, (Onischenko Weis, Liu structural 1F). Similarly, loss actin-related proteins activity (Szerlong 2008), Finally, further classified EV4), bypassed, overlapped so observed directly particular confirmation strains. three nonsynonymous (Datasets EV5 EV6). sequenced, 188 (49%) content, EV7). complement data, high-resolution SGA-based mapping region (Jorgensen 2002), focusing 89 mild did carry EV2 EV7, 47 locus consisting 20 EV8); however, 39 suffered low spore and/or limited sporulation, identifiable locus. Candidate predicted based on: candidate gene; (ii) location genetically mapped locus; reoccurrence isolates mutant; (iv) chromosomes below. All 283 validated crosses complementation S1B, Dataset EV2, (79%) assays. 141 259 (Figs 3A, 22% reported (15%; EV3) hypomorphic (partial loss-of-function) (7%) 2. Network interactionsBypass arrows point Nodes colored grouped gene(s). Gray nodes indicate poorly characterized, black highlight functions figure. Complex involving nodes. 3. fraction suppressor, co-occurring suppressors, unable divided t