Genome-wide RNAi screen reveals a role for the ESCRT complex in rotavirus cell entry Daniela Silva-Ayalaa, Tomás Lópeza, Michelle Gutiérreza, Norbert Perrimonb, Susana Lópeza, and Carlos F. Ariasa,1 aDepartamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; and bDepartment of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 Edited by Mary K. Estes, Baylor College of Medicine, Houston, TX, and approved May 3, 2013 (received for review March 14, 2013) Rotavirus (RV) is the major cause of childhood gastroenteritis described that the VP8 protein of human RV strain HAL1166 worldwide. This study presents a functional genome-scale analysis and the human RV strains belonging to the most frequent VP4 of cellular proteins and pathways relevant for RV infection using genotypes (P4 and P8) bind to A-type histo-blood group antigens RNAi. Among the 522 proteins selected in the screen for their (5, 6). Integrin 2β1 has also been reported to serve as an attach- ability to affect viral infectivity, an enriched group that partic- ment receptor for some RV strains (7), although this integrin, as ipates in endocytic processes was identified. Within these pro- well as integrins vβ3 and xβ2 and the heat-shock protein 70 teins, subunits of the vacuolar ATPase, small GTPases, actinin 4, (HSC70), have been implicated mostly in a postattachment in- and, of special interest, components of the endosomal sorting teraction of the virus that might be involved in cell internalization complex required for transport (ESCRT) machinery were found. (7). Nevertheless, RV strains whose infectivity does not depend Here we provide evidence for a role of the ESCRT complex in the on integrins have also been reported. RRV enters cells by an entry of simian and human RV strains in both monkey and human endocytic pathway that is independent of clathrin and caveolin, epithelial cells. In addition, the ESCRT-associated ATPase VPS4A whereas other RV strains have been shown to enter cells through and phospholipid lysobisphosphatidic acid, both crucial for the a clathrin-dependent endocytosis (8). It has also been reported formation of intralumenal vesicles in multivesicular bodies, were that RV cell entry depends on dynamin and cholesterol (8), al- also found to be required for cell entry. Interestingly, it seems that though contradicting results were recently reported in Madin regardless of the molecules that rhesus RV and human RV strains Darby canine kidney cells (9). RRV infection of monkey kidney use for cell-surface attachment and the distinct endocytic pathway MA104 cells has been shown to depend on the small GTPase used, all these viruses converge in early endosomes and use multi- RAB5, but not on RAB4 or RAB7 (10). The interaction of the vesicular bodies for cell entry. Furthermore, the small GTPases RV spike protein VP4 with surface receptors determines the RHOA and CDC42, which regulate different types of clathrin-inde- endocytic pathway used by RVs to enter cells (11). This protein pendent endocytosis, as well as early endosomal antigen 1 (EEA1), has also been proposed to undergo structural changes during the were found to be involved in this process. This work reports the entry process (9, 12); nonetheless, a functional correlation of the direct involvement of the ESCRT machinery in the life cycle of proposed structural changes with cellular factors that trigger a nonenveloped virus and highlights the complex mechanism that these changes is not known. Recently, several studies have reported the use of genome- these viruses use to enter cells. It also illustrates the efficiency of wide RNAi screens to unravel virus–host cell interactions (13). high-throughput RNAi screenings as genetic tools for comprehen- We recently developed a robust high-throughput screening assay sively studying the interaction between viruses and their host cells. to assess RV replication in cell culture (14). In this study we report a genome-wide siRNA screen that allowed us to identify otaviruses (RVs), members of the family Reoviridae, are the more than 500 proteins and several biological processes poten- Rleading etiologic agents of viral gastroenteritis in infants and tially involved in various steps of the RV life cycle. Of particular young children worldwide, being responsible for an estimated interest, the endosomal sorting complex required for transport 453,000 deaths each year (1). The infectious particle is composed (ESCRT) complex, a major pathway for the lysosomal degra- of three concentric layers of protein that enclose the viral ge- dation of monoubiquitinated membrane proteins (15) and also nome formed by 11 segments of double-stranded RNA. The involved in the abscission step of cytokinesis and in the budding proteins of the outermost layer, VP4 and VP7, are involved in process of several enveloped viruses, was found to be involved in virus attachment and cell entry. Two domains constitute the RV cell entry. This report describes the use of the ESCRT spike protein VP4: VP5 at the base of the spike and VP8 at the complex by a nonenveloped virus and highlights the complex head. Once inside the cell, the triple-layered particle (TLP) loses mechanism that RVs use to enter cells. the surface proteins, leading to a double-layered particle (DLP) that is transcriptionally active. The nascent viral mRNAs can be Results used either for viral protein synthesis or for genome replication. Identification of Cellular Proteins Required for RV Infection Using Newly formed progeny DLPs assemble in cytoplasmic inclusions a Genome-Wide siRNA Screen. The assay involved RRV infection known as viroplasms and bud into the lumen of the ER. The of MA104 (Cercopithecus aethiops) cells previously transfected outer-layer proteins then assemble on DLPs in this compartment with an siRNA library that targets 21,181 individual human genes, (2). It has been recently reported, however, that RV hijacks the followed by evaluation of virus replication by an optimized im- autophagy membrane-trafficking pathway to transport the ER- munofluorescent detection of viral protein synthesis (14). The associated viral proteins required for infectious particle assembly to membranes surrounding viroplasms (3). fi Even though speci c steps of entry have been increasingly well Author contributions: D.S.-A., T.L., M.G., N.P., S.L., and C.F.A. designed research; D.S.-A., characterized in recent years, the involvement of host-cell pro- T.L., and M.G. performed research; N.P. contributed new reagents/analytic tools; D.S.-A., teins in the replication life cycle of the virus has been poorly T.L., M.G., N.P., S.L., and C.F.A. analyzed data; and D.S.-A., T.L., and C.F.A. wrote characterized. The initial interactions of the virus with the cell the paper. surface involve several molecules. Specifically, some RV strains The authors declare no conflict of interest. such as rhesus RV (RRV), initially bind to sialic acid on the cell This article is a PNAS Direct Submission. surface through the VP8 domain of the spike protein VP4, but 1To whom correspondence should be addressed. E-mail: [email protected]. some RVs appear to attach to subterminal sialic acid, such as This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. that present in ganglioside GM1 (4); in addition, it was recently 1073/pnas.1304932110/-/DCSupplemental. 10270–10275 | PNAS | June 18, 2013 | vol. 110 | no. 25 www.pnas.org/cgi/doi/10.1073/pnas.1304932110 Downloaded by guest on September 23, 2021 screening was performed in two steps (Fig. S1A and Materials A B and Methods 100 ). Using this experimental design, 522 genes whose TLPs DLPs 100 expression is required for RV infection were identified (Table * S1). Analysis of the data by functional clustering showed that the 75 75 genes that scored as positives are implicated in a broad array of 50 50 ** ** cellular functions and also suggested several statistically enriched ** ** ** ** 25 25 biological pathways that could be involved in the virus life cycle *** fi (Table S2). Among the pathways identi ed are several that have 0 0 been reported to be relevant for, and in some cases highly regu- siRNA: Irre ARF1 COPB1 COPA Irre ATP6V0C ATP6V1B1 lated during, RV infection, including tight junction (TJ) function C150 D (16), endocytosis (8, 10), and calcium signaling (17), as well as the 100 protein-ubiquitination pathway (18, 19). 125 The functional protein clusters initially identified with the 100 75 * Ingenuity Systems software were enriched with several protein- 75 * ** 50 ** interaction databases. We initially characterized three cellular 50 25 processes: the ubiquitin-proteasome pathway, the TJ network, and 25 *** the endocytosis-related protein system. Regarding the protea- Infectivity (%) 0 0 some-ubiquitin components, in silico proteomics showed a strong siRNA: Irre RAB30 RAB2LA ACTN4 Irre ARF6 CDC42 RHOA cluster in our data set: E3 ligase hits, deubiquitinase PAN2, and E 100 F heat-shock proteins. Components of the 26S proteasome were 100 also present in these hits (Fig. S1B and Table S2). These findings 75 are supported by the recent demonstration of the involvement of 75 50 ** ** the proteasome-ubiquitin pathway in the life cycle of RVs (18, 19). 50 Fifteen proteins belonging to the TJ network were recognized 25 25 by protein databases among the positive hits, including JAM-A 0 0 (junctional adhesion molecule) and claudins [human F11 re- Plasmid: Empty WT N17 V12 siRNA: Irre VPS37D VPS25 ceptor (F11R), claudin 6 (CLDN6), CLDN14, and CLDN9) (Fig. S1C and Table S2). Several cytoplasmic proteins involved in Fig. 1. Characterization of proteins involved in endocytosis and intracellular the assembly and maintenance of TJs were also present in our trafficpathway.(A, B, C, D,andF) MA104 cells were transfected with the in- MICROBIOLOGY data set (PARD6A, CNKSR3, MYL9, MYH1, and MYH8), dicated siRNAs and 72 hpt were either infected with RRV [multiplicity of infec- suggesting that TJs are important for RV infection.