Comparative Interactomics for Virus–Human Protein–Protein

DNA viruses versus RNA viruses viruses RNA versus viruses DNA is properly cited. cited. is properly which permits use,distributi underthe terms article This isanopenaccess Sons Ltd. FEBS© 2016The Authors.PublishedbyWiley John & Pressand BioFEBS (2016) Open doi: 10.1002/2211-5463.12167 thisversionandthe between lead todifferences been through the copyediting, typesetting, and proofreading which may pagination process, forpublicati accepted This articlehasbeen genetic material.Animproved to evade during hostimmune systems infections ma adopted Thestrategies reproduction. survival and Viruses are obligatory intracellular pathogens andcompletelyon their hostsfor depend E-mail: salihadur Tel: +902626052120 TURKEY 41400, Gebze/Kocaeli University Technical Gebze Bioengineering Department of * Article type :Research Article Date:16-Nov-2016 Accepted Revised Date:06-Nov-2016 :25-Aug-2016 Received Date Comparative interactomicsfor virus– 1 Accepted Corresponding author Article Computational Systems BiologyGroup, Departme 2 Department ofChemic

[email protected]

Saliha Durmu on and reproduction in any medium on andreproduction in al Engineering, Bo University, Kocaeli, Turkey Turkey Kocaeli, University, understanding of these viral infection mechanisms is only theseviralinfectionmechanismsis only of understanding

ABSTRACT ABSTRACT ş 1,* on and undergone full peer review buthasnot review undergone fullpeer on and andKutluÖ.Ülgen of the Creative Commons Attribution License, CreativeCommonsAttribution of the

human protein–protein interactions: Version of Record. PleaseVersion cite thisarticle as by viruses to exploit host cell processes and and hostcellprocesses toexploit viruses by ğ aziçi University, y differ largely with the type of the viral viral ofthe type the with y largely differ nt of Bioengineering, Gebze Technical Technical Gebze nt ofBioengineering, , provided the original work the original work , provided 2 İ stanbul, Turkey Turkey stanbul, Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted RNA: Ribonucleicacid acid DNA: Deoxyribonucleic InteractionPPI: Protein-Protein PHI: Pathogen-HostInteraction ABBREVIATIONS ViralNext-generation infection drug strategy, antiviral target Keywords: therapeutics. antiviral next-generation informati crucial human proteinsmay provide observedcommon and specific infection mechanisms interms ofviral strategiesattack to ribonucleoproteins and transporter humanprotei virus-targeted Observing Articlespecificcellular as inintracellular well as processes transport and localization withinthe cell. virusespreferentially RNA hand, On theother able toattack cellular bothhuman metabolic and processes during simultaneously infections. ofDNAandR compare theattackstrategies investigated prope thefunctional getinsightstheir humanhost,to intotheinfe netw PHI the current analyzed comparatively In study, decade. last we this the within scale large at available onlysystems became veri Experimentally advantage. viruses toenter intothehostcells manipulate and cellular the totheir own mechanisms understanding thepa possible through of abetter Pathogen-Host Interaction, in Comparative Pathogen-Host fied protein–protein interacti fied protein–protein rties of human proteins inth rties ofhumanproteins proteins as potential antiviral therapeutic targets. The The targets. antiviraltherapeutic as potential proteins NA viruses. We observedthatDNAvirusesare viruses. We NA ns, we propose heterogeneous nuclear nuclear ns, weproposeheterogeneous ction strategies used by these viral groups. We groups. We viral these by used ction strategies orks belonging to DNA and RNA viruses and RNAviruses and DNA belonging to orks on for further design of broad and specific broad andspecific of design on forfurther interact with human proteins functioningin proteins interact withhuman thogen–host interactions (PHIs) thatenable interactions thogen–host teractomics, DNA virus, RNA virus, virus, virus,RNA DNA teractomics, on (PPI) data of pathogen–host ofpathogen–host data on (PPI) e PHI toobserveand networks, Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted hostproteins and pathogen interactions between bymanipulated andexploited pathogenic on cellular essential inthe functions virus on antiviral drughave beenfocused discovery next-generation the on efforts the Therefore, strains. virus resistant the to effective hardly proteins. Thismakestheproblemmoreserious, conventional therapeuti the resistance towards high mutationrate Their reemerging diseases. and ofemerging because beings human the to danger poseever-increasing infections Viral 1. INTRODUCTION HEADING: RUNNING EBV: virus Epstein-Barr ArticleHNRP: Heterogeneous nu BasedAnnotation System KOBAS: Orthology KEGG andGenomes ofGenes KEGG: Kyoto Encyclopedia GO: GeneOntology PHISTO: Pathogen-Host Interaction Search Tool single-stranded RNA Negative-sense ssRNA(-): ssRNA(+): Positive-sense single-stranded RNA RNA dsRNA: Double-stranded RNA ssRNA: Single-stranded DNA dsDNA: Double-stranded DNA ssDNA: Single-stranded ComparativeInteractomics PPIs forVirus-Human clear ribonucleoprotein clear ribonucleoprotein life-cycle [1, 2]. The cellular processes are are processes Thecellular 2]. [1, life-cycle finding host-oriented drug targets, which act targets,finding whichact host-orienteddrug microorganisms throughmainly physical [3]. Therefore, viral PHI networks should be networks shouldbe PHI viral Therefore, [3]. since most of the current antiviral drugs are drugs are antiviral current ofthe most since s enable viruses to easily develop drug s enablevirusestoeasily drug develop cs, whichmainly inhi bit essentialviral Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Acceptedlife have integratedwithin the styles viruses ofviruses hostcells. DNA sequences large DNA resulting proteome, the size and type ofviral genetic materials maygreat have effects onthe only proteins thatusuallygenomes afew encode of to hundreds up encode can which genomes, disable antiviralresponsesofhostimmune strategies tomanipulatehost cell mechanisms tocontrol their ownlife cycles and also to entercells intothe toreplicate, host propagate. assembleand evolved They todevelop have Owing totheir verysmall genome have restricted sizes, lifecapabilities viruses and must genomes. despite having RNA the Retroviruses, replicate intermediates which through DNA using reverse transcriptase group is ofthis An exception translation. before using polymerase positive-sense RNA RNA RNA thatiscompleme carry ssRNA(-) viruses by cell. host the and translated canbedirectly mRNA like is viruses ofssRNA(+) material Article (ssRNA(+)) grouped aspositive-sense further RNA viruseshavetypically ssRNA,butmay repli viruses These (ssDNA). stranded DNA double- contain usually DNA viruses RNA [6]. grouped basedontheirtype Viral familiesare andvirus-sp broad designing crucial for and similaritiesinth differences viruses toreplicate withinthe persist host and for indispensable are that functions andassociated proteins cellular the identify orderto in functi terms ofthe investigated in thoroughly e infection mechanisms used by different viralgroupse infectionmechanismsusedby different is ecific antiviral therapeutics [1,4,5]. cate using DNA-dependent DNA polymerase. DNA polymerase. usingDNA-dependent cate cell during infections. The understanding of the ofthe understanding duringinfections.The cell onal properties of virus- propertiesof onal systems 7, [4, 8]. ComparedtoDNAvirus also containdsRNA.ssRNA virusescanbe also of nucleic acid as ge nucleicacidas of or negative-sense (ssRNA(-)). The genetic The (ssRNA(-)). negative-sense or ntary to mRNA and must be converted to to beconverted ntary mRNAandmust to stranded DNA (dsDNA) and rarely single- and rarely (dsDNA) DNA stranded . Owing andfunctionality tothesize the of viral proteins, RNA viruses have smaller smaller viruseshave RNA viral proteins, netic material, DNA or material,DNAor netic targeted hostproteins, targeted Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted PHIs 19,033 between RNA viruses,covering thecurrent analyzed comparatively Here, we dataset and intermsofcommon specific infect and579humanprot proteins 70viral data between 830 PHI Pichlmair of RNAvirusesthrough data. characteristics infection special analyzing networks interaction protein viruses-human RNA theirprotein interactionswithhuman comparing a behaviors ofbacterial common andspecific is still lacking [2,14].The general focus co of view systems theaforementioned Nevertheless, pr interspecies virus-human of field the that thehigh-throughput the preliminary effortson viewofviralin a systems required tocapture patho-physiologies,more functional a analysis ofvirus-hostmolecular interactions is ArticleDespite the availabilityof detailed structures, models replication ofvirus machineries, and ch generally infection strategies tocause Consequently,[9]. itcanbestatedthat,DNAa i.e. they interact withthe hostproteins usin ofPHIs. networks through RNAviruse complex homologies eukaryo withtheir ha other Onthe cell. replication withinthe viruses tofinely the metabolism exploit ofinfected cells inorder their topromote own witheukaryote-originated encode proteins th from thehoststotheirgenome,throughout tic counterparts, butstillcan tic counterparts, ronic and acute infections, respectively. respectively. acuteinfections, and ronic complex functional domains and enable DNA DNA functionaldomainsandenable complex g protein-binding toRNAviruses motifsspecific experimental PHI data belonging to DNA and belonging PHI toDNAand data experimental nd, RNA virus proteins cannot exhibit such exhibit cannot proteins RNAvirus nd, 1,061viral proteins and 4,943 humanproteins. proteinsand4,943 1,061viral fection mechanismsfection inhostcells. Considering e evolution. Consequently, their genomes can Consequently,e evolution. their genomescan otein interactions has been developing now. now. developing been interactionshas otein ion strategies used by DNA and RNA viruses. viruses. andRNA DNA usedby strategies ion nd RNAviruseshavedeve experimental studies [4, 10-13], onecanstate 10-13], studies[4, experimental [3,15]. Vidalainand et al. (2012) experimentally found 1681 PHI found1681PHI et al.(2012)experimentally s have probably evolved haveprobably s of viral infectionof mechanisms through PHIs mputational analysisPHI of data isonthe nd viral pathogens during infections, by by infections, during nd viralpathogens eins and then comparatively analyzed this analyzed eins andthencomparatively communicate with host cells communicate withhostcells Tangy (2010) reviewed Tangy (2010)reviewed a different strategy, differentstrategy, a loped somedistinct loped Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted us wereobtainedand virus families(Table2) da viruses. Consequently, PHI Similarly,He reverse transcription. through genetic material.exclude were Retroviruses da interspecies interactome filteringits functionality of thetaxonomic using fromPHISTO PHIs downloaded were virus-human The family-based 2.2. Virus-Human PHI Data also tootherma data belonging (www.phisto.org).interface studiesonPH Ongoing pathogen-targe of analysis topological/functional bioi also providesintegrated ex which for all pathogentypes for data PHI It up-to-date the stores [16]. Article Web inthe PHI database comprehensive a lack of Interaction PHISTO Search (Pathogen-Host 2.1. PHISTO: Retrie AWeb-BasedToolfor ANDMETHODS 2. MATERIALS scarce. caution sinc with shouldbeinterpreted analysis pathoge ofviral understanding RNA viruses interms oftheir infection strategies, providing ansystems-level initial Thishuman PPIs study thefi [16]. presents which fromPHISTO obtained were The PHI data ta. 12 families carry DNAand16 ta. 12familiescarry browse option.28viral familiesar ta belonging to 11 DNA virus to11 ta belonging mmalian species ashostorganism. nformatic tools for visualiz nformatic tools nesis through PHIs. However the results drawnfromthis theresults nesis through However PHIs. perimentally-found PPIsperimentally-found with rst comprehensive comparison between DNA and between DNAand rst comprehensive comparison d fromthe RNA families sincereplicate they Tool) was developed by our group by duetothe wasdeveloped our Tool) val andAnalysisof PHI Networks padnaviruses were were padnaviruses ed throughout the study. Two representative ed throughoutTwo representative thestudy. e PHI data for lots of virus familiesarestill virus for lotsof PHI data e ted human proteins through its user-friendly itsuser-friendly through humanproteins ted is a comprehensive database of pathogen- of database is acomprehensive ISTO are for covering experimental PHI ISTO experimental forcovering are families (Table 1)and15RNA families (Table ation of PHI networks and and networks ation ofPHI human are available. PHISTO PHISTO available. human are e covered by the downloaded the downloaded e coveredby families carry RNA as their excluded from the DNA DNA fromthe excluded Gene Ontology (GO) [17] enrichment analys enrichment [17] (GO) Gene Ontology 2.4. Gene OntologyEnrichmentAnalysis Table 3. virus-targeted humanpr numberof The analyzed. RNAvirusestogether bothDNAand targeted by ones the and set) (viruses-targeted viruses RNA and/or DNA by targeted i.e. viruses, all obtain thecommoninfectionstrategies ofviralpa least fourRNAvirusfamilies(4-R virus families(4-DNAviruses-target viralinfections,humanpr andRNA between DNA RNA viruses withrespect totheir interactionsdeeper withhumana proteins.comparison For c set)were viruses-targeted RNA viruses,i.e. only and targeted set), viruses,i.e.not ta targeted set),only DNA viruse viruses (DNA DNA by sets targeted PHI data toanalyzefunctional the properties of A totalof8sets ofhuman prot 2.3. Human Sets Protein Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted AllthreeGOterms(biological correction. calculationBenjamini with hypergeometricand &Hochberg test then false discoveryrate at with ap-valueof that only termsenriched Th [18]. ofCytoscape BiNGOusing plug-in the Article the PHIviral these families 26 for data aregiven in DNA virusandoneforan PHI networks,onefora onstructed toobservethechar eins interacting withviral pathogens were constructed fromthe NA viruses-targetedset)were ed set),aswellhumanpr rgeted byrgeted DNA viruses- RNAviruses(only any not targeted by any DNA viruses (only RNA RNA (only DNA viruses any by not targeted most 0.05 were considered after an enrichment enrichment an after most 0.05wereconsidered s-targeted set), RNA viruses (RNAviruses- viruses set),RNA s-targeted is of the human protein sets was performed wasperformed is ofthehumanproteinsets e significance level was set to0.05meaning wasset level e significance process, molecular function, andcellular process, molecularfunction, virus-targeted human proteins. Firstly, proteins. the virus-targeted human thogens, setsof humanproteinstargetedby (DNA-RNA viruses-targeted set) were also also set)were (DNA-RNA viruses-targeted oteins covered by each set istabulatedin each oteins coveredby Supplementary oteins interacting withat least fourDNA RNA virus,areinFigure 1.Alldetailsof acteristics specific to DNA and specifictoDNAand acteristics used. On theotherhand,to used.On files 1 and 2. files 1and oteins withat interacting

Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted despite some preliminary attempts tomodel networks couldnotbefitted to distri In fact,thedegree human PHI networks. scale-free cases, the most in 1B). Therefore, lots have usually proteins RNAvirus of these All genomes. small very oftheir because networks PHI in roles have proteins viral very few (Figur tosomeextent virus-human PHI network proteins targeting lotsofhumanproteins.Th human prot are as hubnodes.These interactionsviral between the (Fig ofvirus-humannetworks The visualization 3.1. Virus-TargetedHumanProteins Article3. RESULTS sets. protein for thevirus-targeted In method.was thisstudy,correction p-value &Hochberg and Benjamini test hypergeometric uses platform KOBAS process, enrichment basedoninformatio [19] 2.0) (ver. tool, KOBAS pr human ofthe analysis enrichment Pathway 2.5. Pathway Enrichment Analysis setstudied. targeted humanprotein toidentify ha theterms scanned component) were and human proteins. In a PHI network, few proteins may serve proteins may serve few In network, aPHI proteins. and human anyyet, model mostly because oftheir incompleteness [22], eins targeted by lots of pathogen proteins; and pathogen andpathogen by proteins; lotsofpathogen eins targeted the graph properties PHI [10]. of networks behavior couldnotbeobservedinRNA virus- behavior is scale-free behavior is observed in the DNA is behavior is observedintheDNA scale-free otein sets was performed using the Web-based theWeb-based using setswasperformed otein set to 0.05 to obtain enriched human pathways humanpathways to 0.05obtainenriched set bution ofthevirus-humanprotein interaction bution ure 1) provides some insights on the nature of insightsonthenatureof 1)providessome ure of interactions with human proteins (Figure proteins(Figure withhuman interactions of e 1A). On the other hand, inRNAviruses, otherhand, 1A).Onthe e ving significant association witheachvirus- ving association significant n in KEGG pathway database [20]. In the [20]. database pathway n inKEGG 21suchhumanproteins Table 4.Thelistincludes targeted by at least 8viral families total and the targeting virusfamilies, are presented in Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted and viruses-targeted DNA areonly sets protein human these results, analysis GO enrichment presenting thecertaincharacteristics an ofDNA forfi Enriched pathway terms 3.2.2. Pathway Enrichment important tohighlight infectionmechan common the resultsofhumanproteins mechanismsofth infection to more specificity families, 4-DNAviruses-targeted targetedmultiple viral proteins by highly human for the processesGO virus types. Enriched sp toretrieve 5) (Table only virusproteins RNA ofhumanproteins results ofsets tothe given inSupplem setareavailable each humanprotein attacked DNA/RNAviruses. by Article canbeused terms GOprocess The enriched 3.2.1. GO Enrichment 3.2. Functional Analysis the of found in withthenum virus-targeted humanproteins are targeted andconstituting RNAviruses, by the bothDNA common viral targets. Allofthe Ac 2). is shownusing diagram(Figure aVenn human viruses-targeted The distributionof4,943 Supplementary Analysis Results file 3. Human proteins that are highly targeted by viruses, i.e. i.e. viruses, by targeted arehighly that proteins 3.Human file AnalysisResults interacting withbothDNAandRNA interacting ve specific human proteinsets ve specifichuman Virus-Targeted Human Proteins All enriched GO process, f process, GO All enriched set and 4-RNA viruses-targeted set and4-RNA ber of targeting familiescanbe DNA/RNAvirus e corresponding virus types. On the other hand, hand, On theother virustypes. corresponding e and virusproteins DNA with only interacting onsiderable amount of human proteins (1,354) proteins(1,354) amountofhuman onsiderable ecific attack strategies different these of two to pointoutthehuman processes thatare isms shared by the two types of viruses. ofviruses. thetwotypes sharedby isms d RNA viruses attackd RNAviruses strategies. Similar to with corresponding targeting viralfamilies. proteins based on thei proteins basedon entary file 4. Special attention shouldbe entary file4.Special unction and component terms for terms for component unction and arelistedinTables8-10, set (Table 6) may reflect 6)may reflect set(Table viruses (Table 7) are also also (Table7)are viruses r attacking virus types virustypes r attacking investigation. Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted therapeutics. antiviral mayRNA virusesfoundhere leadtothedevelo and DNA of strategies infection special and Thecommon proteins. viral with interacting through theobservatio viruses, comparatively, initialinsightsaims toprovide interactomes Thisstudy 14,24]. conventional solutions[2, interactionnetw protein underlying analysis of Tounderstandthecomple therapeutic targets. mechanisms toid inorder through PHIs, rais diseases infectious against approaches Thede proteins [23]. the instead oftargeting istoinhibitthe interactionsbe approach inhibit infectionswithoutdeveloping re drug indispensable butnotessential hostcells, forpathogens, for their silencingeffectively may Article insteadoftargetin thepathogens, required by proteins host target which emerging are therapeutics antiviral Thenext-generation rapidly. very canmutate which viruses RNA case of the in especially viruses, by developed resistance essential viral enzymes. Unfortunately, this a Most ofthe current antiviral therapeutics act forinhibiting specific viral proteins, e.g. 4. DISCUSSION in are provided results analysis enrichment 10).Pathway (Table viruses-targeted and DNA-RNA 9), (Table vi (Table8),4-DNA only viruses-targeted RNA

Supplementary file 5 for all of 8virus-ta all of 5for file tween these host factors and pathogen proteins, pathogen proteins, and thesehostfactors tween on the infection mechanisms of DNA and RNA and RNA of DNA ontheinfectionmechanisms sistance rapidly [1, 21, 22]. Another alternative Anotheralternative 21,22]. sistance rapidly [1, velopment of these novel strategic therapeutic therapeutic strategic novel ofthese velopment orks may serve crucial insightstodevelopnon- crucial may orks serve thees need forenlightening theinfection pproach has been ineffective because of drug ofdrug because ineffective hasbeen pproach g pathogen proteins. If these host factors are If hostfactorsare pathogen proteins. g these entify host-oriented putative anti-infective x mechanisms of infections, computational mechanismsofinfections, x n of the characteristics of humanproteins ofthecharacteristics n pment of broad and specific next-generation next-generation ofbroad andspecific pment of computational analysis of virus-human ofvirus-human of computationalanalysis ruses-targeted and 4-RNA viruses-targeted viruses-targeted and4-RNA ruses-targeted rgeted human protein sets under proteinsetsunder human rgeted Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted families[see of DNAvirus vi targeted HNRPs,thenumberoftargeting RNA several otherHNRPs,targeted be targetedfive viral by families [see human protein[4 proposed asapotentialantiviral repo HNRPUwas multipleviruses, by targeted pathways relate proteins associatedwith therole cytoplasm. ofmRNAfromthe inthe to nucleus export recruit They also regulatory nuclear RNAsintomaturemRNAsandinregula areRNA-binding ROA2). HNRPs proteins in thehighly human targeted that revealed Our analyses Article 15]. GBLP, andHNRPK[3, astarget proteins werepreviouslyreported multiple viral families, withinthe mostcomprehensive PHI Some data. human ofthese of targeting virusfamilies (Table 4).The list includes the topviral targets which interact with vira with arehighly interacting that proteins for translationa also regulatory proteins membrane proteins fortransportinggenetic viral material across the nuclear membrane,and factorstopromot cell cycle, humantranscription highly viralproteins within thehost.Therefore, As the main viralstrategy, infection all viruses manipulate cellular toproliferate processes 4.1. HighlyTargetedHumanProteins there are six heterogeneous nuc there aresix Supplementary by proteins[see viral proteins, which functionin proteins,which Supplementary list (HNRPK, ROA1, HNRPC, HNRH1, HNRPF, HNRH1,HNRPF, ROA1,HNRPC, list(HNRPK, nd apoptosis [3, 15, 25, 26]. 15,25,26]. We [3, identifiedhuman apoptosis nd d to DNA and RNA metabolism [27, 28]. Being [27, andRNAmetabolism d toDNA file 3],revealing that they play may crucial roles l proteins,sequentially s for multipleviruses,i.e.P53,NPM,ROA2, s for interact with human proteins functioning in in functioning with humanproteins interact e viral genetic material transcription, nuclear nuclear e viralgenetic materialtranscription, ting gene expression. Specifically, they take Specifically,gene they take expression. ting ]. In study, isfoundto ]. HNRPU thepresent rus familiesisfound to behigher thanthat rted as a hotspot of viral infection, and infection,and ahotspotofviral rted as Supplementary file 3]. Our data additionally indicate additionally indicate Ourdata file 3]. lear ribonucleoproteins (HNRPs) (HNRPs) lear ribonucleoproteins processing heterogeneous processing heterogeneous based on thetotalnumberbased files 1-3]. For allvirus- files1-3]. Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Acceptedcellu components ofthe essential Since they are Translation elongationfactors were during biosynthesis witharesponsibilit protein of binding GTP-dependent proteins promotethe astranslationelonga function EF1A3 EF1A1 and life cycleorganism. withinthe host for their potential tobe next-generation antiviral target, because oftheir crucial roles inviral Highly targeted transpor 4). RNA families(Table localizationfor RNA results activity reveal our and infection strategy ofbacteria [32] metabolic processes ADP withmitochondrial ATP across themitochondr is ADT2 activity of transporter transmembrane Articleregulatory tothe nucleus proteins cells of to host antiviralresponse,sincenuclearimportfact transcriptional machinery.Besides, may viruses InteractingIMA1 with enables viruses toenter the nucleus and consequently to use the host’s nuc proteinfor an adapter nuclear importas IMA1 TCPE. (Karyopher IMA1,ADT2, TCPG,and relatedwithin the cell processes are targeted RNAviruses, and i.e. by highly bothDNA prot that reflected also Moreover, ouranalyses drug targets. of family Theprotein in viralRNAprocessing. . Attacking to human metabolic processes was reported as a common as reported was processes metabolic tohuman . Attacking and viruses [15]. Theproteins, and viruses[15]. reported astargets forviru reported activate the antiviral response [3, 29-31]. The The 29-31]. [3, response activate theantiviral lear receptorKPNB1 (Karyopherin beta 1). eins functioning intr HNRPs may HNRPs asantiviral serve host-oriented aminoacyl-tRNA to the A-site of ribosomesaminoacyl-tRNA A-site of tothe y of achieving accuracy of translation [33]. of translation [33]. y accuracy ofachieving responsible for the exchange of cytoplasmic cytoplasmic of exchange the for responsible ors regulate thetrans lar translational machinery, viruses interact interact viruses translationalmachinery, lar interact with IMA1 in order to inhibitthe order to IMA1 in interact with tion factors in protein biosynthesis. EF1A tion factorsinprotein ter proteins should be ter proteinsshouldbe that they are targeted by larger number of of number larger by targeted thatthey are in alpha 2, KPNA2) functions mainlyin alpha2,KPNA2)functions in ial membrane,servin TCPG andTCPE areresponsible ses, in early studies [34-36]. studies[34-36]. ses, inearly ansport and localization port ofinnateimmuneport investigated further investigated g rolesin crucial Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted investigation potentialas fortheir antiviral forserving drug targets. elongation translation factor and localization, ribonucleoproteins,prot mentioned humanproteins; yet. Above- targets drug forthese available is usage therapeutic noantiviral Nevertheless, TBB5, onlyHowever, ADT2, GRP78, P53,andTB found TBB5,TBA1A were P53,TCPG,HS90B, and humanproteins Among highly the targeted apoptosis toassistviru and completion oftranscription cell, apoptosisisinhibited by corresponding tovi response an innateimmune Articlecontro strategically and shouldbe apoptotic celldeath.Apoptosisis avery crucia hand,P53isthefam of translation.Ontheother genes, asatranscripti transcription ofnumerous transcriptionactivity.Both factor ofthese Among highly 15]. the targ strategies [3, Interacting withhuman transcri (Table 7). elongation asthetopbiological co process, translational found We thehostcell. within biosynthesis ofviralproteins with themfor s dissemination [37-39]. ption factors was reported ason was ption factors ral infection. In the early stage of viral life cycle in the host inthe lifecycle viral stage of the early In ral infection. translation of viral genetictranslation ofviral material, viruses try toinduce lled by viruses for a successful viral infection. Apoptosisis infection. viral successful a for viruses lled by proteins are multifunctional. functionsproteins in YBOX1 mmonly andRNAviruses bothDNA by targeted in Table 4, EF1A1, ADT2, TBA1C, GRP78, TBA1C, GRP78, ADT2, Table 4,EF1A1, in eted human proteins, YBOX1 and P53 have andP53have humanproteins, YBOX1 eted ous tumor supressor acting as an activator for for an activator ous tumorsupressoracting as on factor. It also contributes to the regulation totheregulation It alsocontributes on factor. l process during thevira process during l s and transcription factors require further further require factors andtranscription s virus-human protein interactions. After virus-humanproteininteractions.After A1A are approved for commercial drugs. commercial drugs. for approved A1A are eins functioning in intracellular transport transport inintracellular eins functioning as drug targets listed in DrugBank [40]. [40]. inDrugBank listed targets as drug e ofthe main viral infection l infection progress, l infectionprogress, Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Acceptedattacked by multiple RNAvirusfamilies are enriched inspecific processeswithin the cellular For theRNA growth [4]. instead ofcellular biology,transcription orchromosome witha human that DNAvirusestendtotargetcrosstalking It wasreported processes. target cellular to high preference their out 6)pointed (Table viruses Further investigation ofthe enriched processes ofhuman proteins attacked by multiple DNA [4]. infection a successful for RNA processing metabolismandalso that areinvolvedinRNA Itwithin the reported cell(Table that was 5). RNA viruses are related mostly proces to RNA termsen GOprocess in human.Ontheotherhand, mechanisms ofinfectedcells totheir ownadvantage, generallyresulting chronic infections in Article DNAvirusescan Using thisPHI mechanism, be ablecellular toattackand metabo human conclusion tothe may lead 5) viruses (Table te process GO enriched ofthe Our observation 45]. [44, usedasfeat arewidely terms GO andpathway comput verificationof asin aswell 15, 41,42] PHI ne of bioinformatic analysis ofpathogen analyses enrichment GO andpathway Mechanisms Human 4.2. Targeted tworks to understand the attack strategies of pathogens [3, 4, [3, of pathogens strategies attack the tounderstand tworks lic processessimultaneously, during infections. RNA viruses extensively target human proteins human proteins target extensively viruses RNA that DNA viruses have specifically evolved to evolved specifically have DNAviruses that rms for human proteins targeted by only DNA DNA only by targeted forhumanproteins rms ures incomputationalPHI studies ures prediction possible aimofpromo possible viruses, we found that the human proteins found thatthehuman proteins we viruses, protein and RNA transport topromoteviral protein andRNAtransport sing, intracellular transport and localization ationally PHIs predicted finely exploit the cellular and metabolic thecellularandmetabolic exploit finely -targeted host proteins are widely used in usedin arewidely hostproteins -targeted riched in human proteins targeted by only only targetedby riched inhumanproteins proteins linking the cell cycle witheither cycle proteinslinking thecell ting viral replication [43]. Additionally, [43]. Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted itis theotherhand, On PHI 1). (Table data whichconstitute DNA virusfamily Herpesviridae, ca and viral infection (EBV) virus Epstein-Barr only are set protein human viruses-targeted 4-DNA in terms pathway enriched The analyses. enrichmentwith GO provide results parallel related targetedviruses, pathways byRNA only Cellcycle path pathways. of enrichedhuman of strategies different infection RNA viruses only by and viruses DNA by only targeted sets protein for human terms pathway enriched of the investigation A comparative viral proteins. the cellular mechanisms forthese processes andrecruit they hostribosomes fortranslation of th of synthesis, of thelack simply because target humanproteinsfunctioning withinth Articletypes. Basedontheseobservations,wecanstateth includes cellular and processes, metabolic which withinthecurrent viruses both DNAandRNA by targeted proteins human in enriched term process GO top as the elongation translational ineukaryoticgene expression most highly-targeted processistransla human 7).The (Table results strong statistically arevery indicating low, terms GOprocess enriched humanproteins Incase of the material transcription. mechanisms (TableAll viruses need 6). host’stranscriptional machineryfor viral genetic theseviralgroups.Thereisnocommontermintwolists hosts was reported repeatedly hostswasreported targeted by both DNA and RNA viruses, the p-values of the the p-valuesof bothDNAandRNAviruses, targeted by eir own such machineries. All viruses depend on viruses dependon All suchmachineries. eir own tional elongation.Translati way targeted by only DNA virusesandRNA- DNA only by targeted way e processes of gene expression andprotein e processesgene expression of estimated that 15% of all human tumors are human tumors are all that15%of estimated rcinogenesis (Table 9). EBV is a species of of a species is EBV 9). (Table rcinogenesis (Table 8) reveals additional support for the the additional supportfor reveals 8) (Table experimental PHI data. The remaining list The remaining PHI data. experimental can be considered as targets of both virus virus ofboth astargets considered can be at the common viral infection strategy isto nearly half of the DNA viruses-human viruses-human oftheDNA nearly half [46-48]. Here, we presented Here, wepresented [46-48]. onal control of viral onal controlofviral Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open 5: file Supplementary Accepted 4: file Supplementary proteins 3: file Supplementary 2: file Supplementary 1: file Supplementary SUPPLEMENTARY FILES manuscript. the KÜÖprepared and SD thestudy. performed SD thestudy. conceived andKÖÜ SD CONTRIBUTIONS AUTHORS' infectious disesases. id human andhopefully and between pathogens PHIexperimentally-verified da Articlein thenearfuture. pathogen-host systems investigationsfor further ofinfection mechanisms and DNA comparing by pursued networks was In thisstudy, understa an initialsystem-level 5. CONCLUSIONS use hostribos Both viruses (Table 10). ribosom weobtained targets oftwovirustypes, system terms andimmune processing related pathway enrichment analysis viruses-targeted of4-RNA brings the terms set ofprotein i.e. viruses mainlycaused DNA by viruses, Pathway enrichment results for thehuman protein sets GO enrichment results for thehuman protein sets RNA viruses-human PHI data DNA viruses-human PHI data Number of targeting DNA/RNA virus families for each targeted human targeted for each families virus DNA/RNA ofNumber targeting ta willfurtherimproveourunde ome for viral proteinsynthesis. ome forviral nding of viral infection mechanisms through PHI mechanismsthroughnding ofviralinfection PHI Herpesviruses Papillomaviruses and [49].The Ongoing studiesandincreasingOngoing amountsof forward (Table 9). Finally,(Tableforward 9). common forthe RNA viruses, aiming to provide a framework framework a aimingtoprovide RNA viruses, e term enriched with a very small p-value p-value small very a with enriched e term entify novel and effective therapeutics for for therapeutics entify andeffective novel inthe light ofmoreprecise information on rstanding of the interplay oftheinterplay rstanding Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted Article REFERENCES 7. 6. 5. 4. 3. 2. 1.

byretroviruses. exploited Goff SP(2007)Hostfactors 35:235-41. Baltimore D(1971)Expression pathogen proteininteractions. Klein-Seetha J, Kshirsagar M,Carbonell strategies. immune modulatorsperturb thehumanmo Alvisi G,Mu K, A,Kandasamy Pichlmair interacting withviruse Dyer MD,MuraliTM,SobralBW (2008) pathogen-host interactions. Durmu Genome Medicine insightshost interactomics:new andoppor de ChasseyL, B, Meyniel-Schicklin Vonders ş S,ÇakırT,Guthke,R(2015)Areview Nature 487:486-90. 6:115. 6:115. s and other pathogens. otherpathogens. s and Frontiers inMicrobiology Bioinformatics of animalvirusgenomes. raman J (2013) Multitask learning for host- for (2013)Multitasklearning raman J lecular networkby unique commonand 29:i217-26. cher J, AndréP,LotteauJ, Virus- V(2014) cher PLoS Pathogens PLoS lhern O, Sacco R, et al. (2012) Viral Viral (2012) R,etal. lhern O,Sacco tunities for antiviral drug discovery. discovery. tunities forantiviraldrug The landscape of human proteins Thelandscapeofhuman on computational systems biologyon computationalsystems of 6:235. Nature Bacteriological Reviews Bacteriological 5:253-63. 4:e32.

doi:10.1093/bib/bbv059. protein interactionnetworks LahiriPan A, C,RajendiranA,Shanmugh proteincomplexes. HIV-human Global landscapeof Jager S,CimermancicP,GülbahçeN,J reveal interactions host-influenza I, B,Shapira S,Gat-Viks Dricot Shum Hepatitis Cvirusinfection protein network. L, V,Tafforeau Navratil de Chassey B, National AcademyofSciences Epstein-Barr virusandhum L, K,Xing Calderwood MA,Venkatesan Infection Virus-hos FVidalain PO,Tangy (2010) cycle. life virus influenza Y ( S,Kawaoka T,Watanabe Watanabe 12:1134-43. 12:1134-43. Cell HostMicrobe for infectious diseases. diseases. forinfectious 104:7606-11. 104:7606-11. s pathways in H1N1 infection. inH1N1 s pathways an proteininteraction maps. t interactions inRNA viruses. t interactions A (2009) Aphysical andregulatoryA (2009) mapof ohnson JR,McGovernKE,et al. (2012) 2010) Cellular networks involved inthe Cellularnetworksinvolved 2010) Hiet MS, Aublin-Gex A, etal.(2008) MS, Aublin-Gex Hiet Molecular SystemsBiology Molecular 7:427-39. am B (2015)Computational analysisam of Chase MR, Vazquez A, et al.(2007) A,et MR,Vazquez Chase Nature Briefings inBioinformatics 481:365-70. Cell Proceedings ofthe Proceedings 139:1255-67. 4:230. Microbes and Microbes and

7:e1002164. factors. dependency of HIV analysis prediction and D,Tyle Badger Murali TM,Dyer MD, Res information, knowledgeandprinciple: Kanehisa M,GotoS,Sato Acids Res identification annotation and for server 2.0:aweb S, et al. (2011)KOBAS Dong Ding J, Y,Wu J, Xie C,MaoX,Huang 21:3448-9. ontologycat ofgene representation assess over to plugin ACytoscape BiNGO: M(2005) Kuiper K, S,Heymans Maere unification ofbiology. forthe Tool Ontology: Gene (2000) Botstein D BallC,Blake J, Ashburner M, searchtool. pathogen-host interaction Durmu Microbiology pathogens through pathogen-human Durmu 42:D199-205. 42:D199-205. ş ş Tekir S,Çakır T, Ardıç E,Sayılırba TekirS,ÇakırT, ÜlgenInfec KÖ(2012) 39:W316-22. 39:W316-22. 3:46. Nature Y,KawashimaM,Furumichi 25:25-9. egories inbiologicalegories networks. Bioinformatics protein-protein interactions. protein-protein backtometabolism inKEGG. of enriched pathways and diseases. anddiseases. pathways enriched of r BM, Katze MG (2011) Network-based MG(2011)Network-based BM, Katze r ş AS,KonukG,et al.(2013) PHISTO: tion strategies of bacterial andviral tion strategies ofbacterial 29:1357-8. PLoS ComputationalBiology M, Tanabe M (2014) Data, M,TanabeM(2014) Bioinformatics Bioinformatics Nucleic Acids Acids Nucleic Frontiers in Nucleic Nucleic

multifunctional regulatoryroles. incellula ribonucleoproteins (hnRNPs) Chaudhury P,HowePH A,Chander A/B. functions of He Y,SmithR(2009)Nuclear Oncogene basal control complex is differentially ta Thomas M,Massimi P, C,Borg Navarro papillomavirus E2proteins and TBP-associated factors. Carrillo E,GarridoGariglio P(2004) interactions. L Wong (2013)Progress in ZhouJ, H,Jin 72. identifyantimicrobial drug novel targets. (2013)Proteininte Zoraghi NE R,Reiner interactions inthe post-genomic era. Networks ofprotein-protei Durmu Cell MolLife Sci ş Tekir S, Ülgen KÖ (2013) System bi KÖ(2013)System TekirS,Ülgen 24:6222-30. 24:6222-30. Journal of Bioinformatics andComputational Biology Journal ofBioinformatics 66:1239-56. n interactionwithinpat RNA Biotechnolgy Journal Biotechnolgy 16:1449-62. 16:1449-62. rgeted by HPV-16 and HPV-18 E6 proteins.rgeted HPV-16 andHPV-18 by JP, Banks L Banks JP, (2005)ThehScrib/Dlgapico- Current OpinioninMicrobiologyCurrent heterogeneous nuclear ribonucleoproteins ribonucleoproteins nuclear heterogeneous r processes: Focus on hnRNP E1’s E1’s Focus onhnRNP r processes: computationalstudi raction networks as starting points to pointsto starting networksas raction Specific in vitro interaction between Specific invitrointeractionbetween (2010) Heterogeneous nuclear (2010)Heterogeneous ology of pathogen-host interaction: ology ofpathogen-host hogens and pathogen-human hogens andpathogen-human Intervirology 8:85-96. es of host-pathogen es ofhost-pathogen 11:1230001. 47:342-9. 47:342-9. 16:566-

71:6433-44. the 3' Nilevirusgenomic ofWest RNA. stem-loopregion BrintonBlackwell (1997)Translation JL, MA Trends inBiochemSci Andersen GR,NissenP,Nyborg (2003)Elong J Academy ofSciences leve mRNA the at expressed Attardi G(1988)Twodis Houldsworth J, Retrovirology sensitivity toVpx karyopherin by aclassical mediated is SAMHD1 L,G Apolonia Schaller T,PollpeterD, Reticulum/Golgi Membrane. Endoplasmic ontheRough ImportFactors Function Sequestering by Nuclear Co Syndrome Acute Respiratory Severe M,Kopecky-Br Heise B, M,Yount Frieman Traffic se localization nuclear alpha/beta-recognized of Nuclear localization dengue virusnons Pryor Rawlinson SM, MJ, Butcher RE,Ba 8:795-807. 11:29. 85:377-81. MAC 28:434-41. 28:434-41. induced and ubiquitination proteasomal degradation. Journal ofVirology l in adult human liver. adult humanliver. l in oujon C, Malim MH (2014) Nuclear import of oujon C,MalimMH(2014)Nuclearimportof tinct genes forADP/A tructural protein 5 through itsimportin 5through tructural protein ronavirus ORF6 Antagonizes STAT1 ORF6ronavirus Antagonizes rton CL, al.(2007) rton TA,et Waterhouse omberg SA, Palese P, Baric RS (2007) Baric P, SA,Palese omberg quences isintegraltoviralinfection. elongation factor-1 alpha interacts with alpha interacts elongation factor-1 81(18):9812-24. 81(18):9812-24. ation factorsinproteinbiosynthesis. α / β 1 dependent pathway and confers 1 dependentpathway confers and Proceedings of the National ofthe Proceedings Journal ofVirology TP translocase are are TP translocase

anthracis,Francisella tularensis, and Yersinia pestis. (2010) Thehuman-bacterial etal. J, D, Bassaganya-Riera, Shattuck CG, M,Rivera Dufford C, Dyer MD,Neff and exploration. Woolsey (2006)DrugBank: a J C,GuoAC,Shrivastava DS,Knox Wishart B Cells. VirusCanSimulta Epstein-Barr Oncogene of Pratt ZL,Sugden J, Zhang B (2012)Th WorldGastroenterol J BlumBaumert HE(2007)He T, Fischer R, infection. G (1999)Apoptosis: Everett H,McFadden 4VirusRNA. Dengue Elongation Factor-1 M,Villegas-Sepúlvedaa De Nova-Ocampoa Journal ofVirology Immunodefici Human withthe Specifically Luban Cimarelli A, J(1999)Translation J Virol Trends inMicrobiology 86(8):4380-93. 86(8):4380-93. Nucleic Acids Res Acids Nucleic 73:5388-401. α , La, and PTB Interact with the 3 the with Interact PTB La, and , 13(36):4865-72. 13(36):4865-72. Virology Virology pathogen protein interacti pathogen protein 295:337-47. comprehensive resource for comprehensive 7(4):160-5. 7(4):160-5. 34:D668-72. 34:D668-72. e Latent MembraneProtein1(LMP1) e neously Induce and Inhibit Apoptosis in patitis Cvirusinfection andapoptosis. patitis ency Virus Type 1 Gag Polyprotein. 1Gag Type Virus ency S, Hassanali M, Stothard P, Chang Z, P,Chang Hassanali M,Stothard S, N, delAngel RM(2002)Translation Elongation Factor 1-Alpha Interacts Elongation Interacts Factor 1-Alpha an innateimmuneresponsetovirus PLoS ONE on networks of Bacillus on networks ′ Untranslated Region of Region of Untranslated in silico drug discovery in silicodrug discovery 5:e12089. Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted Article 48. 47. 46. 45. 44. 43. 42.

factors. factors. (2012)Thedependence Nagy PD,Pogany J Nature ReviewsMicrobiology I D,Mohr Viralsubversionof Walsh (2011) Eukaryotes. MG( Gale M,TanSL, Katze pathogen-host protein-pr Durmu Nourani E,KhunjushF, Microbiology proteinin transferring host-pathogen S, CarbonellJ, Kshirsagar M,Schleker PPIs. HIV-1-human sources topredict Ray based BandyopadhyayS (2016)ANMF S, doi:10.1145/1854776.1854785. Conference onBioinformaticsandComputational Biology pathways.human signal transduction ( J Klein-Seetharaman I,Singh O, Tastan Nature Reviews Microbiology Nature Reviews Microbiology andMolecu Microbiology 6:36. otein interactions. 2000) TranslationalControlof 9:860-75. ş S(2015)Computational appr teractions knowledge 10:137-49. lar Biology Reviews lar Biology BMC Bioinformatics Proceedings of theFirst ACMInternationalProceedings Klein-Seetharaman J 2010) Comparison of virus interactions with ofvirusinteractions 2010) Comparison Frontiers inMicrobiology of viral RNA replication on co-opted host RNAreplication onco-opted of viral the hostproteinsynthesis machinery. the approach for integrating multiple data 64(2):239-80. 64(2):239-80. tonew tasks. , NiagaraFalls, NY, 17-24. NY, 17-24. , NiagaraFalls, 17:121. Viral Gene Expression in ViralGeneExpression oaches for prediction of forprediction oaches (2015) Techniques for for (2015) Techniques 6:94. Frontiers inFrontiers TOTAL (dsDNA)Siphoviridae (dsDNA) Poxviridae (dsDNA) Polyomaviridae (ssDNA) Parvoviridae (dsDNA) Papillomaviridae (dsDNA) Myoviridae (dsDNA) Herpesviridae (ssDNA) Circoviridae (dsDNA) Baculoviridae (dsDNA) Asfarviridae (dsDNA) Adenoviridae (Genetic material) family DNA virus

Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted ArticleFigure 2. protein interactionnetwork. interaction network. proteins. human are and bluenodes Figure 1. FIGURE LEGENDS

49.

etiology of human disease. etiology ofhuman disease. carci (2000)Viral Butel JS The number of humanproteinstargeted numberof The Virus-Human PHI networks obtained from obtained PHI networks Virus-Human

B) Table 1. Influenza AvirusStrain WSN/1933/ # of species# of Contents of DNA viruses-human PHI data data ContentsofDNAviruses-humanPHI 10 17 61 10 5 2 2 1 1 1 9 3

Carcinogenesis nogenesis: Revela nogenesis:

A) # of strains# of TABLES Human Herpesvirus 4 – Human protein-protein protein-protein Human 4– Herpesvirus Human 106 19 20 35 13 3 6 2 3 2 1 2

by DNA viruses and/or RNA viruses viruses virusesand/orRNA by DNA 21(3):405-26. 21(3):405-26.

PHISTO. Red nodes are viral proteins viral are nodes PHISTO. Red # of PHIs of # tion of molecular mechanisms and mechanisms ofmolecular tion 10,051 4,033 4,836 444 356 305 60 3 4 4 1 5

TS61 (H1N1)–Humanprotein-

# of pathogen# of proteins 640 391 78 18 91 43 3 5 3 2 1 5

# of human # of proteins 3,658 1,731 2,288 343 261 235 56 3 3 3 1 4

TOTAL Togaviridae ((+)ssRNA) Rhabdoviridae ((-)ssRNA) Reoviridae (dsRNA) Picornaviridae ((+) ssRNA) Paramyxoviridae ((-) ssRNA) Orthomyxoviridae ((-) ssRNA) Hepeviridae ((+)ssRNA) Flaviviridae ((+)ssRNA) ssRNA) ((-) Filoviridae Coronaviridae ((+) ssRNA) Bunyaviridae ((-)ssRNA) Bornaviridae ((-) ssRNA) Birnaviridae (dsRNA) ssRNA) ((+) Arteriviridae ssRNA) ((-) Arenaviridae (Genetic material) family RNA virus Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open

Accepted Article DNA-RNA viruses-targeted 4-RNA viruses-targeted 4-DNA viruses-targeted viruses-targeted RNA Only viruses-targeted DNA Only RNA viruses-targeted DNA viruses-targeted Set Human Protein Viruses-targeted

Table 2.

Table 3.

# of species# of

ContentsofRNA viruses-humanPHI data 69 14 4 5 4 4 3 1 8 3 4 9 1 1 2 6

Virus-targeted human proteinsets Virus-targeted human 4 ormore DNA 4 ormore RNAvirus families Both DNA and RNAviruses DNAand Both

DNA and/or RNAviruses DNA and/or # of strains# of Only DNA viruses DNA Only Targeting viruses Only RNA viruses RNA Only DNA viruses RNA viruses 158 22 49 30 10 7 2 4 4 1 1 2 6 5 7 8

virus families

# of PHIs of #

5,681 1,704 8,982 904 172 182 115 10 34 68 17 27 63

3 1 1

# of human of proteins # of pathogen# of proteins 105 191 421 42 16 11 11 11 4,943 1,354 1,285 2,304 2,639 3,658 9 2 6 1 1 3 6 6

84 60

# of human# of proteins 1,623 2,639 650 876 151 140 104 29 68 14 22 57 6 2 1 1

protein subunit beta-2-like 1 -GBLP Guaninenucleotide-binding NPM - Nucleophosmin P53 - Cellular tumor antigen p53 -TBB5 Tubulin beta chain protein GRP78 -kDa 78 glucose-regulated ribonucleoprotein A1 -ROA1 Heterogeneous nuclear -TBA1C alpha-1C Tubulin chain 2 translocase -ADT2 ADP/ATP IMA1 - Importin subunit alpha-1 EF1A1 - Elongation factor 1-alpha 1 element-binding protein 1 YBOX1 - Nuclease-sensitive ribonucleoprotein K -HNRPK Heterogeneous nuclear Human Protein Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted Article

Table 4.

Herpesviridae, Papillomaviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Highlyhuman proteins targeted Papillomaviridae, Parvoviridae, Papillomaviridae, Parvoviridae, Adenoviridae, Herpesviridae, Adenoviridae, Herpesviridae, Adenoviridae, Herpesviridae, Adenoviridae, Herpesviridae, Papillomaviridae, Poxviridae Papillomaviridae, Poxviridae Papillomaviridae, Poxviridae Asfarviridae, Herpesviridae, Polyomaviridae, Poxviridae Polyomaviridae, Poxviridae Herpesviridae, Poxviridae DNA virus families DNA virus Polyomaviridae Poxviridae Poxviridae Poxviridae Poxviridae Poxviridae Targeting

Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae, Coronaviridae, Orthomyxoviridae, Arteriviridae, Orthomyxoviridae, Flaviviridae, Orthomyxoviridae, Flaviviridae, Orthomyxoviridae, Flaviviridae, Orthomyxoviridae, Orthomyxoviridae, Togaviridae Filoviridae, Orthomyxoviridae, Paramyxoviridae, Togaviridae Paramyxoviridae, Paramyxoviridae, Togaviridae Paramyxoviridae, Paramyxoviridae, Togaviridae Paramyxoviridae, Togaviridae Paramyxoviridae, Paramyxoviridae, Reoviridae Arteriviridae, Coronaviridae, Arenaviridae, Bunyaviridae, Rhabdoviridae, Togaviridae Bunyaviridae, Flaviviridae, Arteriviridae, Flaviviridae, Bunyaviridae, Filoviridae, Bunyaviridae, Filoviridae, Arteriviridae, Filoviridae, Filoviridae, Flaviviridae, Filoviridae, Flaviviridae, Reoviridae, Togaviridae Reoviridae, Reoviridae, Togaviridae Reoviridae, Reoviridae, Togaviridae Reoviridae, Reoviridae,Togaviridae RNA virus families RNA virus Paramyxoviridae Flaviviridae, Flaviviridae, Targeting

ribonucleoproteins A2/B1 -ROA2 Heterogeneous nuclear ribonucleoprotein F HNRPF -nuclear Heterogeneous -TBA1A alpha-1A Tubulin chain ribonucleoprotein H nuclear -HNRH1 Heterogeneous 90-beta HS90B -Heat shock protein HSP epsilon -TCPE T-complex protein 1 subunit ribonucleoproteins C1/C2 -HNRPC Heterogeneous nuclear 1-alpha-like 3 EF1A3 - Putative elongation factor gamma -TCPG T-complex protein 1 subunit

Herpesviridae, Papillomaviridae, Papillomaviridae, Herpesviridae, Papillomaviridae, Herpesviridae, Herpesviridae, Papillomaviridae Herpesviridae, Papillomaviridae Adenoviridae, Herpesviridae, Adenoviridae, Herpesviridae Herpesviridae, Poxviridae Herpesviridae, Poxviridae Herpesviridae, Poxviridae Papillomaviridae Poxviridae Poxviridae

Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae, Orthomyxoviridae, Paramyxoviridae Orthomyxoviridae, Paramyxoviridae Paramyxoviridae, Rhabdoviridae, Arteriviridae, Orthomyxoviridae, Flaviviridae, Orthomyxoviridae, Flaviviridae, Orthomyxoviridae, Filoviridae, Orthomyxoviridae, Filoviridae, Orthomyxoviridae, Paramyxoviridae, Togaviridae Paramyxoviridae, Paramyxoviridae, Togaviridae Paramyxoviridae, Paramyxoviridae, Reoviridae Paramyxoviridae, Reoviridae Arenaviridae, Bunyaviridae, Arenaviridae, Bunyaviridae, Arenaviridae, Bunyaviridae, Arteriviridae, Bunyaviridae, Arteriviridae, Bunyaviridae, Bunyaviridae, Filoviridae, Bunyaviridae, Filoviridae, Arteriviridae, Filoviridae, Filoviridae, Flaviviridae, Filoviridae, Flaviviridae, Togaviridae Reoviridae Reoviridae

Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open positive regulation of apoptosis and nucleic acid metabolic process nucleobase, nucleoside, nucleotide regulation of cell cycle regulation of molecular function macromolecule modification organisms interspecies interaction between cell cycle protein modification process organelle organization modification post-translational protein cellular protein metabolic process primary metabolic process metabolic process cellular componentorganization macromolecule metabolic process process positive regulation of biological positive regulation of cellular process cellular metabolic process process cellular macromolecule metabolic cellular process set DNAviruses-targeted only Enriched GO Process Terms in

Accepted Article Table 5.

Top 20 enriched GO process terms in only DNA viruses-targeted and only RNA termsin only DNAviruses-targeted GOprocess Top20enriched

viruses-targeted human protein sets humanprotein viruses-targeted

1.06E-08 1.05E-08 9.08E-09 8.70E-09 3.28E-09 7.65E-10 3.30E-10 3.30E-10 1.88E-10 5.25E-11 4.14E-12 1.92E-13 1.26E-13 1.99E-14 1.34E-15 4.49E-16 1.47E-18 4.61E-19 2.86E-19 4.94E-26 p-value

nucleic acidmetabolic process RNA localization mRNA processing cellular metabolic process and nucleic acid metabolic process nucleobase, nucleoside, nucleotide mRNA metabolic process RNA metabolic process RNA splicing RNA processing cellular process gene expression set RNAviruses-targeted only Enriched GO Process Terms in macromolecule localization mRNA transport metabolic process and nucleic acid transport nucleobase, nucleoside, nucleotide metabolic process cellular nitrogen compound cellular componentorganization establishment of RNA localization RNA transport nucleic acidtransport

3.25E-07 7.77E-08 4.45E-08 2.63E-08 1.25E-08 1.07E-08 2.81E-09 2.68E-09 2.68E-09 9.57E-11 4.75E-14 2.53E-15 1.39E-06 7.69E-07 7.33E-07 4.02E-07 3.25E-07 8.10E-08 8.10E-08 8.10E-08 p-value

cellular process protein localization in nucleus regulationviral of transcription morphology orphysiology modification by hostof symbiont nuclear transport nucleocytoplasmic transport nuclear import protein import intonucleus morphogenesis anatomical structure formation involved in transcription modulation by hostof symbiont organism involved insymbiotic interaction modulation oftranscriptionotherin modulation by hostof viral transcription positive regulation of cellular process multi-organism process positive regulation of biological process interspecies interaction betweenorganisms set 4-DNA viruses-targeted in ProcessTerms GO Enriched vasculature development positive regulation of viral reproduction blood vessel development regulation of protein modification process

targeted human protein sets targeted humanprotein

6.42E-04 4.51E-04 4.12E-04 2.82E-04 1.59E-04 1.59E-04 1.59E-04 3.77E-05 2.50E-05 2.25E-06 1.53E-08 1.07E-03 1.07E-03 1.05E-03 1.04E-03 8.59E-04 7.63E-04 6.42E-04 5.50E-04 5.50E-04 p-value

DNA viruses-targeted and 4-RNAviruses- and DNA viruses-targeted RNA splicing macromolecular complex subunit protein folding chromatin assembly ordisassembly macromolecular complex assembly DNA packaging nucleosome organization assembly complex protein-DNA chromatin assembly nucleosome assembly subunit organization cellular macromolecular complex assembly cellular macromolecular complex response to unfolded protein unfolded to response translational elongation process cellular macromolecule metabolic cellular componentbiogenesis cellular componentassembly gene expression change DNA conformation cellular process organization in 4-RNA viruses-targeted set set 4-RNAviruses-targeted in ProcessTerms GO Enriched

3.42E-10 9.83E-11 9.59E-07 6.99E-08 4.66E-08 4.52E-08 3.33E-08 2.78E-08 2.89E-09 2.89E-09 2.18E-09 1.78E-09 1.25E-06 9.59E-07 5.46E-07 3.93E-07 1.43E-07 7.12E-08 6.99E-08 6.99E-08 p-value

AcceptedNotch signaling pathway Small cell lung cancer pathway signaling TNF p53 signaling pathway Viral carcinogenesis Huntington's disease Oxidative phosphorylation Cell cycle set DNAviruses-targeted only Enriched Pathway Terms in Article Table 8. Top 20 enriched GO process termsin DNA- GOprocess Top20enriched Enriched pathway terms in only DNA inonly Enrichedpathway DNA terms

OPoesTr p-value GO Process Term metabolic process intracellular transport cellular macromolecular complex subunit organization cellular componentassembly cellular macromolecular complex assembly primary metabolic process macromolecular complex subunit organization macromolecular complex assembly cellular componentbiogenesis macromolecule biosynthetic process cellular protein metabolic process cellular macromolecule biosynthetic process cellular metabolic process macromolecule metabolic process cellular process interspecies interaction betweenorganisms gene expression translation cellular macromolecule metabolic process translational elongation

targeted human protein sets targeted humanprotein

3.80E-02 3.80E-02 3.49E-02 2.59E-02 2.23E-02 1.09E-02 1.04E-02 2.55E-04 p-value

Ribosome biogenesis in eukaryotes Aminoacyl-tRNA biosynthesis Pathogenic Escherichia coli infection mRNA surveillance pathway Spliceosome RNA transport set RNA viruses-targeted Enriched Pathway Terms inonly

viruses-targeted and only RNA viruses- andonly viruses-targeted

RNA viruses-targeted humanproteinset RNA viruses-targeted

2.32E-29 1.64E-29 1.95E-31 4.07E-32 7.66E-33 4.86E-34 4.41E-34 8.78E-39 6.46E-42 4.86E-43 6.88E-46 4.62E-46 2.28E-46 1.21E-51 3.15E-62 3.67E-26 7.41E-27 7.64E-28 7.17E-29 7.09E-29

3.05E-02 2.16E-02 1.41E-02 5.36E-04 6.43E-08 1.18E-11 p-value

Accepted Article Table 9. Enriched pathway terms in4-DNAviruse Enrichedpathway terms

4.96E-03 1.06E-03 p-value human proteinsets

Phagosome Legionellosis Spliceosome Antigen processing and presentation Protein processing inendoplasmic reticulum Ribosome Pathogenic Escherichia coli infection Alcoholism Systemic lupus erythematosus viruses-targeted set 4-RNA in Terms Pathway Enriched s-targeted and 4-RNA viruses-targeted viruses-targeted and4-RNA s-targeted

5.20E-03 1.94E-03 1.69E-04 2.52E-02 2.04E-02 7.74E-03 1.14E-03 1.74E-05 1.79E-06 p-value

Sons Ltd. FEBS© 2016TheAuthors.Published byWiley John & Pressand BioFEBS (2016) Open Accepted Article Table 10. Enriched pathway termsinDNA-RNA Enrichedpathway Ribosome Pathway Term Chronic myeloid leukemia Alcoholism Measles C Hepatitis mRNA surveillance pathway B Hepatitis Small cell lung cancer Toxoplasmosis Influenza A Pathogenic Escherichia coli infection Systemic lupus erythematosus RNA transport Herpes simplex infection Viral carcinogenesis Spliceosome Protein processing inendoplasmic reticulum Proteasome Epstein-Barr virus infection

viruses targeted human protein set protein viruses targeted human

1.23E-02 1.23E-02 9.56E-03 4.82E-03 1.26E-04 5.69E-05 3.04E-06 8.68E-07 4.81E-08 1.23E-11 1.23E-11 1.58E-22 4.95E-02 4.13E-02 1.93E-02 1.82E-02 1.78E-02 1.76E-02 1.46E-02 p-value

r ess and Joh ess and n Wiley&