Virology 466-467 (2014) 15–26

Contents lists available at ScienceDirect

Virology

journal homepage: www.elsevier.com/locate/yviro

Review Revisiting the genome packaging in viruses with lessons from the “Giants”

Venkata Chelikani, Tushar Ranjan, Kiran Kondabagil n

Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India article info abstract

Available online 3 July 2014 Genome encapsidation is an essential step in the life cycle of viruses. Viruses either use some of the most Keywords: powerful ATP-dependent motors to compel the genetic material into the preformed capsid or make use of the Genome packaging positively charged proteins to bind and condense the negatively charged genome in an energy-independent Classification manner. While the former is a hallmark of large DNA viruses, the latter is commonly seen in small DNA and NCLDV RNA viruses. Discoveries of many complex giant viruses such as mimivirus, megavirus, pandoravirus, etc., Energy-independent belonging to the nucleo-cytoplasmic large DNA virus (NCLDV) superfamily have changed the perception of Energy-dependent genome packaging in viruses. From what little we have understood so far, it seems that the genome packaging Encapsidation mechanism in NCLDVs has nothing in common with other well-characterized viral packaging systems such as Packaging ATPase the portal-terminase system or the energy-independent system. Recent findings suggest that in giant viruses, the genome segregation and packaging processes are more intricately coupled than those of other viral systems. Interestingly, giant viral packaging systems also seem to possess features that are analogous to bacterial and archaeal chromosome segregation. Although there is a lot of diversity in terms of host range, type of genome, and genome size among viruses, they all seem to use three major types of independent innovations to accomplish genome encapsidation. Here, we have made an attempt to comprehensively review all the known viral genome packaging systems, including the one that is operative in giant viruses, by proposing a simple and expanded classification system that divides the viral packaging systems into three large groups (types I–III) on the basis of the mechanism employed and the relatedness of the major packaging proteins. Known variants within each group have been further classified into subgroups to reflect their unique adaptations. & 2014 Elsevier Inc. All rights reserved.

Contents

Introduction...... 15 Classification of packaging systems ...... 16 Type I: energy-independent packaging systems ...... 17 Type II: portal-translocase system ...... 19 Type IIA (T4-like) ...... 20 Type IIB (ϕ29-like) ...... 20 Type IIC (ϕ6-like) ...... 21 Type IID (adenovirus-like) ...... 21 Type III: FtsK/HerA-type system...... 21 Type IIIA (mimivirus-like)...... 22 Type IIIB (PRD1-like)...... 23 Type IIIC (M13-like) ...... 23 Conclusion...... 23 Acknowledgments...... 23 References...... 23

Introduction n Corresponding author at. Indian Institute of Technology-Bombay, Powai, Mum- bai 400076, India. Tel.: þ91 22 2576 7758; fax: þ91 222572 3480. E-mail addresses: [email protected], Genome condensation and packaging are complex and essen- [email protected] (K. Kondabagil). tial processes common to all three forms of life as well as to http://dx.doi.org/10.1016/j.virol.2014.06.022 0042-6822/& 2014 Elsevier Inc. All rights reserved. 16 V. Chelikani et al. / Virology 466-467 (2014) 15–26 viruses that parasitize them. No single definition of “genome the relatedness of the components. We have limited ourselves to condensation” could explain the diversity of packaging systems discussing one well-understood system in greater detail under because the mechanism and the extent of compaction vary widely each major type. Variant mechanisms within each major type will in biological systems. Several centimeters of eukaryotic genome is also be discussed briefly. condensed into the micrometer-sized nucleus (Teif and Bohinc, Type I mechanism includes viruses in which capsid assembly 2011) with the help of highly charged histone proteins (Van Holde, and genome condensation are more or less coupled and do not 1989). Genomic DNA in prokaryotes is condensed with the help of require the input of energy (Kutluay and Bieniasz, 2010). Initiation polyamines and proteins such as histone-like nucleoid structuring of capsid protein nucleation (recognition) occurs at the genome protein (H-NS), heat-unstable nucleoid protein (HU), factor for terminus, where several forms of packaging signals are present inversion stimulation (FIS), integration host factor (IHF), and DNA- (Choi and Rao, 2003)(Fig. 1). Viruses that employ type II and type binding protein from starved cells (DPS) into an irregularly-shaped III modes of packaging critically require ATP for genome pumping viscous region known as the nucleoid, which occupies about a into the preassembled capsid (Fig. 1). The type II system includes quarter of the intracellular volume (Teif and Bohinc, 2011; Wiggins most tailed phages that employ typical terminase-portal ensemble et al., 2010). Viral genome packaging mechanisms provide the for genome encapsidation (Hegde et al., 2012; Rao and Black, most condensed state of the genome among all forms of biological 2005). Most of the tailed phages (T4, T7, etc.) in this category entities (Catalano, 2005; Teif and Bohinc, 2011). Most DNA and encode typical components of the packaging machinery, namely, RNA viruses with smaller genomes (o20 Kb) use the energy- small terminase, large terminase, and portal protein (Rao and independent system, where the capsid is assembled around the Black, 2005; Catalano, 2005). We placed ϕ29 phage into the genome, resulting in its condensation and packaging, whereas separate subgroup B under type II; it does not encode a small large viruses use ATP-driven motors to pump the nucleic acid into terminase (although it encodes terminal protein, which is func- the preformed capsid (Burroughs et al., 2007). In recent times, tionally homologous to small terminase) but critically requires an significant progress has been made in understanding the mechan- RNA component known as pRNA (packaging RNA, which is not a ism of genome packaging in both types of viruses. Solution typical component of the terminase-portal system) for genome structures of retroviral Gag cleavage products and atomic struc- translocation (Grimes et al., 2002)(Table 1). In viruses belonging tures of some DNA and RNA packaging motors have been solved to the Cystoviridae family (e.g., ϕ6) a critical NTPase functions both (Agirrezabala et al., 2005; Amarasinghe et al., 2000; Du et al., as the portal and the translocase (Pirttimaa et al., 2002). High- 2011; Lebedev et al., 2007; Mancini et al., 2004; Momany et al., resolution crystal structure and phylogenetic analyses indicate 1996; Saad et al., 2006; Simpson et al., 2001; Sun et al., 2008). that ϕ6 packaging NTPase has a recA-type nucleotide-binding Furthermore, in vitro packaging assays and single-molecule stu- motif fold similar to large terminases, probably suggesting dies in the energy-dependent packaging systems have shown that mechanistic similarity (Hegde et al., 2012; Omari et al., 2013). This the viral packaging enzymes are some of the most powerful motor protein is also capable of utilizing any type of NTP for biological motors (Gottlieb et al., 1992b; Kondabagil et al., 2006; genome translocation (Poranen et al., 2001). We have placed Masker and Serwer, 1982; Smith, 2011). phage ϕ6 and other phages of the Cystoviridae family in a separate Large and extremely large viruses of the nucleo-cytoplasmic large subgroup, C, under type II (Table 1). In earlier classifications, DNA virus (NCLDV) clade appear to have evolved a completely adenovirus was always grouped with ϕ29 (Ostapchuk and different strategy for packaging their genome into the capsid. They Hearing, 2003; Mencia et al., 2011). Since adenoviruses lack an carry extremely large genomes (on an average, 5–20 times larger apparent RNA component, we have tentatively placed them under than normal phage genomes) and are thought to use a mechanism a separate subgroup, D. However, they do code for a terminal that is comparable to chromosome segregation in bacteria and protein (Tamanoi and Stillman, 1982). Adenoviral packaging sys- archaea (Chelikani et al., 2014). The DNA packaging ATPase of tems remain poorly understood, and there is no clarity on the NCLDVs and the prokaryotic viruses with an inner lipid membrane identity of the DNA pumping ATPase (Christensen et al., 2012). The belong to the FtsK/SpoIIIE/HerA superfamily (ATP-dependent DNA identification and characterization of this critical component will pumping motors of bacteria and archaea) (Iyer et al., 2004). Other help in the proper placement of adenoviral packaging systems. components involved in prokaryotic chromosome segregation, such The type III system mainly consists of large dsDNA viruses or giant as recombinases and topoisomerases, are also encoded by several viruses that possess a unique genome packaging machinery members of the NCLDV and might play a crucial role in their genome related to prokaryotic ones. It is hypothesized that this group of packaging (Chelikani et al., 2014). Surprisingly, Marseillevirus and viruses requires three major components, namely, packaging Lausannevirus, members of NCLDVs, encode histone-like proteins ATPase, recombinase, and topoisomerase (Chelikani et al., 2014) that are critical for eukaryotic genome packaging (Boyer et al., 2009; (Fig. 1). Of these three major components, only the packaging Thomas et al., 2011). Thus, genome packaging mechanisms of ATPase is invariably of viral origin, whereas the other two NCLDVs seem to share features that are seen in all types of cellular components are coded either by the virus or the host. Comparative life, bacteria, archaea, and eukaryotes. analyses of DNA pumping ATPases by Iyer et al. (2004) clearly Viruses largely use three types of mechanisms for genome suggested that packaging ATPases of PRD1 and M13 are related to encapsidation, two of which require ATP/NTP-dependent DNA the FtsK/HerA family ATPases of NCLDVs. Apart from the presence pumping motors. An attempt has been made here to provide a of the NCLDV-type packaging ATPase, PRD1-like phages possess an comprehensive review of all the known viral genome packaging internal membrane, which is a characteristic feature of the NCLDVs mechanisms, and a simple classification system dividing the (Iyer et al., 2004; Burroughs et al., 2007). Filamentous phages, such packaging systems into three large groups on the basis of the as M13, start their assembly at the host plasma membrane, and the mechanism employed has been proposed. These will be useful in packaging ATPase docks the single-stranded DNA (ssDNA) close to understanding the origin and evolution of packaging mechanisms. the assembly site. Several viral components (membrane proteins) also help in genome encapsidation (Russel and Model, 1986). We have placed PRD1-like phages and M13-like filamentous phages Classification of packaging systems under separate subgroups, B and C, respectively, under type III (Table 1). In this article, we have made an effort to classify the viral In the proposed classification system, we have taken only the genome packaging systems based on the strategy employed and overall mechanism of genome packaging and the presence and V. Chelikani et al. / Virology 466-467 (2014) 15–26 17

Viral genome packaging

Type I packaging Type II packaging Type III packaging

Nucleation of capsid proteins Docking of the viral genome by Assembly of internal lipid onto the genome the packaging proteins onto the membranes and the procapsid portal situated at a unique vertex ATP independent on the procapsid Resolution and docking of the viral Assembly of viral particles genome by the segro-packasome Genome translocation into the machinery onto the procapsid at the capsid by the packaging proteins vertex or non-vertex opening ATP/NTP dependent Genome translocation into the capsid Assembly of viral particles by the packaging ATPase ATP dependent

Assembly of viral particles

Fig. 1. Major types of viral packaging systems. relatedness of its components into account. For example, although viral genome to the host plasma membrane, where virus assembly M13 is a filamentous phage and does not have much in common takes place. At this stage, envelope proteins gp120 and gp40 with NCLDVs, we have placed M13-like phages under the same (encoded by the env gene) assemble onto the plasma membrane major group because they both encode FtsK-type packaging (Seibert et al., 1995)(Fig. 2B). During virion maturation, the Gag ATPases (Iyer et al., 2004). This showcases great diversity in viral polyprotein gets cleaved by the retroviral protease into four packaging systems arising from convergent mechanisms, lateral proteins—matrix (MA or p17), capsid (CA or p24), nucleocapsid acquisitions, and dynamic adaptations in the rapidly evolving (NC or p7), and p6—and two unstructured but functionally host-parasite interactions. important polypeptides known as SP1 and SP2 (spacer polypep- tides 1 and 2) (Jones and Stuart, 1996; Lu et al., 2011)(Fig. 2B Type I: energy-independent packaging systems inset). The MA domain (1–132 aa) of the Gag protein is responsible for the transport of the Gag polyprotein to the plasma membrane Small DNA and RNA viruses that do not require energy and (Meyers et al., 2008; Saad et al., 2006). The MA domain contains a specialized packaging machinery for genome encapsidation are critical cotranslationally acquired myristoyl group that is attached included in type I (Table 1). Capsid assembly and genome to the N-terminal glycine residue (Chukkapalli and Ono, 2011). The condensation in these viruses are usually coupled by the coating hidden myristoyl moiety of the monomer gets exposed when Gag of the nucleic acid with the viral capsid proteins, leading to the oligomerizes to form a trimeric structure. The exposed myristoyl assembly of a virion (Kutluay and Bieniasz, 2010)(Fig. 2). Although groups of the Gag trimer bind to the plasma membrane with there are quite a few mechanistic variations within this group higher affinity and stabilize the plasma membrane–Gag interac- (some are mentioned in Table 1), we have not subgrouped them tions. The CA (133–377 aa) protein is made of two distinct further because only three major types of interactions are suffi- domains: an amino-terminal domain (NTD) and a carboxy- cient for packaging, namely, (1) protein–protein interactions for terminal domain (CTD) (Fig. 2B inset) connected by a flexible capsid assembly, (2) DNA/RNA–protein interactions for the nuclea- linker. Proteolytic cleavage and dissociation from Gag protein lead tion of capsid proteins on the genome, and (3) sequence- to the nucleation of the CA domain to form a roughly conical- independent and sequence-dependent DNA/RNA–protein interac- shaped shell around the RNA genome and other viral components. tions that stabilize the encapsidated genome and minimize The conserved region in CTD is crucial for Gag oligomerization, encapsidation of nonviral nucleic acids (Catalano, 2005; Vriend and any mutations in this region adversely affect viral assembly et al., 1986). The unique packaging signal or origin of assembly (Du et al., 2011). The NTD is believed to play an important role in sequence (OAS) such as stem-loop-like structures, 30-tRNA-like stabilizing the capsid through a sixfold interaction, and interac- sequence (TLS), and the 50-untranslated region (UTR) at the tions between CTD and NTD of the adjacent units are also deemed genome termini recognized by the capsid protein (CP) helps to important for stability. The conserved inter-domain hinge region distinguish the viral genome from cellular genetic material (Choi also adds considerable plasticity to the CA domain and helps in and Rao, 2003). Apart from these packaging signals, some auxiliary linking NTD–CTD, CTD–CTD, and NTD–NTD, leading to polymorph- factors, such as host tRNA, viral replicase, etc., also enhance ism unlike other viruses that have a more defined capsid structure genome packaging (Rixon, 1993). Human immunodeficiency virus (Cardone et al., 2009; Du et al., 2011). The Gag–Gag lattice (HIV) is a typical and well-known example of this type of interactions—made by the CTD of CA, SP1 spacer, and NC region packaging system and is discussed briefly below (Fig. 2). —are also crucial for the maturation of virus (Ganser-Pornillos et The structural component of HIV-1 and retroviruses is the al., 2008). The CTD of CA and NTD of the spacer polypeptide SP1 Gag polyprotein that has all the components needed for genome are also essential for the formation of immature virions (Fig. 2B packaging and virus assembly. During viral replication, the inte- inset). Mutational studies on SP1 showed loss of viral infection and grated genome of HIV is transcribed into mRNA that produces the a severe effect on morphogenesis (Kräusslich et al., 1995). structural protein Gag (Zheng et al., 2005). It has been estimated The NC domain (378–508) is the fourth domain of the Gag that about 3000–5000 copies of Gag proteins are needed for the protein and is responsible for the formation of the innermost layer assembly of each HIV particle (Briggs et al., 2004; Van Engelenburg and is associated with the genome. The NC domain binds to the et al., 2014). The Gag protein recognizes the specific packaging conserved Ψ-site (120 nt-long stretch of RNA containing a packa- signal (50UTR) at the dimeric ssRNA end (Fig. 2A) and directs the ging signal) near the 50-end of the viral RNA and forms an RNA– 18 V. Chelikani et al. / Virology 466-467 (2014) 15–26

Table 1 Classification of genome packaging in viruses.

Type I packaging system Subgroup None Genome ssRNA/dsRNA/ssDNA/dsDNA types Examples (þ) ssRNA: Tobacco mosaic virus (TMV), Turnip yellow mosaic virus (TYMV), Brome mosaic virusa (BMV), Dianthovirusesa, Comovirusa, Fabavirusa, Nepovirusa, Cucumovirusa, Alfamovirusa, Tombusvirus, Tymovirus, Sobemovirus, Luteovirus, Carmovirus, Human immunodeficiency virus (HIV), λN, Flock house virusa (FHV), Togavirus, Rous sarcoma virus, Simian immunodeficiency virus (SIV), Lentivirus, Bovine leukemia virus, Rabies virus, Influenza A virusa, Yeast PR6; dsDNA: SV40, Human hepatitis B virus; dsRNA: Totivirus; ssDNA: Geminivirus Components Nucleocapsid protein Deviation 1. In FHV, packaging of one RNA molecule is dependent on the replication of the other RNA molecule. 2. In influenza A virus, all eight segments of genome have unique packaging signals at the ends. 3. SV40 DNA forms minichromosomes that are wound into nucleosomes with the help of host histone proteins. 4. Rhabdoviruses replicate their genome in inclusion bodies (similar to viral factory).

Type II packaging system Subgroup A T4-like Genome ssDNA/dsDNA types Examples dsDNA: Phages T4, T3/T7, T5, λ, P1, P2, P4, P22, and SPP1, herpes simplex virus-1; ssDNA: Phage ϕX174, Adeno-associated virus (AAV2) Components Portal protein, large terminase, and small terminase Deviation 1. Phage λ has a linear concatemerized genome and uses host encoded IHF and HU proteins for bending the DNA to facilitate terminase binding. 2. Phages SPP1 and P22 require head completion and capsid decoration proteins to prevent the leakage of genome. 3. In AAV2, Rep protein (required for replication) targets the viral genome to the portal and translocates it into the capsid. Helicase activity of the Rep protein is essential for genome translocation. 4. Phage HK97 makes use of HNH nuclease (gp74) for genome packaging. Subgroup B ϕ29-like Genome dsDNA Type Examples Phages ϕ29, ϕ15, PZA, PZE, BS32, B103, and M2Y Components Connector (portal protein), terminal protein, packaging ATPase, and pRNA Deviation – Subgroup C ϕ6-like Genome dsRNA type Examples Phages ϕ6–ϕ14a, Rotavirusa Components Polymerase complex (capsid protein, RNA polymerase, packaging NTPase, and stabilizing protein) Deviation Φ8 and Φ13 NTPase exhibits helicase activity. Subgroup D Adenovirus-likeb Genome dsDNA Type Examples Human adenoviruses A-G, Frog adenovirus, and Ovine adenovirus D Components Proteins IVa2, L4-22K/33K, and L1-52/55K Deviation –

Type III packaging system Subgroup A Mimivirus-likeb Genome dsDNA Type Examples Mimivirus, Vaccinia virus, Paramecium bursaria chlorella virus (PBCV), Cafeteria roenbergensis virus (CroV), Megavirus, Asfarvirus, Iridovirus, Ascovirus, Marseillevirus, Pandoravirus, and Virophages Components Packaging ATPase, recombinase, and type II topoisomerase Deviations 1. Vaccinia virus has dsDNA with hairpin-like structure at the end. 2. Poxviridae and Asfarviridae family viruses recruit type II topoisomerase from the host. 3. Marseillevirus and Laussanevirus encode histone-like protein. Subgroup B PRD1-like Genome dsDNA Type Examples Phages PRD1, PR3, Bam35c, L17, PR4, AP50, and PR772 Components Packaging ATPase, spike protein, and membrane integral protein Deviation – Subgroup C M13-likeb Genome ssDNA type Examples Phages M13, Pf1, Fd, Pf3, Xf, Ff, If1, and F1 Components Probable packaging ATPase, coat protein, and minor proteins. Deviation –

a Segmented genome. b Mechanism of genome packaging is not well understood. protein complex (Amarasinghe et al., 2000). The zinc finger in the copies of the viral genome is transported to plasma membrane NC domain makes sequence-specific contacts with exposed loop viral assembly sites, where several thousands of Gag proteins are residues (Ganser-Pornillos et al., 2008). Genome packaging does already localized, leading to the formation of immature virus not occur in the presence of mutations that inhibit zinc binding particle (Lu et al., 2011). During maturation, HIV also packages (Amarasinghe et al., 2000). It is believed that an RNA–protein its reverse transcriptase and integrase enzymes (encoded by pol complex comprising a small number of Gag proteins and two gene), which are required for infection (Seibert et al., 1995) V. Chelikani et al. / Virology 466-467 (2014) 15–26 19

SP1 SP2

MA CANTD CACTD NC p6 N C Cleavage sites

Lipid Raft gp120 of host PM gp41

5’UTR CA Gag gp120 RT & Single stranded RT & gp41 Integrase RNA dimer-Gag MA complex Envelope Integrase NC

Fig. 2. Schematic of the genome packaging mechanism in HIV. (A) Docking of the Gag-RNA complex to the host plasma membrane (PM): assembly of Gag polyproteins on the 50 UTR (packaging signal) of the viral RNA and docking of the complex to the host PM for viral assembly. (B) Genome packaging and assembly: encapsidation of the viral genome by Gag on the inner surface of the host PM and assembly of the envelop proteins (gp120 and gp41) onto the PM. (C) Mature virion production: maturation of the HIV virion, and incorporation of reverse transcriptase (RT) and integrase into the mature virion particle. Domain organization of the Gag polyprotein is shown in the inset. MA— matrix domain, CA—capsid domain, NC—nucleocapsid domain, SP1 and SP2 are space regions. NTD and CTD stand for N-terminal domain and C-terminal domain, respectively.

Assembly of neck, tail, base plate, tail fibers

gp16 gp17

Branched Procapsid (gp23, gp24) concatemer with portal protein(gp20)

Fig. 3. Schematic of the genome packaging mechanism in phage T4. (A) Docking of the viral genome onto the procapsid: oligomerization of the small terminase on the pac site. The large terminase (gp17) recognizes the small terminase (gp16) bound to the pac-site and assembles to form a hetero-oligomeric complex while the capsid assembly pathway produces the procapsid. (B) Genome encapsidation through the portal: the terminase-DNA complex binds to the portal (gp20) situated at a unique vertex of the preformed head and the genome is translocated into the procapsid through the portal with the help of ATP hydrolysis. (C) Production of mature virion particles: after packaging of a one unit length genome, the nuclease domain of large terminase releases the concatemer by making a second cut followed by the assembly of neck proteins, tail, base plate and tail fibers. Small and large terminase proteins are also released and reused for packaging another head.

(Fig. 2C). Complete assembly takes about 5–6 min (Jouvenet et al., whereas in FHV, two segments are copackaged into a single virion, and 2008, 2009). the packaging of one segment is facilitated by the other (Hutchinson et The genomes of plant viruses are either monopartite or multi- al., 2010; Marshall and Schneemann, 2001; Venter et al., 2009). partite (segmented) (Rao, 2006). Monopartite plant viruses, such as Another deviation (Table 1) in type I genome packaging was observed tymovirus and tombusvirus, exhibit a single genome component in Simian virus 40 (SV40), which has minichromosomes wrapped in packaged into one virion and sgRNA (subgenomic RNA) packaged into histone proteins from the host to form a nucleosome-like structure a separate particle, whereas bipartite viruses, such as comovirus, that is similar to eukaryotic chromosome in architecture (Polisky and nepovirus, and dianthovirus, package two RNA molecules into two McCarthy, 1975; Saper et al., 2013). Genome encapsidation in rhabdo- distinct virions (comovirus and nepovirus) or into one virion (dia- virusesisverysimilartotheothervirusesinthisgroup,buttheir nthovirus) (Rao, 2006). In tripartite viruses, such as bromovirus and replication takes place in a specialized inclusion body similar to a “viral cucumovirus, two large RNA molecules are packaged into two virions, factory” inside the cytoplasm (Lahaye et al., 2009)(Table 1). butthethirdRNAanditssgRNAarecopackagedintoathirdvirion (Rao, 2006). The sgRNA make up secondary RNA molecules necessary Type II: portal-translocase system for replication as well as packaging. The reason for the packaging of a segmented genome is not well understood (Lane, 1974; Mossop and The type II system consists of all phages and viruses that make Francki, 1979; Rao, 2006; Simon et al., 2004). Like plant viruses, use of machinery comprising a portal protein and terminase-type influenza virus and flock house virus (FHV) genomes are also enzyme/s or other translocases that package the genome in an segmented. In influenza virus, eight segments of the genome with ATP-dependent manner into the preformed capsid. This type of eight different packaging signals are packaged into a single virion, machinery is ubiquitous in bacterial viruses, especially in the order 20 V. Chelikani et al. / Virology 466-467 (2014) 15–26

Caudovirales that comprises tailed bacteriophages, and is also terminase functions (Al-Zahrani et al., 2009; Hegde et al., 2012; Rao found in Herpesviridae (Camacho et al., 2003; Mancini et al., and Black, 2005). It is hypothesized that the small terminase protein 2004; Ortega and Catalano, 2006; Sun et al., 2008). We have gp16 recognizes the end of the genome, leading to its oligomerization classified the type II system into four subtypes (A: T4-like, B: ϕ29- and recruitment of the large terminase gp17 (Al-Zahrani et al., 2009) like, C: ϕ6-like, and D: adenovirus-like) on the basis of their (Fig. 3A). The motor protein makes the first cut in the concatemer to unique composition and the mechanism of genome packaging generate one end of the genome and docks it onto the doughnut- (Table 1). The phage T4-like system consists of portal protein and shaped portal protein oligomer situated at the unique vertex on the terminase enzymes and is prominent among tailed bacterio- capsid (Fig. 3B). Components of the packaging machinery progres- phages. Terminase enzymes cut the DNA either nonspecifically sively interact and harmonize a complex series of reactions to produce upon completion of packaging in a head-full manner at pac sites, aDNA-filled head containing a little over one viral genome per head leading to packaging little over one full copy of the genome (Hegde et al., 2012). A combination of atomic structures, cryo-electron (e.g., phage T4) (Black, 1995) or at specific sites known as cos reconstruction, and mutational/functional studies helped to decipher (e.g., phage λ)(Feiss et al., 1983). In ϕ29-like packaging, the small the mechanism of DNA translocation in phage T4 (Sun et al., 2008). terminase is absent, but two other components, a single-stranded Once one end of the genomic DNA is docked onto the portal, the packaging RNA known as pRNA and a terminal protein, are present binding of ATP to the N-terminal ATPase domain and the binding of (Guo et al., 1987a; Simpson et al., 2000)(Table 1). In the ϕ6-like DNA to the C-terminal nuclease domain of the motor protein gp17 (in packaging system, the same protein functions as both portal and its tense state) cause conformational changes, resulting in ATP hydro- packaging protein and is also capable of hydrolyzing any type of lysis (Fig. 3B). The subsequent release of Pi and ADP causes the rotation NTP (Gottlieb et al., 1992a), in contrast to other type II subgroups of N-terminal subdomain II by about 6 degrees, which facilitates the that rely exclusively on ATP. The putative portal/NTPase oligomers movement of the C-domain towards the N-domain via a flexible hinge are present at all the 12 vertices of the capsid, and one of these that temporarily aligns the charged pairs between the N- and C- NTPase complexes present at a specific vertex carries out genome domains. This movement of the C-terminal domain by about 7 Å packaging. All the other subgroups in type II encode distinct results in the movement of 2 bp of DNA bound to the C-terminal packaging and portal proteins. Another interesting feature in ϕ6- domain into the capsid. The release of ADP and Pi from the catalytic like packaging is that it requires NTPase activity for genome center (relaxed state) returns the large terminase gp17 to its original packaging, but that the presence of NTPs is sufficient (no NTPase state, which is now ready for binding another molecule of ATP and activity) for genome delivery (Paatero et al., 1998; Poranen et al., translocation of DNA. When the capsid is nearly full, internal forces 2001). In addition, the packaging NTPase possesses helicase pushtheportalproteinslightlyoutward,whichinturnexposesand activity as well (Kainov et al., 2006). Due to the diversity in the activates the nuclease domain of gp17 to cleave the end of the composition of the packaging machinery, the overall mechanism genome. Cryo-electron microscopic reconstructions suggest that the of genome packaging varies in subgroups of the type II packaging individual monomers of the pentameric gp17 takes turns in pushing system. It has recently been shown that in Escherichia coli phage HK97, the DNA into the capsid (Sun et al., 2008). Motor protein gp17 alone the terminase enzymes (designated as TerL and TerS for terminase shows poor ATPase activity but is enhanced by about a hundredfold in large and small subunits, respectively) critically require the presence of the presence of gp16 (Baumann and Black, 2003; Leffers and Rao, a phage-coded HNH-type nuclease (gp74) for efficient genome packa- 2000). The nuclease and the DNA translocation activities of gp17 are gingandheadmorphogenesis(Kala et al., 2014; Moodley et al., 2012). also regulated by the small terminase protein gp16 (Al-Zahrani et al., Many of the highly mobile staphylococcal pathogenicity islands (SaPIs) 2009). Once the head is full, the packaging machinery makes a second hijack the terminase-type packaging machinery for their own benefit cut, resulting in the dissociation of the concatemer and the terminase (Ram et al., 2012). The SaPI genomes carry either pac sites or cos sites complex from the vertex (Zhang et al., 2011). The filled head then in their genome so that they get efficiently packaged into phage proceeds toward assembly completion by acquiring other components particles, thereby reducing the number of phage particles packaged like neck, tail, base plate, and tail fibers to generate a fully assembled with phage genomes (Ubeda et al., 2009). Many SaPIs use their own virus particle (Fig. 3C). After genome packaging, phages SPP1 and P22 terminase-type packaging system and have a cos site for encapsidation in this group require capsid decoration proteins to prevent the leakage for infectious phage-like particles. Some islands such as SaPIbov5 do of genome (White et al., 2012)(Table 1). not contain a terminase enzyme but possess both pac and cos sites in their genome so that they can use either type of helper phage (cos or Type IIB (ϕ29-like) pac phage) and its machinery for their packaging (Quiles-Puchalt et al., 2014; Ubeda et al., 2007). This clearly suggests that viral genome A major difference between the terminase-portal packaging system packaging systems are actively involved in evolutionary processes by and the one operative in Bacillus subtlis phage ϕ29 is the requirement facilitating lateral gene transfers. Fig. 3 shows a schematic representa- of an RNA component known as the prohead RNA (pRNA-120 tion of the overall mechanism of type II genome packaging with phage nucleotides) (Table 1). Phage ϕ29 multiplies its genome by a T4 as an example. The mechanism of each subgroup is briefly protein-primed mechanism (Kamtekar et al., 2004). The 30-hydroxyl discussed below. group for elongation is provided by a serine residue of the priming protein known as the terminal protein (gp3), which is covalently Type IIA (T4-like) attached to the 50 (dAMP) end of its linear dsDNA genome (Salas et al., 1996). The terminal protein gp3 plays a central role in both replication PhageT4genomereplicationpathwaysyieldahighlybranched, and packaging (Harding et al., 1978; Peñalva and Salas, 1982; Salas et metabolically active concatemeric intermediate that is used as a al., 1978). Along with pRNA, the ϕ29 packaging machinery includes a substrate for packaging. The packaging machinery of bacteriophage dodecameric connector or the portal protein (gp10, situated at the T4 is a hetero-oligomeric complex comprising three proteins: a prohead vertex) and an ATPase (gp16). During packaging, the terminal dodecameric 61 kDa portal protein (gp20), which is the structural protein (gp3), attached to the end of a unit-length genome, acts as a component and is part of the unique vertex of the capsid; a nucleation site for the gp16 ATPase, and gp16 directs the genome to pentameric 70 kDa large terminase motor (gp17), which has all the the connector of an empty capsid where pRNA is already bound catalytic functions required for packaging (ATPase, translocase, and (Grimes et al., 2002). The hexameric form of pRNA binds the capsid nuclease); and an 11- to 12-meric 18 kDa small terminase (gp16), protein (gp8), the connector (gp10), and the packaging ATPase (gp16), which is required for DNA recognition and regulation of large leading to the assembly of the packasome complex. The monomeric V. Chelikani et al. / Virology 466-467 (2014) 15–26 21 pRNA folds into a DNA translocation domain and a procapsid binding component of the viral replicase complex (McDonald and Patton, domain (Morais et al., 2008; Reid et al., 1994). The pRNA binding 2011; Jayaram et al., 2002)(Table 1). Although the genome domain of the packaging ATPase recognizes and binds to the pRNA- packaging mechanism in rotavirus is poorly understood, it was prohead complex, and in the process, gp16 docks the DNA-gp3 tentatively placed in subgroup IIC because, in analogy to the ϕ6 complex onto the connector. Hydrolysis of ATP by gp16 induces packaging NTPase, the NSP2 protein assembles as an octamer, conformational changes, leading to the translocation of DNA into binds to ssRNA, and exhibits NTPase activity (Vende et al., 2003). the capsid (Chemla et al., 2005; Grimes and Anderson, 1990). The dodecameric connector channel size is dynamically altered by about Type IID (adenovirus-like) 30% to ensure one-way traffic of DNA into the capsid, and pRNA helps in synchronizing this movement with gp16 ATPase/translocase func- Adenovirus packages its 36 kb linear dsDNA genome into the tion (Zhang et al., 2012). The pRNA component dissociates from the preformed nonenveloped icosahedral capsid (Fabry et al., 2005). It mature virus particle after the completion of genome packaging, is hypothesized that genome packaging in adenoviruses takes whereas the connector remains as part of the viral structure. The place in a polar fashion, from left to right of the genome (Gräble gp16 and gp3 of phage ϕ29arebelievedtobethefunctionalanalogsof and Hearing, 1990). A series of redundant bipartite sequences the large and small subunits of the terminase complex (Rao and Feiss, named “a repeats” present at the left end, between 200 and 400 2008). nucleotides of the genome, is critical for genome packaging (Gräble and Hearing, 1992)(Table 1). At least three adenovirus- Type IIC (ϕ6-like) encoded proteins—IVa2, L4-22K/L4-33K, and L1-52/55K—specifi- cally interact with the packaging sequence and are required for Phage ϕ6 is a pseudomonas-infecting lytic phage with a unique packaging (Wu et al., 2012; Yang and Maluf, 2010). It is not clear 14 kb segmented dsRNA genome. The three segments of RNA are whether IVa2 has the packaging ATPase/NTPase activity, but it is packaged as single strands (ssRNA) into the preformed capsid, and critically required both for packaging and the transcriptional the second strand is generated with the help of an RNA-dependent activation of a late promoter (Christensen et al., 2012). Most RNA polymerase (protein P2) inside the capsid (Gottlieb et al., studies so far have focused on understanding the interaction 1990; Pirttimaa and Bamford, 2000). The presence of an outer lipid requirements between specific DNA elements of the genome and bilayer (Vidaver et al., 1973) and the sequential packaging of the the packaging proteins IVa2 and L4-22K/33K (Ewing et al., 2007; three segments of genome make this group very different from Gräble and Hearing, 1990; Ostapchuk et al., 2006; Tyler et al., T4- and ϕ29-like systems. The three genome segments are named 2007). From the available literature, it seems that adenovirus according to their sizes: small (S, 2.9 kb), medium (M, 4.1 kb), and packages its genome into the preformed capsid in an energy- large (L, 6.4 kb), and each of these strands has a unique loop-like dependent manner. But no packaging ATPase or portal protein has structure at the 50 end known as the pac site, which is required for been clearly identified, although the presence of IVa2 protein as a packaging (Pirttimaa and Bamford, 2000). The selection of these hexamer/octamer complex at the unique vertex has been demon- three segments of genome is carried out by a polymerase complex strated (Christensen et al., 2008). Since this assembly process is whose affinity toward the segments increases with segment size analogous to common features of portal-translocase systems, it is (Juuti and Bamford, 1995). The essential components of genome tentatively placed here as a separate group. packaging in ϕ6 are the polymerase complex (P1, P2, P4, and P7 The terminase-type genome packaging motors are some of the proteins) and the nucleocapsid (P8) protein. Protein P1 is a major most powerful molecular motors that can generate forces in excess component of the procapsid and is also likely to be involved in the of 60 pN and translocate DNA at rates of up to 2000 bp/s (Fuller et initial recognition of ssRNAs (Onodera et al., 1998). The packaging al., 2007a; Rao and Black, 2005) and help in the condensation of three segments of ssRNA into the procapsid is carried out by the of the genome inside the capsid to near-crystalline density multifunctional hexameric NTPase P4. Interestingly, P4 NTPase can (500 mg/ml) (Lander et al., 2006; Smith et al., 2001). It is hydrolyze NTPs, rNTPs, dNTPs, and even ddNTPS in the presence of estimated that phage T4 needs about 105 ATP molecules to Mg2 þ to derive energy for genome encapsidation (Poranen et al., package one molecule of its genome (Fuller et al., 2007a). The 2001). There are 12 NTPases, but only one of them acts as a packaging density in ϕ29 is similar to other phages (Rickgauer et scaffold for capsid assembly, and the same NTPase is involved in al., 2008), and the force generated by the motor (57 pN) (Chemla genome packaging (Pirttimaa et al., 2002). The other 11 NTPases et al., 2005; Smith et al., 2001) is comparable to the force might be involved in genome delivery during infection, which is generated by the phage T4 packaging motor (Fuller et al., not the case for packaging ATPases of other subgroups in type II 2007a). The initial rate of genome packaging in ϕ29 is estimated (Makeyev and Grimes, 2004; Poranen et al., 2001). Although P7 to be 100 bp/s at a saturating concentration of ATP, and the whole has no enzymatic activity, it is thought to play a role in the stable genome is packaged in about 5 min by the motor (Smith et al., packaging of the ssRNA genome (Juuti and Bamford, 1997; Juuti et 2001). The requirement of one ATP for every two base pairs al., 1998). The capsid also expands during genome encapsidation translocated was first established in ϕ29 (Guo et al., 1987b) and (Juuti and Bamford, 1997; Juuti et al., 1998). Other members of this later turned out to be valid for all the packaging systems studied subgroup, such as phages ϕ8 and ϕ13, encode an NTPase that also so far (Cue and Feiss, 2001; Fuller et al., 2007a; Guo, 1994; Guo et exhibits helicase activity (Kainov et al., 2006)(Table 1). al., 1987b; Lin and Black, 1998; Smith et al., 2001). Rotavirus, a member of the Reoviridae family, has 11 dsDNA segments and shares several features of its genome packaging Type III: FtsK/HerA-type system mechanisms with both influenza virus (without ATP hydrolysis) and ϕ6 (NTP hydrolysis) (McDonald and Patton, 2011). Two The type III system comprises all viruses with a P-loop FtsK/ possible models for genome encapsidation in this virus were HerA superfamily ATPase and is mainly seen in members of the proposed: (1) co-condensation of nucleic acid and the capsid NCLDV clade and phages with an inner lipid membrane like PRD1, protein (Berosis et al., 2013), and (2) packaging of all 11 genome filamentous phages such as M13, and virophages (Burroughs et al., segments into the preassembled capsid in a manner similar to 2007; Iyer et al., 2006). Deviations within this group are built phage ϕ6(McDonald and Patton, 2011). Like the ϕ6 NTPase protein around an invariable nucleic acid pumping ATPase that is related P4, the nonstructural multifunctional NSP2 protein of rotavirus to the essential prokaryotic cell division and chromosome segre- exhibits NTPase activity and ssRNA binding, and it is also a gation proteins such as FtsK and HerA, rather than packaging 22 V. Chelikani et al. / Virology 466-467 (2014) 15–26

Star gate KOPS-like packaging ATPase binding site Surface fibers Topoisomerase type II Capsid

Recombinase dif-like Packaging ATPase assembly Non-vertex Internal initiation site packaging site membranes

Fig. 4. Schematic of a hypothetical model for genome packaging in mimivirus. (A) Oligomerization of packaging ATPase on the catenated genome: the packaging ATPase oligomerizes at specific sites (yet to be identified probably analogous to bacterial KOPS site) of the catenated genome (dimeric or multimeric-not known yet, for simplicity a dimer is shown) which is the end product of replication in mimivirus. (B) Assembly of the segro-packasome machinery: after oligomerization of the packaging ATPase that slides on the genome towards the assembly site (analogous to bacterial dif-site) where it encounters other components, recombinase and topoisomerase II (and possibly other unknown components) to form a complex that resolves the catenated genome. (C) Translocation of the viral genome through a nonvertex packaging site: the packaging ATPase translocates the decatenated genome powered by ATP hydrolysis into the preassembled capsid through a transient non-vertex opening situated on the opposite face of the stargate. Two strands of the dsDNA genome could be translocated simultaneously. (D) Mature virion production: after completion of genome encapsidation, the nonvertex opening is sealed and the packaging ATPase complex leaves the capsid.

ATPases of other known viruses (Iyer et al., 2004). Many of the is further covered by 120 nm-long fibers on the outside (Raoult et NCLDVs carry extremely large genomes (in excess of 1000 kb), and al., 2004; Xiao et al., 2005). Mimivirus has evolved a unique two- the molecular machinery that carries out the complex operation of portal system: (1) a nonvertex transient conduit for genome genome segregation and encapsidation with remarkable fidelity packaging and (2) a stargate-like structure for genome delivery remains to be understood. Our recent studies suggest that the during infection (Kuznetsov et al., 2010; Xiao et al., 2009; genome segregation and packaging machinery of mimivirus and Zauberman et al., 2008). Fig. 4 shows the schematic representation many other NCLDVs subfamilies have many similarities with the of a possible mechanism of genome packaging in mimivirus bacterial chromosome segregation and cell division machinery mainly based on few available studies (Chelikani et al., 2014; (Chelikani et al., 2014). On the basis of the available literature and Mutsafi et al., 2013; Zauberman et al., 2008). Mimivirus and many our observations, we suggest subdividing the type III packaging other NCLDVs encode a packaging ATPase, a putative type II systems into mimivirus-like, PRD1-like, and M13-like systems topoisomerase, and recombinases that are integral parts of the (Table 1). The components of genome packaging in mimivirus- prokaryotic chromosome segregation and translocation machinery like packaging include a packaging ATPase, a type II topoisome- (Aussel et al., 2002). Hundreds of copies of the mimiviral genome rase, recombinase/s, and possibly several as yet unidentified are made during the synthesis phase inside the viral factory components (Table 1). The replication of genome in mimivirus (Suzan-Monti et al., 2007), which are likely to be catenated and and many other NCLDV families (except in the Poxviridae and have to be resolved before packaging (Fig. 4A). A proposed Asfarviridae virus families) probably results in the synthesis of mechanism suggests that the mimivirus packaging ATPase oligo- catenated genomes. The three packaging components interact merizes around a strand of genome and translocates on it until it with one another in a spatiotemporal manner to form a complex encounters the entangled region (Fig. 4A), which then might that is competent for both resolving the catenated genomes into recruit type II topoisomerase, and this complex is further guided unit lengths and translocating them into empty capsids (Chelikani toward specific sites on the genome (analogous to bacterial dif et al., 2014). The other two subgroups, PRD1-like and M13-like sites, where the recombinase is most likely to be already bound) phages, do not encode topoisomerases or recombinases, but the (Chelikani et al., 2014). The assembled segro-packasome resolves critical packaging ATPase is related to the one in mimivirus (FtsK- the catenated genome into unit lengths (Fig. 4B). The packaging HerA superfamily). The overall packaging mechanism is also not ATPase that is still bound to a copy of the resolved genome docks well understood in these phages. So far, phage M13 was assumed at the membrane–capsid protein interface and pumps the DNA to possess a passive packaging system (type I) due to the co- into the capsid (Chelikani et al., 2014)(Fig. 4C). The packaging condensation of capsid and genome (Guo and Lee., 2007; Oram ATPase was not identified in the proteomic analysis of the purified and Black, 2011). However, phage M13 encodes an FtsK type mimivirus particles (Renesto et al., 2006), suggesting that it leaves packaging ATPase (gp1) that is required for its assembly (Iyer et the nonvertex packaging site after packaging and is probably al., 2004; Russel, 1995), hence, we have placed them under a reused (Fig. 4D). The genome packaging in vaccinia virus is slightly separate category. Since virophages also encode packaging ATPase different, and genome replication in this virus leads to the of the FtsK/HerA superfamily (Fischer and Suttle, 2011; La Scola et formation of a dimeric tail-to-tail cruciform-like structure at the al., 2008), they are included in type IIIA. Fig. 4 shows the schematic distal end (Traktman, 1996). At this junction, the packaging ATPase representation of the overall mechanism of type III genome complex assembles and resolves the cruciform-like structure packaging with mimivirus as an example. (Table 1). The vaccinia virus does not encode type II topoisome- rase, but experimental evidence suggests that vaccinia virus Type IIIA (mimivirus-like) recruits host type II topoisomerase for decatenation (Lin et al., 2008)(Table 1). The packaging ATPase assembly docks a copy of In terms of genome and particle size, mimivirus (host Acantha- the genome onto the capsid vertex for packaging and leaves the moeba polyphaga) is bigger than most viruses and some small capsid after genome translocation Thus, the overall composition of bacteria (La Scola et al., 2003). The genome of mimivirus is the packaging machinery is probably similar to mimivirus and surrounded by lipid membranes inside the icosahedral capsid that other NCLDVs. V. Chelikani et al. / Virology 466-467 (2014) 15–26 23

Type IIIB (PRD1-like) Conclusion

Phage PRD1 is a member of the Tectoviridae family and contains All the known viruses, and even some naked DNA elements, an internal lipid membrane that plays an important role during appear to use at least three basic mechanisms to accomplish genome infection by forming a tubular structure (Grahn et al., 2002). packaging. These mechanisms vary from the simple coating of the Essential components of the PRD1 packaging machinery are P9 genome with capsid proteins, as seen in most small viruses, to the ATPase, two membrane proteins (P20, P22), and a minor protein highly complex genome packaging mechanisms of NCLDVs that (P6) (Karhu et al., 2007)(Table 1). Genome packaging in bacter- resemble prokaryotic chromosome segregation and pumping mechan- iophage PRD1 requires a fully assembled empty prohead with an isms. Here, we have made an attempt to classify viral packaging internal lipid membrane through which the dsDNA genome is systems into three large groups and, based on variations within these packaged by the P9 ATPase situated at a specific vertex (Strömsten groups, into several subgroups. The mechanism of genome packaging et al., 2003). The unique vertex of PRD1 forms a channel through for each group and subgroup has been discussed using one typical the capsid into the inner membrane via the P20 and P22 example. Several recent studies on viral packaging motors and membrane proteins. The minor protein P6, which attaches itself components involved in genome packaging helped us to understand to the virion through P20 and P22 membrane proteins, is neces- these processes in greater detail (Morais et al., 2008; Mutsafi et al., sary for the binding of the putative P9 ATPase (Strömsten et al., 2013; Simpson et al., 2000; Sun et al., 2012, 2008; Zauberman et al., 2003). Unlike other packaging ATPases, P9-ATPase remains with 2008). Many systems such as the ones operative in NCLDVs, baculo- the mature virion, and no portal protein has been identified in viruses, rotaviruses, and adenoviruses remain to be understood. The PRD1 (Strömsten et al., 2003, 2005). Microscopic studies suggest fact that bacterial genomic islands have hijacked the terminase- that the PRD1 capsid does not undergo expansion after genome packaging systems for their own advantage suggests that the viral packaging unlike some of the well-studied phages in type II packaging mechanisms play an important role in the coevolution of genome packaging (Butcher et al., 1995; Fuller et al., 2007b; bacteria and their phages and also facilitate a trans-species lateral Jardine and Coombs, 1998). movement of genomic islands. We believe that the suggested classi- fication of viral packaging systems will help us to better understand packaging mechanisms. Type IIIC (M13-like)

Many filamentous phages, such as M13, assemble at the plasma Acknowledgments membrane and are released without host lysis (Bull et al., 2004). Phage M13 genome has nine open reading frames, which encode This work was supported by grants from the Board of Research 11 proteins (Russel, 1995), the majority of which are membrane in Nuclear Sciences (2012/37B/26/BRNS) and IIT-Bombay seed Grant proteins (eight), indicating their probable role during the release (P11IRCCSG004) to KK. VC acknowledges the post-doctoral fellowship from the host membrane (Makowski, 1984; Webster and Lopez, from IIT-Bombay and TR acknowledges Junior Research Fellowship 1985). Thousands of copies of the major coat protein (pVIII) from Council of Scientific and Industrial Research (CSIR), India. We are condense onto its 6.4 kb circular ssDNA genome in a helical grateful to the reviewers and the editor for their suggestions to fashion. An imperfect complementary structure at the end of the improve the manuscript. genome acts as a packaging signal (Russel, 1995). Although this suggests that M13 belongs to type I packaging system, some mutational studies indicate that the phage M13 encoded probable References packaging ATPase pI, membrane protein pIV, and a host-encoded thioredoxin are critical for its assembly (Horabin and Webster, Agirrezabala, X., Martín-Benito, J., Valle, M., González, J.M., Valencia, A., Valpuesta, J.M., 1986; Russel and Model, 1986)(Table 1). The pI protein contains a Carrascosa, J.L., 2005. Structure of the connector of bacteriophage T7 at 8 Å resolution: structural homologies of a basic component of a DNA translocating single transmembrane domain and, part of its amino-terminus machinery. J. Mol. Biol. 347 (5), 895–902. region remains in the cytoplasm (Russel, 1995). This region Al-Zahrani, A.S., Kondabagil, K., Gao, S., Kelly, N., Ghosh-Kumar, M., Rao, V.B., 2009. contains an ATP binding motif, and mutations in this region The small terminase, gp16, of bacteriophage T4 is a regulator of the DNA packaging motor. J. Biol. Chem. 284 (36), 24490–24500. disrupt phage assembly (Russel, 1995). The cytoplasmic region of Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Chancellor, K.J., Wu, Z.R., the pI protein also interacts with the packaging signal of the Summers, M.F., 2000. NMR structure of the HIV-1 nucleocapsid protein bound genome (Russel, 1995). The interaction of pI with DNA is further to stem-loop SL2 of the Ψ-RNA packaging signal. Implications for genome recognition. J. Mol. Biol. 301 (2), 491–511. stabilized by thioredoxin, and ATP hydrolysis by the pI protein also Aussel, L., Barre, F.-X., Aroyo, M., Stasiak, A., Stasiak, A.Z., Sherratt, D., 2002. FtsK is a helps in the displacement of the DNA-binding protein pV. At the DNA motor protein that activates chromosome dimer resolution by switching same time, the pVIII coat protein present on the inner membrane, the catalytic state of the XerC and XerD recombinases. Cell 108 (2), 195–205. Baumann, R.G., Black, L.W., 2003. Isolation and characterization of T4 bacteriophage adjacent to the pI protein, starts wrapping onto the DNA (Russel, gp17 terminase, a large subunit multimer with enhanced ATPase activity. J. Biol. 1995). The role of the pI protein is not entirely clear, but the Chem. 278 (7), 4618–4627. presence and criticality of this distant relative of packaging Berosis, M., Sapin, C., Erk, I., Poncet, D., Cohen, J., 2013. Rotavirus nonstructural protein NSP5 interact with major core protein VP2. J. Virol. 77 (3), 1757–1763. ATPases in type III systems (Iyer et al., 2004) have prompted us Black, L.W., 1995. DNA packaging and cutting by phage terminases: control in phage to place it as a separate type III subgroup. T4 by a synaptic mechanism. Bioessays 17 (12), 1025–1030. Baculoviruses are relatively large viruses with rod-shaped capsids Boyer, M., Yutin, N., Pagnier, I., Barrassi, L., Fournous, G., Espinosa, L., Robert, C., containing circular dsDNA genomes (80–180 kbp) that infect a wide Azza, S., Sun, S., Rossmann, M.G., 2009. Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc. range of invertebrates (Rohrmann, 2011). All the sequenced baculo- Natl. Acad. Sci. 106 (51), 21848–21853. viruses encode a motor protein (Ac66/ORF66) that appears to be Braunagel,S.C.,Russell,W.K.,Rosas-Acosta,G.,Russell,D.H.,Summers,M.D.,2003. related to eukaryotic structural and chromosome maintenance pro- Determination of the protein composition of the occlusion-derived virus of Autographa californica nucleopolyhedrovirus. Proc. Natl. Acad. Sci. 100 (17), teins (SMC) and has been implicated in genome packaging (Braunagel 9797–9802. et al., 2003; Deng et al., 2007; Rohrmann, 2011). This probably Briggs, J.A.G., Simon, M.N., Gross, I., Kräusslich, H.G., Fuller, S.D., Vogt, V.M., Johnson, M. represents a fourth group where the eukaryotic machinery is utilized C., 2004. The stoichiometry of Gag protein in HIV-1. Nat. Struct. Mol. Biol. 11 (7), 672–675. for viral genome packaging. However, it is too early to place Bull, J.J., Pfennig, D.W., Wang, I.-N., 2004. Genetic details, optimization and phage baculoviruses in a separate packaging category. life histories. Trends Ecol. Evol. 19 (2), 76–82. 24 V. Chelikani et al. / Virology 466-467 (2014) 15–26

Burroughs, A., Iyer, L., Aravind, L., 2007. Comparative genomics and evolutionary Guo, P., Peterson, C., Anderson, D., 1987b. Prohead and DNA-gp3-dependent ATPase trajectories of viral ATP dependent DNA-packaging systems. Genome Dyn. 3, 48–65. activity of the DNA packaging protein gp16 of bacteriophage φ29. J. Mol. Biol. Butcher, S.J., Bamford, D.H., Fuller, S.D., 1995. DNA packaging orders the membrane 197 (2), 229–236. of bacteriophage PRD1. EMBO J. 14 (24), 6078–6086. Guo, P.X., Erickson, S., Anderson, D., 1987a. A small viral RNA is required for in vitro Camacho, A.G., Gual, A., Lurz, R., Tavares, P., Alonso, J.C., 2003. Bacillus subtilis packaging of bacteriophage φ 29 DNA. Science 236 (4802), 690–694. bacteriophage SPP1 DNA packaging motor requires terminase and portal Harding, N.E., Ito, J., David, G.S., 1978. Identification of the protein firmly bound to proteins. J. Biol. Chem. 278 (26), 23251–23259. the ends of bacteriophage φ29 DNA. Virology 84 (2), 279–292. Cardone, G., Purdy, J.G., Cheng, N., Craven, R.C., Steven, A.C., 2009. Visualization of a Hegde, S., Padilla-Sanchez, V., Draper, B., Rao, V.B., 2012. Portal-large terminase missing link in retrovirus capsid assembly. Nature 457 (7230), 694–698. interactions of the bacteriophage T4 DNA packaging machine implicate a Catalano, C., 2005. Viral genome packaging machines, viral genome packaging molecular lever mechanism for coupling ATPase to DNA translocation. J. Virol. machines: genetics, Structure, and Mechanism. Springer, US, pp. 1–4. 86 (8), 4046–4057. Chelikani, V., Ranjan, T., Zade, A., Shukla, A., Kondabagil, K., 2014. Genome Horabin, J.I., Webster, R.E., 1986. Morphogenesis of f1 filamentous bacteriophage: segregation and packaging machinery in acanthamoeba polyphaga mimivirus increased expression of gene I inhibits bacterial growth. J. Mol. Biol. 188 (3), is reminiscent of bacterial apparatus. J. Virol. 88 (11), 6069–6075. 403–413. Chemla, Y.R., Aathavan, K., Michaelis, J., Grimes, S., Jardine, P.J., Anderson, D.L., Hutchinson, E.C., von Kirchbach, J.C., Gog, J.R., Digard, P., 2010. Genome packaging Bustamante, C., 2005. Mechanism of force generation of a viral DNA packaging in influenza A virus. J. Gen. Virol. 91 (2), 313–328. motor. Cell 122 (5), 683–692. Iyer, L.M., Balaji, S., Koonin, E.V., Aravind, L., 2006. Evolutionary genomics of nucleo- Choi, Y.G., Rao, A.L.N., 2003. Packaging of brome mosaic virus RNA3 is mediated cytoplasmic large DNA viruses. Virus Res. 117 (1), 156–184. through a bipartite signal. J. Virol. 77 (18), 9750–9757. Iyer, L.M., Makarova, K.S., Koonin, E.V., Aravind, L., 2004. Comparative genomics of Christensen, J.B., Byrd, S.A., Walker, A.K., Strahler, J.R., Andrews, P.C., Imperiale, M.J., the FtsK-HerA superfamily of pumping ATPases: implications for the origins of 2008. Presence of the adenovirus IVa2 protein at a single vertex of the mature chromosome segregation, cell division and viral capsid packaging. Nucleic virion. J. Virol. 82 (18), 9086–9093. Acids Res. 32 (17), 5260–5279. Christensen, J.B., Ewing, S.G., Imperiale, M.J., 2012. Identification and characterization Jardine, P.J., Coombs, D.H., 1998. Capsid expansion follows the initiation of DNA of a DNA binding domain on the adenovirus IVa2 protein. Virology 433 (1), packaging in bacteriophage T4. J. Mol. Biol. 284 (3), 661–672. 124–130. Jayaram, H., Taraporewala, Z., Patton, J.T., Prasad, B.V.V., 2002. Rotavirus protein Chukkapalli, V., Ono, A., 2011. Molecular determinants that regulate plasma involved in genome replication and packaging exhibits a HIT-like fold. Nature membrane association of HIV-1 Gag. J. Mol. Biol. 410 (4), 512–524. 417 (6886), 311–315. Cue, D., Feiss, M., 2001. Bacteriophage λ DNA packaging: DNA site requirements for Jones, I., Stuart, D., 1996. Journey to the core of HIV. Nat. Struct. Mol. Biol. 3 (10), termination and processivity. J. Mol. Biol. 311 (2), 233–240. 818–820. Deng, F., Wang, R., Fang, M., Jiang, Y., Xu, X., Wang, H., Chen, X., Arif, B.M., Guo, L., Jouvenet, N., Bieniasz, P.D., Simon, S.M., 2008. Imaging the biogenesis of individual Wang, H., 2007. Proteomics analysis of Helicoverpa armigera single nucleo- HIV-1 virions in live cells. Nature 454 (7201), 236–240. capsid nucleopolyhedrovirus identified two new occlusion-derived virus-asso- Jouvenet, N., Simon, S.M., Bieniasz, P.D., 2009. Imaging the interaction of HIV-1 ciated proteins, HA44 and HA100. J. Virol. 81 (17), 9377–9385. genomes and Gag during assembly of individual viral particles. Proc. Natl. Acad. Du,S.,Betts,L.,Yang,R.,Shi,H.,Concel,J.,Ahn,J.,Aiken,C.,Zhang,P.,Yeh,J.I.,2011. Sci. 106 (45), 19114–19119. Structure of the HIV-1 full-length capsid protein in a conformationally trapped Juuti, J.T., Bamford, D.H., 1995. RNA binding, packaging and polymerase activities of unassembled state induced by small-molecule binding. J. Mol. Biol. 406 (3), the different incomplete polymerase complex particles of dsRNA bacteriophage 371–386. φ6. J. Mol. Biol. 249 (3), 545–554. Ewing, S.G., Byrd, S.A., Christensen, J.B., Tyler, R.E., Imperiale, M.J., 2007. Ternary Juuti, J.T., Bamford, D.H., 1997. Protein P7 of phage φ6 RNA polymerase complex, complex formation on the adenovirus packaging sequence by the IVa2 and L4 acquiring of RNA packaging activity by in vitro assembly of the purified protein 22-kilodalton proteins. J. Virol. 81 (22), 12450–12457. onto deficient particles. J. Mol. Biol. 266 (5), 891–900. Fabry, C., Rosa‐Calatrava, M., Conway, J.F., Zubieta, C., Cusack, S., Ruigrok, R.W.H., Juuti,J.T.,Bamford,D.H.,Tuma,R.,Thomas,G.J.,1998.StructureandNTPaseactivityof Schoehn, G., 2005. A quasi‐atomic model of human adenovirus type 5 capsid. the RNA-translocating protein (P4) of bacteriophage φ6. J. Mol. Biol. 279 (2), EMBO J. 24 (9), 1645–1654. 347–359. Feiss, M., Widner, W., Miller, G., Johnson, G., Christiansen, S., 1983. Structure of the Kainov, D.E., Tuma, R., Mancini, E.J., 2006. Hexameric molecular motors: P4 packaging bacteriophage lambda cohesive end site: location of the sites of terminase ATPase unravels the mechanism. Cell. Mol. Life Sci. 63 (10), 1095–1105. binding (cosB) and nicking (cosN). Gene 24 (2), 207–218. Kala, S., Cumby, N., Sadowski, P.D., Hyder, B.Z., Kanelis, V., Davidson, A.R., Maxwell, Fischer, M.G., Suttle, C.A., 2011. A virophage at the origin of large DNA transposons. K.L., 2014. HNH proteins are widespread component of phage DNA packaging Science 332 (6026), 231–234. machines. Proc. Natl. Acad. Sci. 111 (16), 6022–6027. Fuller, D.N., Raymer, D.M., Kottadiel, V.I., Rao, V.B., Smith, D.E., 2007a. Single phage Kamtekar, S., Berman, A.J., Wang, J., Lázaro, J.M., de Vega, M., Blanco, L., Salas, M., T4 DNA packaging motors exhibit large force generation, high velocity, and Steitz, T.A., 2004. Insights into strand displacement and processivity from the dynamic variability. Proc. Natl. Acad. Sci. 104 (43), 16868–16873. crystal structure of the protein-primed DNA polymerase of bacteriophage φ29. Fuller,D.N.,Raymer,D.M.,Rickgauer,J.P.,Robertson,R.M.,Catalano,C.E., Mol. Cell 16 (4), 609–618. Anderson, D.L., Grimes, S., Smith, D.E., 2007b. Measurements of single DNA Karhu, N.J., Ziedaite, G., Bamford, D.H., Bamford, J.K.H., 2007. Efficient DNA molecule packaging dynamics in bacteriophage λ reveal high forces, high packaging of bacteriophage PRD1 requires the unique vertex protein P6. J. motor processivity, and capsid transformations. J. Mol. Biol. 373 (5), Virol. 81 (6), 2970–2979. 1113–1122. Kondabagil, K.R., Zhang, Z., Rao, V.B., 2006. The DNA translocating ATPase of Ganser-Pornillos, B.K., Yeager, M., Sundquist, W.I., 2008. The structural biology of bacteriophage T4 packaging motor. J. Mol. Biol. 363 (4), 786–799. HIV assembly. Curr. Opin. Struct. Biol. 18 (2), 203–217. Kräusslich, H.G., Fäcke, M., Heuser, A.M., Konvalinka, J., Zentgraf, H., 1995. The Gottlieb, P., Strassman, J., Mindich, L., 1992a. Protein P4 of the bacteriophage spacer peptide between human immunodeficiency virus capsid and nucleo- φ 6 procapsid has a nucleoside triphosphate-binding site with associated capsid proteins is essential for ordered assembly and viral infectivity. J.Virol. 69 nucleoside triphosphate phosphohydrolase activity. J. Virol. 66 (10), (6), 3407–3419. 6220–6222. Kutluay, S.B., Bieniasz, P.D., 2010. Analysis of the initiating events in HIV-1 particle Gottlieb, P., Strassman, J., Qiao, X., Frilander, M., Frucht, A., Mindich, L., 1992b. assembly and genome packaging. PLoS Pathog. 6 (11), e1001200. in vitro packaging and replication of individual genomic segments of bacter- Kuznetsov, Y.G., Xiao, C., Sun, S., Raoult, D., Rossmann, M., McPherson, A., 2010. iophage φ 6 RNA. J. Virol. 66 (5), 2611–2616. Atomic force microscopy investigation of the giant mimivirus. Virology 404 (1), Gottlieb, P., Strassman, J., Qiao, X.Y., Frucht, A., Mindich, L., 1990. in vitro replication, 127–137. packaging, and transcription of the segmented double-stranded RNA genome of La Scola, B., Audic, S., Robert, C., Jungang, L., de Lamballerie, X., Drancourt, M., bacteriophage φ6: studies with procapsids assembled from plasmid-encoded Birtles, R., Claverie, J.M., Raoult, D., 2003. A giant virus in amoebae. Science 299 proteins. J. Bacteriol. 172 (10), 5774–5782. (5615), 2033. Gräble, M., Hearing, P., 1990. Adenovirus type 5 packaging domain is composed La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., Merchat, M., of a repeated element that is functionally redundant. J. Virol. 64 (5), Suzan-Monti, M., Forterre, P., Koonin, E., 2008. The virophage as a unique 2047–2056. parasite of the giant mimivirus. Nature 455 (7209), 100–104. Gräble, M., Hearing, P., 1992. cis and trans requirements for the selective packaging Lahaye, X., Vidy, A., Pomier, C., Obiang, L., Harper, F., Gaudin, Y., Blondel, D., 2009. of adenovirus type 5 DNA. J. Virol. 66 (2), 723–731. Functional characterization of Negri bodies (NBs) in rabies virus-infected cells: Grahn, A.M., Daugelavičius, R., Bamford, D.H., 2002. Sequential model of phage evidence that NBs are sites of viral transcription and replication. J. Virol. 83 (16), PRD1 DNA delivery: active involvement of the viral membrane. Mol. Microbiol. 7948–7958. 46 (5), 1199–1209. Lander, G.C., Tang, L., Casjens, S.R., Gilcrease, E.B., Prevelige, P., Poliakov, A., Potter, C. Grimes, S., Anderson, D., 1990. RNA dependence of the bacteriophage φ29 DNA S., Carragher, B., Johnson, J.E., 2006. The structure of an infectious P22 virion packaging ATPase. J. Mol. Biol. 215 (4), 559–566. shows the signal for headful DNA packaging. Science 312 (5781), 1791–1795. Grimes, S., Jardine, P.J., Anderson, D., 2002. ed.Bacteriophage φ29 DNA packaging, Lane, L.C., 1974. The bromoviruses. Adv. Virus Res. 19, 151–220. Advances in Virus Research, 58. Academic Press, California, USA, pp. 255–294 Lebedev, A.A., Krause, M.H., Isidro, A.L., Vagin, A.A., Orlova, E.V., Turner, J., Dodson, (Volume). E.J., Tavares, P., Antson, A.A., 2007. Structural framework for DNA translocation Guo, P., 1994. Introduction: principles, perspectives and potential applications in via the viral portal protein. EMBO J. 26 (7), 1984–1994. viral assembly. Semin. Virol. 5, 1–3. Leffers, G., Rao, V.B., 2000. Biochemical characterization of an ATPase activity Guo, P., Lee, T.J., 2007. Viral nanomotors for packaging of dsDNA and dsRNA. Mol. associated with the large packaging subunit gp17 from bacteriophage T4. J. Biol. Microbiol. 64 (4), 886–903. Chem. 275 (47), 37127–37136. V. Chelikani et al. / Virology 466-467 (2014) 15–26 25

Lin, H., Black, L.W., 1998. DNA requirementsin vivofor phage T4 packaging. Virology Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., La Scola, B., Suzan, 242 (1), 118–127. M., Claverie, J.M., 2004. The 1.2-megabase genome sequence of mimivirus. Lin, Y.C.J., Li, J., Irwin, C.R., Jenkins, H., DeLange, L., Evans, D.H., 2008. Vaccinia virus Science 306 (5700), 1344–1350. DNA ligase recruits cellular topoisomerase II to sites of viral replication and Reid, R.J., Bodley, J.W., Anderson, D., 1994. Characterization of the prohead-pRNA assembly. J. Virol. 82 (12), 5922–5932. interaction of bacteriophage φ29. J. Biolo.Chem. 269 (7), 5157–5162. Lu, K., Heng, X., Summers, M.F., 2011. Structural determinants and mechanism of Renesto, P., Abergel, C., Decloquement, P., Moinier, D., Azza, S., Ogata, H., Fourquet, P., HIV-1 genome packaging. J. Mol. Biol. 410 (4), 609–633. Gorvel, J.-P., Claverie, J.-M., 2006. Mimivirus giant particles incorporate a Makeyev, E.V., Grimes, J.M., 2004. RNA-dependent RNA polymerases of dsRNA large fraction of anonymous and unique gene products. J.Virol. 80 (23), bacteriophages. Virus Res. 101 (1), 45–55. 11678–11685. Makowski, L.S., 1984. Structural diversity in filamentous bacteriophages. Biological Rickgauer, J.P., Fuller, D.N., Grimes, S., Jardine, P.J., Anderson, D.L., Smith, D.E., 2008. macromolecules and assemblies. Virus Structures, vol. 1. Wiley-Interscience, Portal motor velocity and internal force resisting viral DNA packaging in New York, pp. 203–253. bacteriophage φ29. Biophys. J. 94 (1), 159–167. Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I., 2004. Rixon, F.J., 1993. Structure and assembly of herpesviruses. Semin. Virol. 4, 135–144. Atomic snapshots of an RNA packaging motor reveal conformational changes Rohrmann, G.F., 2011. Baculovirus Molecular Biology: second edition. National linking ATP hydrolysis to RNA translocation. Cell 118 (6), 743–755. Center for Biotechnology Information (US), Bethesda (MD) (Bookshelf ID: Marshall, D., Schneemann, A., 2001. Specific packaging of nodaviral RNA2 requires NBK49492). the N-terminus of the capsid protein. Virology 285 (1), 165–175. Russel, M., 1995. Moving through the membrane with filamentous phages. Trends Masker, W.E., Serwer, P., 1982. DNA packaging in vitro by an isolated bacteriophage Microbiol. 3 (6), 223–228. T7 procapsid. J. Virol. 43 (3), 1138–1142. Russel, M., Model, P., 1986. The role of thioredoxin in filamentous phage assembly. McDonald, S.M., Patton, J.T., 2011. Assortment and packaging of the segmented Construction, isolation, and characterization of mutant thioredoxins. J. Biol. rotavirus genome. Trends Microbiol. 19 (3), 136–144. Chem. 261 (32), 14997–15005. Mencia, M., Gella, P., Camacho, A., de Vega, M., Salas, M., 2011. Terminal protein- Saad, J.S., Miller, J., Tai, J., Kim, A., Ghanam, R.H., Summers, M.F., 2006. Structural primed amplification of heterologous DNA with a minimal replication system basis for targeting HIV-1 Gag proteins to the plasma membrane for virus based on phage φ29. Proc. Natl. Acad. Sci. 108 (46), 18655–18660. assembly. Proc. Natl. Acad. Sci. 103 (30), 11364–11369. Meyers, A., Chakauya, E., Shephard, E., Tanzer, F.L., Maclean, J., Lynch, A., William- Salas, M., Mellado, R.P., Viñuela, E., Sogo, J.M., 1978. Characterization of a protein son, A.-L., Rybicki, E.P., 2008. Expression of HIV-1 antigens in plants as potential covalently linked to the 50 termini of the DNA of Bacillus subtilis phage φ29. J. subunit vaccines. BMC Biotechnol. 8 (1), 53. Mol. Biol. 119 (2), 269–291. Momany, C., Kovari, L.C., Prongay, A.J., Keller, W., Gitti, R.K., Lee, B.M., Gorbalenya, A. Salas, M., Miller, J.T., Leis, J., Depamphilis, M.L., 1996. Mechanisms for priming DNA E., Tong, L., McClure, J., Ehrlich, L.S., 1996. Crystal structure of dimeric HIV-1 synthesis, DNA Replication in Eukaryotic Cells. Cold Spring Harbor Laboratory capsid protein. Nat. Struct. Mol. Biol. 3 (9), 763–770. Press, NY, pp. 131–176 (Cold Spring Harbor). Moodley, S., Maxwell, K.L., Kanelis, V., 2012. The protein gp74 from the Saper, G., Kler, S., Asor, R., Oppenheim, A., Raviv, U., Harries, D., 2013. Effect of bacteriophage HK97 functions as a HNH endonuclease. Protein Sci. 2 (16), capsid confinement on the chromatin organization of the SV40 minichromo- 809–818. some. Nucleic Acids Res. 41 (3), 1569–1580. Morais, M.C., Koti, J.S., Bowman, V.D., Reyes-Aldrete, E., Anderson, D.L., Rossmann, Seibert, S.A., Howell, C.Y., Hughes, M.K., Hughes, A.L., 1995. Natural selection on the M.G., 2008. Defining molecular and domain boundaries in the bacteriophage gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. φ29 DNA packaging motor. Structure 16 (8), 1267–1274. Evol. 12 (5), 803–813. Mossop, D.W., Francki, R.I.B., 1979. Comparative studies on two satellite RNAs of Simon, A.E., Roossinck, M.J., Havelda, Z., 2004. Plant virus satellite and defective cucumber mosaic virus. Virology 95 (2), 395–404. interfering RNAs: new paradigms for a new century. Annu. Rev. Phytopathol. Mutsafi, Y., Shimoni, E., Shimon, A., Minsky, A., 2013. Membrane assembly during 42, 415–437. the infection cycle of the giant mimivirus. PLoS Pathog. 9 (5), e1003367. Simpson, A.A., Leiman, P.G., Tao, Y., He, Y., Badasso, M.O., Jardine, P.J., Anderson, D.L., Omari, K.E., Meier, C., Kainov, D., Sutton, G., Grimes, J.M., Poranen, M.M., Bamford, Rossmann, M.G., 2001. Structure determination of the head-tail connector of D.H., Tuma, R., Stuart, D.I., Mancini, E.J., 2013. Tracking in atomic detail the bacteriophage φ29. Acta Crystallogr. Sect. D 57 (9), 1260–1269. functional specializations in viral RecA helicases that occur during evolution. Simpson,A.A.,Tao,Y.,Leiman,P.G.,Badasso,M.O.,He,Y.,Jardine,P.J.,Olson,N.H.,Morais, Nucleic Acids Res. 41 (20), 9396–9410. M.C.,Grimes,S.,Anderson,D.L.,Baker,T.S.,Rossmann,M.G.,2000.Structureofthe Onodera, S., Qiao, X., Qiao, J., Mindich, L., 1998. Isolation of a mutant that changes bacteriophage φ29 DNA packaging motor. Nature 408 (6813), 745–750. genomic packaging specificity in φ6. Virology 252 (2), 438–442. Smith, D.E., 2011. Single-molecule studies of viral DNA packaging. Curr. Opin. Virol. Oram, M., Black, L.W., 2011. Mechanisms of genome packaging, Structural Virology. 1 (2), 134–141. RSC Publishing, London, UK, pp. 213–219. Smith, D.E., Tans, S.J., Smith, S.B., Grimes, S., Anderson, D.L., Bustamante, C., 2001. Ortega, M.E., Catalano, C.E., 2006. Bacteriophage lambda gpNu1 and Escherichia coli The bacteriophage φ29 portal motor can package DNA against a large internal IHF proteins cooperatively bind and bend viral DNA: implications for the force. Nature 413 (6857), 748–751. assembly of a genome-packaging motor. Biochemistry 45 (16), 5180–5189. Strömsten, N.J., Bamford, D.H., Bamford, J.K.H., 2003. The unique vertex of bacterial virus Ostapchuk, P., Hearing, P., 2003. Minimal cis-acting elements required for adeno- PRD1 is connected to the viral internal membrane. J. Virol. 77 (11), 6314–6321. virus genome packaging. J. Virol. 77 (9), 5127–5135. Strömsten, N.J., Bamford, D.H., Bamford, J.K.H., 2005. Invitro DNA packaging of Ostapchuk, P., Anderson, M.E., Chandrasekhar, S., Hearing, P., 2006. The L4 22- PRD1: a common mechanism for internal-membrane viruses. J. Mol. Biol. 348 kilodalton protein plays a role in packaging of the adenovirus genome. J. Virol. (3), 617–629. 80 (14), 6973–6981. Sun, S., Gao, S., Kondabagil, K., Xiang, Y., Rossmann, M.G., Rao, V.B., 2012. Structure Paatero, A.O., Mindich, L., Bamford, D.H., 1998. Mutational analysis of the role of and function of the small terminase component of the DNA packaging machine nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex in T4-like bacteriophages. Proc. Natl. Acad. Sci. 109 (3), 817–822. of bacteriophage φ6. J. Virol. 72 (12), 10058–10065. Sun, S., Kondabagil, K., Draper, B., Alam, T.I., Bowman, V.D., Zhang, Z., Hegde, S., Peñalva, M.A., Salas, M., 1982. Initiation of phage φ 29 DNA replication in vitro: Fokine, A., Rossmann, M.G., Rao, V.B., 2008. The structure of the phage T4 DNA formation of a covalent complex between the terminal protein, p3, and packaging motor suggests a mechanism dependent on electrostatic forces. Cell 50-dAMP. Proc. Natl. Acad.Sci. 79 (18), 5522–5526. 135 (7), 1251–1262. Pirttimaa, M.J., Bamford, D.H., 2000. RNA secondary structures of the bacteriophage Suzan-Monti, M., La Scola, B., Barrassi, L., Espinosa, L., Raoult, D., 2007. Ultra- φ6 packaging regions. RNA 6 (6), 880–889. structural characterization of the giant volcano-like virus factory of Acantha- Pirttimaa, M.J., Paatero, A.O., Frilander, M.J., Bamford, D.H., 2002. Nonspecific nucleo- moeba polyphaga mimivirus. PLoS One 2 (3), e328. side triphosphatase P4 of double-stranded RNA bacteriophage φ6 is required for Tamanoi, F., Stillman, B.W., 1982. Function of adenovirus terminal protein in the single-stranded RNA packaging and transcription. J. Virol. 76 (20), 10122–10127. initiation of DNA replication. Proc. Natl. Acad. Sci. 79 (7), 2221–2225. Polisky, B., McCarthy, B., 1975. Location of histones on simian virus 40 DNA. Proc. Teif, V.B., Bohinc, K., 2011. Condensed DNA: condensing the concepts. Prog. Biophys. Natl. Acad. Sci. 72 (8), 2895–2899. Mol. Biol. 105 (3), 208–222. Poranen, M.M., Paatero, A.O., Tuma, R., Bamford, D.H., 2001. Self-assembly of a viral Thomas, V., Bertelli, C., Collyn, F., Casson, N., Telenti, A., Goesmann, A., Croxatto, A., molecular machine from purified protein and RNA constituents. Mol. Cell 7 (4), Greub, G., 2011. Lausannevirus, a giant amoebal virus encoding histone 845–854. doublets. Environ. Microbiol. 13 (6), 1454–1466. Quiles-Puchalt, N., Carpena, N., Alonso, J.C., Novick, R.P., Marina, A., Penadés, J.R., Traktman, P., 1996. Poxvirus DNA replication, DNA Replication in Eukaryotic Cells, 775. 2014. Staphylococcal pathogenicity island DNA packaging system involving cos- Cold Spring Harbor Laboratory Press, NY, pp. 775–795 (Cold Spring Harbor). site packaging and phage-encoded HNH endonucleases. Proc. Natl. Acad. Sci. Tyler, R.E., Ewing, S.G., Imperiale, M.J., 2007. Formation of a multiple protein 111 (16), 6016–6021. complex on the adenovirus packaging sequence by the IVa2 protein. J. Virol. 81 Ram, G., Chen, J., Kumar, K., Ross, H.F., Ubeda, C., Damle, P.K., Lane, K.D., Penadés, J.R., (7), 3447–3454. Christie, G.E., Novick, R.P., 2012. Staphylococcal pathogenicity island interference Ubeda, C., Maiques, E., Tormo, M., Campoy, S., Lasa, I., Barbe, J., Novick, R.P., Penades, with helper phage reproduction is a paradigm of molecular parasitism. Proc. Natl. J.R., 2007. SaPI operon I is required for SaPI packaging and is controlled by LexA. Acad.Sci.109(40),16300–16305. Mol. Microbiol. 65 (1), 41–50. Rao, A.L.N., 2006. Genome packaging by spherical plant RNA viruses. Annu. Rev. Ubeda, C., Olivarez, N.P., Barry, P., Wang, H., Kong, X., Matthew, A., Tallent, S.M., Phytopathol. 44, 61–87. Christie, G.E., Novick, R.P., 2009. Specificity of staphylococcal phage and SaPI Rao, V.B., Black, L.W., 2005. DNA packaging in bacteriophage T4, Viral Genome DNA packaging as revealed by integrase and terminase mutations. Mol. Packaging Machines: Genetics, Structure, and Mechanism, pp. 40–58. Microbiol. 72 (1), 98–108. Rao, V.B., Feiss, M., 2008. The bacteriophage DNA packaging motor. Annu. Rev. Van Engelenburg, S.B., Shtengel, G., Sengupta, P., Waki, K., Jarnik, M., Ablan, S.D., Genet. 42, 647–681. Freed, E.O., Hess, H.F., Lippincott-Schwartz, J., 2014. Distribution of ESCRT 26 V. Chelikani et al. / Virology 466-467 (2014) 15–26

machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits. Wu, K., Orozco, D., Hearing, P., 2012. The adenovirus L4-22K protein is multi- Science 343 (6171), 653–656. functional and is an integral component of crucial aspects of infection. J. Virol. Van Holde, K.E., 1989. Chromatin. Cell 59 (2), 243–244. 86 (19), 10474–10483. Vende, P., Tortorici, M.A., Taraporewala, Z.F., Patton, J.T., 2003. Rotavirus NSP2 Xiao, C., Chipman, P.R., Battisti, A.J., Bowman, V.D., Renesto, P., Raoult, D., Rossmann, interferes with the core lattice protein VP2 in initiation of minus-strand M.G., 2005. Cryo-electron microscopy of the giant mimivirus. J. Mol. Biol. 353 – synthesis. Virology 313 (1), 261 273. (3), 493–496. Venter, P.A., Marshall, D., Schneemann, A., 2009. Dual roles for an arginine-rich Xiao, C., Kuznetsov, Y.G., Sun, S., Hafenstein, S.L., Kostyuchenko, V.A., Chipman, P.R., fi motif in speci c genome recognition and localization of viral coat protein to Suzan-Monti, M., Raoult, D., McPherson, A., Rossmann, M.G., 2009. Structural fl RNA replication sites in ock house virus-infected cells. J. Virol. 83 (7), studies of the giant mimivirus. PLoS Biol. 7 (4), e1000092. – 2872 2882. Yang, T.-C., Maluf, N.K., 2010. Self-association of the adenoviral L4-22K protein. Vidaver, A.K., Koski, R.K., Van Etten, J.L., 1973. Bacteriophage φ6: a lipid-containing Biochemistry 49 (45), 9830–9838. virus of Pseudomonas phaseolicola. J. Virol. 11 (5), 799–805. Zauberman, N., Mutsafi, Y., Halevy, D.B., Shimoni, E., Klein, E., Xiao, C., Sun, S., Vriend, G., Verduin, B.J.M., Hemminga, M.A., 1986. Role of the N-terminal part of the Minsky, A., 2008. Distinct DNA exit and packaging portals in the virus coat protein in the assembly of cowpea chlorotic mottle virus: a 500 MHz Acanthamoeba polyphaga mimivirus. PLoS Biol. 6 (5), e114. proton nuclear magnetic resonance study and structural calculations. J. Mol. Zhang, H., Schwartz, C., De Donatis, G.M., Guo, P., 2012. Push through one-way valve Biol. 191 (3), 453–460. – Webster, R., Lopez, J., 1985. Structure and Assembly of the Class I Filamentous mechanism of viral DNA packaging. Adv.Virus Res. 83, 415 465. Bacteriophage. Jones & Bartlett, Boston, pp. 235–268. Zhang, Z., Kottadiel, V.I., Vafabakhsh, R., Dai, L., Chemla, Y.R., Ha, T., Rao, V.B., 2011. White, H.E., Sherman, M.B., Brasilès, S., Jacquet, E., Seavers, P., Tavares, P., Orlova, E.V., A promiscuous DNA packaging machine from bacteriophage T4. PLoS Biol. 9 (2), 2012. Capsid structure and its stability at the late stages of bacteriophage SPP1 e1000592. fi assembly. J.Virol. 86 (12), 6768–6777. Zheng, Y.-H., Lovsin, N., Peterlin, B.M., 2005. Newly identi ed host factors modulate Wiggins, P.A., Cheveralls, K.C., Martin, J.S., Lintner, R., Kondev, J., 2010. Strong HIV replication. Immunol. Lett. 97 (2), 225–234. intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc. Natl. Acad. Sci. 107 (11), 4991–4995.