Downloaded from www.microbiologyresearch.org by IP: 54.145.126.58 On: Thu, 04 May 2017 14:29:06 Short Communication Insertion and deletion analyses identify regions of non-structural protein 5A of Hepatitis C virus that are dispensable for viral genome replication Shuanghu Liu, Israrul H. Ansari, Subash C. Das and Asit K. Pattnaik Correspondence Asit K. Pattnaik apattnaik2@unl.edu Department of Veterinary and Biomedical Sciences and Nebraska Center for Virology, University of Nebraska-Lincoln (UNL), E126 Beadle Center, 1901 Vine Street, Lincoln, NE 68588-0666, USA Received 4 August 2005 Accepted 4 November 2005 Hepatitis C virus (HCV) non-structural protein 5A (NS5A) plays an essential role in viral genome replication. A series of transposon-mediated insertion mutants and deletion mutants of NS5A was used to examine the colony-forming ability of HCV subgenomic replicons encoding the mutant proteins. The results reveal that two regions of NS5A can tolerate insertions: one spanning residues 240–314, which contain the interferon sensitivity-determining region (ISDR), and the other spanning residues 349–417 at the carboxy terminus. The majority of these sites also tolerated insertion of enhanced green fluorescent protein. Furthermore, replicons encoding NS5A with deletions in ISDR or in the carboxy-terminal regions were replication-competent, indicating that these regions of NS5A are not necessary for replication. Taken together, the results suggest that the central region spanning the ISDR and the carboxy-terminal region of the molecule are dispensable for the functions of NS5A in viral genome replication. Hepatitis C virus (HCV) is an enveloped virus belonging to the genus Hepacivirus within the family Flaviviridae. The positive-sense, ~9?6 kb RNA genome is translated to produce a polyprotein, which is processed proteolytically to generate the mature structural and non-structural (NS) proteins (Major & Feinstone, 1997). The NS proteins are involved in viral genome replication, whereas the structural proteins participate in virion assembly and release (Bartenschlager & Lohmann, 2000; Rosenberg, 2001). Development of cell lines supporting replication of subgenomic replicons of HCV has revealed that adaptive mutations within the NS proteins are required for efficient replication of the replicons derived from genotype 1a and 1b genomes (Lohmann et al., 1999; Blight et al., 2000, 2003; Krieger et al., 2001; Yi & Lemon, 2004), although a similarly constructed replicon derived from a genotype 2a virus replicates efficiently with few or no adaptive mutations (Kato et al., 2003). The NS5A protein is multifunctional. It contains an inter- feron sensitivity-determining region (ISDR) spanning aa 237–276 and may play a role in resistance to alpha interferon (Polyak et al., 1999). It contains an amphipathic a-helix and a zinc-binding domain at the amino terminus, which are required for replication (Brass et al., 2002; Elazar et al., 2003; Tellinghuisen et al., 2004, 2005). In addition, the phosphor- ylation pattern of NS5A plays an important role in HCV genome replication (Evans et al., 2004b; Appel et al., 2005). It also interacts with a multitude of cellular proteins and alters the host cells to support viral RNA replication (Gale et al., 1998; Chung et al., 2000; Park et al., 2002; Evans et al., 2004a; Gao et al., 2004). Transposon-mediated insertion mutagenesis (Goryshin & Reznikoff, 1998) is a powerful tool that allows insertion of short peptides into proteins encoded in cloned DNA to evaluate permissive sites in the protein. It can also be used to assess regions of the protein that are dispensable for its functions. In the present study, we used an Ez-Tn5 In-Frame Linker Insertion kit (Epicentre Biotechnologies) to intro- duce 57 bp in-frame insertions (corresponding to 19 aa in the protein) randomly into a plasmid encoding the NS5A protein. As the amphipathic a-helix and the zinc-binding domain, which are required for replication, are located in the amino-terminal region, this region of the protein was excluded for insertion mutagenesis. We took advantage of the presence of a unique MluI site (corresponding to aa 92 in NS5A) for subsequent manipulation of the NS5A coding region. To facilitate subcloning of NS5A, an MluI site was engineered between aa 431 and 432 in NS5A (Fig. 1a) within the parental subgenomic replicon Con1S/G-Neo (Blight et al., 2000), henceforth referred to as Con1. This manipula- tion, which resulted in insertion of two residues (Thr and Arg) in NS5A at this position, did not affect colony-forming ability of the new replicon, Con1-MluI (Fig. 1b). Sub- sequently, the entire NS5A coding region of the new repli- con was subcloned into the pGEM3 vector and used as template for transposon-mediated insertion mutagenesis as described previously (Das & Pattnaik, 2005). A panel of 0008-1407 G 2006 SGM Printed in Great Britain 323 Journal of General Virology (2006), 87, 323–327 DOI 10.1099/vir.0.81407-0