http://www.diva-portal.org This is the published version of a paper published in PROTEOMES. Citation for the original published paper (version of record): Sobhy, H. (2016) A Review of Functional Motifs Utilized by Viruses. PROTEOMES, 4(1): 3 http://dx.doi.org/10.3390/proteomes4010003 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-124204 proteomes Review A Review of Functional Motifs Utilized by Viruses Haitham Sobhy Received: 22 October 2015; Accepted: 13 January 2016; Published: 21 January 2016 Academic Editor: Jacek R. Wisniewski Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; [email protected] or [email protected]; Tel.: +46-90-785-67-81 Abstract: Short linear motifs (SLiM) are short peptides that facilitate protein function and protein-protein interactions. Viruses utilize these motifs to enter into the host, interact with cellular proteins, or egress from host cells. Studying functional motifs may help to predict protein characteristics, interactions, or the putative cellular role of a protein. In virology, it may reveal aspects of the virus tropism and help find antiviral therapeutics. This review highlights the recent understanding of functional motifs utilized by viruses. Special attention was paid to the function of proteins harboring these motifs, and viruses encoding these proteins. The review highlights motifs involved in (i) immune response and post-translational modifications (e.g., ubiquitylation, SUMOylation or ISGylation); (ii) virus-host cell interactions, including virus attachment, entry, fusion, egress and nuclear trafficking; (iii) virulence and antiviral activities; (iv) virion structure; and (v) low-complexity regions (LCRs) or motifs enriched with residues (Xaa-rich motifs). Keywords: clathrin endocytosis; low-complexity repeats; ubiquitylation; agnoprotein; APOBEC; pentraxin; PDZ domain; retinoblastoma; inhibitor of apoptosis (IAP); transposition 1. Introduction Interactions between viral and cellular proteins are required for virus entry, replication, or egress from the cell. These interactions are facilitated by peptide sequences, so-called domains or motifs [1,2]. These sequences could be either (i) short linear motifs (SLiM), 3–11 residues, e.g., RGD; (ii) structural motifs or domains, about 30 residues, e.g., tetratricopeptide repeat (TPR), zinc finger or ankyrin; or (iii) they may contain a repeated residue(s) (e.g., Leu-rich, SR-rich, AR-rich or PEST-rich motifs). The consensus motif follows the PROSITE pattern [3]. The consensus is formed of a regular expression pattern, e.g., Px(2)[ED]. In the pattern, a single-letter amino acid abbreviation is indicated. The alternative (degenerated) residues in a position are bracketed, while “x” letter denotes any residue in the position. The number between parentheses refers to the number of occurrences of a residue. Viruses utilize a number of functional motifs to attach and enter into host cells, or interact with cellular proteins. This article aims to review the current understanding of motifs utilized by viruses for fruitful infection, highlighting the function of motifs and/or proteins harboring these motifs, in an attempt to classify the motifs based on the molecular function of the harboring proteins. The motifs can be classified into five main categories (Figure1): (i) motifs that mediate immune response; (ii) virus-host interactions, including entry and cellular trafficking; (iii) virulence and antiviral activities, which may disturb cellular processes; (iv) virion structure; and (v) motifs enriched with residues. Proteomes 2016, 4, 3; doi:10.3390/proteomes4010003 www.mdpi.com/journal/proteomes Proteomes 2016, 4, 3 2 of 21 Proteomes 2016, 4, 3 2 of 20 Figure 1. Five categories of motifs were reviewed, based on function of proteins harboring the motif.motif. 2. Motif Motif Involved Involved in in Immune Immune Response Response and and post-translational post-translational modification modification processes processes Immune response. response. B andB and T cells T cellsemploy employ two types two typesof receptors of receptors with positive with positiveand negative and negativeregulators, regulators, the so-called the so-called immunoreceptor immunoreceptor tyrosine-based tyrosine-based activation activation motif motif(ITAM) (ITAM) and andthe theimmunoreceptor immunoreceptor tyrosine-based tyrosine-based inhibition inhibition motif motif (ITIM), (ITIM), respectively respectively [4]. [4]. These These receptors receptors are responsible for immune response and signal transduction in immune cells. They bear either ITAM (Yxx[LI]x66–8´Yxx[LI])8Yxx[LI]) or or ITIM ITIM ([SIVL]xYxx[IVL]) ([SIVL]xYxx[IVL]) motifs motifs.. The The dendritic dendritic cell cell (DC) immunoreceptorimmunoreceptor (DCIR), a C-typeC-type lectinlectin receptorreceptor expressedexpressed onon DCs,DCs, acts as an attachmentattachment factor for humanhuman immunodeficiencyimmunodeficiency virus type 1 (HIV-1)(HIV-1) [[5].5]. DCIR contains ITIM, which binds to the Glu-Pro-SerGlu-Pro-Ser (EPS) motif.motif. Chemical inhibitors directed againstagainst thisthis motifmotif preventprevent attachmentattachment ofof HIV-1HIV-1 toto DCs.DCs. Post-translational modification modification processes. processes.Cellular Cellular processes, processes, such as ubiquitylation, such as ubiquitylation, SUMOylation andSUMOylation ISGylation, and require ISGylation, particular require motifs particular for proteins motifs to for bind proteins and initiate to bind them. and Ininitiate adenoviruses, them. In proteinadenoviruses, VI recruits protein Nedd4 VI recruits E3 ubiquitin Nedd4 ligases E3 ubiquitin by the PPxY ligases motif, by facilitatingthe PPxY itsmotif, ubiquitylation facilitating [its6]. Theubiquitylation SLQxLA, [6]. VxHxMY, The SLQxLA, HCCH VxHxMY, (Hx5Cx17 ´HCCH18Cx3´ (Hx5H)5Cx and17–18 PPLPCx3–5H) motifs and PPLP in the motifs viral in infectivity the viral factorinfectivity (Vif) factor protein (Vif) bind protein to Cullin5,bind to Cullin5, ElonginB ElonginB and C, and inducing C, inducing protein protein polyubiquitination polyubiquitination and proteasome-mediatedand proteasome-mediated degradation degradation [7–10 [7–10].]. SUMOylation is a post-translational post-translational modification modification process by which small protein (SUMO, small ubiquitin-related modifier) modifier) binds to a wide range of cellular proteins, modifying their functions by adding aa bulkybulky moiety,moiety, and and promoting promoting particular particular protein-protein protein-protein interactions interactions [11 [11,12].,12]. SUMOylation SUMOylation of substratesof substrates is initiated is initiated by theby the binding binding of SUMO of SUMO with with lysine lysine residue residue in the in SUMOylation the SUMOylation consensus consensus motif, 'motif,Kx[DE], φKx[DE], where where' denotes φ denotes large hydrophobic large hydrophobic residues residues (F, I, L or(F, V).I, L It or is V). noteworthy It is noteworthy that the that SUMO the motifSUMO is motif not the is exclusivenot the exclusive motif for motif SUMOylation, for SUMOyl andation, the SUMO and the substrate SUMO can substrate be modified can be in modified different sites,in different such as sites, the SxSsuch ( ''as thexSxS[DE][DE][DE]) SxS (φφxSxS[DE][DE][DE]) and [VI]x[VI][VI] and [VI]x[VI][VI] motifs [12– motifs14]. A [12–14]. number A of number viruses (includingof viruses (including herpesviruses herpesviruses and hepatitis and C hepatitis virus, HCV) C virus, were HCV) able towere trigger able SUMOylation-dependent to trigger SUMOylation- mechanismsdependent mechanisms by recruiting by E2recruiting and E3 ubiquitinE2 and E3 ligases ubiquitin [15– ligases18]. SUMO [15–18]. was SUMO suggested was suggested to play roles to inplay the roles nuclear in the localization nuclear localization of viral cargo of viral [19], cargo suggesting [19], suggesting their roles their in virus roles replication in virus replication [17]. Notably, [17]. theNotably, sentrin-specific the sentrin-specific proteases proteases (SENPs) family(SENPs) are fami SUMOly are proteases, SUMO proteases, which are which able toare detach able to SUMOs detach fromSUMOs their from substrates their substrates [20]. Interfering [20]. Interfering with the proteins with the involved proteins in (de-)SUMOylationinvolved in (de-)SUMOylation processes via SENPsprocesses was via suggested SENPs aswas a potentialsuggested technique as a potential for developing technique an antiviralfor developing agent [ 17an,18 antiviral,21]. agent [17,18,21].Viral proteins, such as paramyxovirus C and V proteins, mouse cytomegalovirus (CMV) pM27,Viral and proteins, Kaposi' ssuch sarcoma-associated as paramyxovirus herpesvirus C and V proteins, K3, K5 mouse and viral cytome interferongalovirus regulatory (CMV) pM27, factor 3,and can Kaposi's inhibit signalsarcoma-associated transduction andherpesvirus activators K3, of transcriptionK5 and viral (STAT)interferon or majorregulatory histocompatibility factor 3, can complexinhibit signal [22–30 transduction]. These interactions and activators downregulate of transcription the interferon (STAT) (IFN)or major pathway, histocompatibility regulate the expressioncomplex [22–30]. of interferon-stimulated These interactions genes downregulate (ISGs), and suppress the interferon both cytokine-mediated (IFN) pathway, immunity regulate andthe anti-viralexpression defense