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Dive into the research topics where Viktor Deineko is active.

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Featured researches published by Viktor Deineko.


Bioinformatics | 2015

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; Ashkan Golshani; Jack Greenblatt; Walid A. Houry; Andrew Emili; Quaid Morris; Gary D. Bader; Mohan Babu

MOTIVATION The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli. RESULTS We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses. CONTACT [email protected]; [email protected] SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.


Cell Reports | 2016

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli

Ashwani Kumar; Natalia Beloglazova; Cedoljub Bundalovic-Torma; Sadhna Phanse; Viktor Deineko; Alla Gagarinova; Gabriel Musso; James Vlasblom; Sofia Lemak; Mohsen Hooshyar; Zoran Minic; Omar Wagih; Roberto Mosca; Patrick Aloy; Ashkan Golshani; John Parkinson; Andrew Emili; Alexander F. Yakunin; Mohan Babu

As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response.


Molecular Systems Biology | 2017

Systematic protein-protein interaction mapping for clinically relevant human GPCRs

Kate Sokolina; Saranya Kittanakom; Jamie Snider; Max Kotlyar; Pascal Maurice; Jorge Gandía; Abla Benleulmi-Chaachoua; Kenjiro Tadagaki; Atsuro Oishi; Victoria Wong; Ramy H. Malty; Viktor Deineko; Hiroyuki Aoki; Shahreen Amin; Zhong Yao; Xavier Morató; David Otasek; Hiroyuki Kobayashi; Javier A. Menendez; Daniel Auerbach; Stephane Angers; Nataša Pržulj; Michel Bouvier; Mohan Babu; Francisco Ciruela; Ralf Jockers; Igor Jurisica; Igor Stagljar

G‐protein‐coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. To obtain a global view of GPCR‐mediated signaling and to identify novel components of their pathways, we used a modified membrane yeast two‐hybrid (MYTH) approach and identified interacting partners for 48 selected full‐length human ligand‐unoccupied GPCRs in their native membrane environment. The resulting GPCR interactome connects 686 proteins by 987 unique interactions, including 299 membrane proteins involved in a diverse range of cellular functions. To demonstrate the biological relevance of the GPCR interactome, we validated novel interactions of the GPR37, serotonin 5‐HT4d, and adenosine ADORA2A receptors. Our data represent the first large‐scale interactome mapping for human GPCRs and provide a valuable resource for the analysis of signaling pathways involving this druggable family of integral membrane proteins.


Molecular Biology of the Cell | 2015

Rab5-family guanine nucleotide exchange factors bind retromer and promote its recruitment to endosomes

Björn D. M. Bean; Michael Davey; Jamie Snider; Matthew Jessulat; Viktor Deineko; Matthew Tinney; Igor Stagljar; Mohan Babu; Elizabeth Conibear

The retromer complex regulates vesicle transport at endosomes. Different members of the VPS9 domain–containing Rab5-family guanine nucleotide exchange factors interact with the yeast retromer complex and mediate its endosomal localization.


Journal of Proteome Research | 2015

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships.

Ke Jin; Gabriel Musso; James Vlasblom; Matthew Jessulat; Viktor Deineko; Jacopo Negroni; Roberto Mosca; Ramy H. Malty; Diem-Hang Nguyen-Tran; Hiroyuki Aoki; Zoran Minic; Tanya Freywald; Sadhna Phanse; Qian Xiang; Andrew Freywald; Patrick Aloy; Zhaolei Zhang; Mohan Babu

Although detailed, focused, and mechanistic analyses of associations among mitochondrial proteins (MPs) have identified their importance in varied biological processes, a systematic understanding of how MPs function in concert both with one another and with extra-mitochondrial proteins remains incomplete. Consequently, many questions regarding the role of mitochondrial dysfunction in the development of human disease remain unanswered. To address this, we compiled all existing mitochondrial physical interaction data for over 1200 experimentally defined yeast MPs and, through bioinformatic analysis, identified hundreds of heteromeric MP complexes having extensive associations both within and outside the mitochondria. We provide support for these complexes through structure prediction analysis, morphological comparisons of deletion strains, and protein co-immunoprecipitation. The integration of these MP complexes with reported genetic interaction data reveals substantial crosstalk between MPs and non-MPs and identifies novel factors in endoplasmic reticulum-mitochondrial organization, membrane structure, and mitochondrial lipid homeostasis. More than one-third of these MP complexes are conserved in humans, with many containing members linked to clinical pathologies, enabling us to identify genes with putative disease function through guilt-by-association. Although still remaining incomplete, existing mitochondrial interaction data suggests that the relevant molecular machinery is modular, yet highly integrated with non-mitochondrial processes.


Journal of Molecular Biology | 2015

A Comprehensive Membrane Interactome Mapping of Sho1p Reveals Fps1p as a Novel Key Player in the Regulation of the HOG Pathway in S. cerevisiae.

Mandy H. Y. Lam; Jamie Snider; Monique Rehal; Victoria Wong; Farzaneh Aboualizadeh; Luka Drecun; Olivia Wong; Bellal Jubran; Meirui Li; Mehrab Ali; Matthew Jessulat; Viktor Deineko; Rachel R. Miller; Mid Eum Lee; Hay-Oak Park; Alan R. Davidson; Mohan Babu; Igor Stagljar

Sho1p, an integral membrane protein, plays a vital role in the high-osmolarity glycerol (HOG) mitogen-activated protein kinase pathway in the yeast Saccharomyces cerevisiae. Activated under conditions of high osmotic stress, it interacts with other HOG pathway proteins to mediate cell signaling events, ensuring that yeast cells can adapt and remain viable. In an attempt to further understand how the function of Sho1p is regulated through its protein-protein interactions (PPIs), we identified 49 unique Sho1p PPIs through the use of membrane yeast two-hybrid (MYTH), an assay specifically suited to identify PPIs of full-length integral membrane proteins in their native membrane environment. Secondary validation by literature search, or two complementary PPI assays, confirmed 80% of these interactions, resulting in a high-quality Sho1p interactome. This set of putative PPIs included both previously characterized interactors, along with a large subset of interactors that have not been previously identified as binding to Sho1p. The SH3 domain of Sho1p was found to be important for binding to many of these interactors. One particular novel interactor of interest is the glycerol transporter Fps1p, which was shown to require the SH3 domain of Sho1p for binding via its N-terminal soluble regulatory domain. Furthermore, we found that Fps1p is involved in the positive regulation of Sho1p function and plays a role in the phosphorylation of the downstream kinase Hog1p. This study represents the largest membrane interactome analysis of Sho1p to date and complements past studies on the HOG pathway by increasing our understanding of Sho1p regulation.


Molecular and Cellular Biology | 2015

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.

Matthew Jessulat; Ramy H. Malty; Diem-Hang Nguyen-Tran; Viktor Deineko; Hiroyuki Aoki; James Vlasblom; Katayoun Omidi; Ke Jin; Zoran Minic; Mohsen Hooshyar; Daniel Burnside; Bahram Samanfar; Sadhna Phanse; Tanya Freywald; Bhanu Prasad; Zhaolei Zhang; Franco J. Vizeacoumar; Nevan J. Krogan; Andrew Freywald; Ashkan Golshani; Mohan Babu

ABSTRACT The nonhomologous end-joining (NHEJ) pathway is essential for the preservation of genome integrity, as it efficiently repairs DNA double-strand breaks (DSBs). Previous biochemical and genetic investigations have indicated that, despite the importance of this pathway, the entire complement of genes regulating NHEJ remains unknown. To address this, we employed a plasmid-based NHEJ DNA repair screen in budding yeast (Saccharomyces cerevisiae) using 369 putative nonessential DNA repair-related components as queries. Among the newly identified genes associated with NHEJ deficiency upon disruption are two spindle assembly checkpoint kinases, Bub1 and Bub2. Both observation of resulting phenotypes and chromatin immunoprecipitation demonstrated that Bub1 and -2, either alone or in combination with cell cycle regulators, are recruited near the DSB, where phosphorylated Rad53 or H2A accumulates. Large-scale proteomic analysis of Bub kinases phosphorylated in response to DNA damage identified previously unknown kinase substrates on Tel1 S/T-Q sites. Moreover, Bub1 NHEJ function appears to be conserved in mammalian cells. 53BP1, which influences DSB repair by NHEJ, colocalizes with human BUB1 and is recruited to the break sites. Thus, while Bub is not a core component of NHEJ machinery, our data support its dual role in mitotic exit and promotion of NHEJ repair in yeast and mammals.


G3: Genes, Genomes, Genetics | 2016

Novel Interactome of Saccharomyces cerevisiae Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH) Screen

Ednalise Santiago; Pearl Akamine; Jamie Snider; Victoria Wong; Matthew Jessulat; Viktor Deineko; Alla Gagarinova; Hiroyuki Aoki; Zoran Minic; Sadhna Phanse; Andrea San Antonio; Luis A. Cubano; Brian C. Rymond; Mohan Babu; Igor Stagljar; José R. Rodríguez-Medina

Nonmuscle myosin type II (Myo1p) is required for cytokinesis in the budding yeast Saccharomyces cerevisiae. Loss of Myo1p activity has been associated with growth abnormalities and enhanced sensitivity to osmotic stress, making it an appealing antifungal therapeutic target. The Myo1p tail-only domain was previously reported to have functional activity equivalent to the full-length Myo1p whereas the head-only domain did not. Since Myo1p tail-only constructs are biologically active, the tail domain must have additional functions beyond its previously described role in myosin dimerization or trimerization. The identification of new Myo1p-interacting proteins may shed light on the other functions of the Myo1p tail domain. To identify novel Myo1p-interacting proteins, and determine if Myo1p can serve as a scaffold to recruit proteins to the bud neck during cytokinesis, we used the integrated split-ubiquitin membrane yeast two-hybrid (iMYTH) system. Myo1p was iMYTH-tagged at its C-terminus, and screened against both cDNA and genomic prey libraries to identify interacting proteins. Control experiments showed that the Myo1p-bait construct was appropriately expressed, and that the protein colocalized to the yeast bud neck. Thirty novel Myo1p-interacting proteins were identified by iMYTH. Eight proteins were confirmed by coprecipitation (Ape2, Bzz1, Fba1, Pdi1, Rpl5, Tah11, and Trx2) or mass spectrometry (AP-MS) (Abp1). The novel Myo1p-interacting proteins identified come from a range of different processes, including cellular organization and protein synthesis. Actin assembly/disassembly factors such as the SH3 domain protein Bzz1 and the actin-binding protein Abp1 represent likely Myo1p interactions during cytokinesis.


Nature Biotechnology | 2017

Global landscape of cell envelope protein complexes in Escherichia coli

Mohan Babu; Cedoljub Bundalovic-Torma; Charles Calmettes; Sadhna Phanse; Qingzhou Zhang; Yue Jiang; Zoran Minic; Sun Young Kim; Jitender Mehla; Alla Gagarinova; Irina A. Rodionova; Ashwani Kumar; Hongbo Guo; Olga Kagan; Oxana Pogoutse; Hiroyuki Aoki; Viktor Deineko; J. Harry Caufield; Erik Holtzapple; Zhongge Zhang; Ake Vastermark; Yogee Pandya; Christine Chieh-Lin Lai; Majida El Bakkouri; Yogesh Hooda; Megha Shah; Dan Burnside; Mohsen Hooshyar; James Vlasblom; Sessandra V. Rajagopala


Cell Reports | 2016

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

Alla Gagarinova; Geordie Stewart; Bahram Samanfar; Sadhna Phanse; Carl A. White; Hiroyuki Aoki; Viktor Deineko; Natalia Beloglazova; Alexander F. Yakunin; Ashkan Golshani; Eric D. Brown; Mohan Babu; Andrew Emili

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