Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba Polyphaga Mimivirus
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PLoS BIOLOGY Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus Nathan Zauberman1, Yael Mutsafi1, Daniel Ben Halevy1, Eyal Shimoni2, Eugenia Klein2, Chuan Xiao3, Siyang Sun3, Abraham Minsky1* 1 Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel, 2 Electron Microscopy Center, The Weizmann Institute of Science, Rehovot, Israel, 3 Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the ‘‘stargate’’, allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane–containing viruses. Citation: Zauberman N, Mutsafi Y, Ben Halevy D, Shimoni E, Klein E, et al. (2008) Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus. PLoS Biol 6(5): e114. doi:10.1371/journal.pbio.0060114 Introduction surrounded by a lipid membrane that underlies an icosahe- dral capsid [17–19]. The capsid is, in turn, covered by closely The prevailing model for genome translocations in packed 120-nm-long fibers that form a dense matrix at their icosahedral viruses entails a molecular motor that is localized attachment site [17–19]. The closely packed fibers and the at a single vertex and comprises a packaging ATPase and a dense layer at the base of these fibers represent a unique portal complex [1–5]. The particular structural features feature of the Mimivirus. In addition, a single modified vertex revealed by the vertex-portal assembly have been argued to has been detected in mature particles [18]. facilitate both genome delivery [6] and genome encapsidation With a 1.2–mega base pair (Mbp) dsDNA genome and a [3,6,7]. Although the functional implications of these features particle size of ;750 nm, the Mimivirus represents the largest have been recently challenged [8,9], their apparent conserva- virus documented so far, blurring the established division tion led to the paradigm that a single vertex-portal system between viruses and single-cell organisms [17,18,20]. Promp- plays a crucial and general role in both genome injection and ted by these unique features, we conducted high-resolution packaging in icosahedral viruses [6]. studies of the Mimivirus life cycle within its amoeba host, Vertex-portal assemblies were, however, characterized only focusing on genome delivery and packaging stages that in herpesviruses that contain an external lipid membrane remain poorly understood in all members of the NCLDV [3,4,10], and in tailed double-stranded DNA (dsDNA) bacter- clade. By performing cryo-scanning electron microscopy and iophages in which membranes are absent [1,5–7,11]. This electron tomography on cryo-preserved host cells at different point is noteworthy in light of recent studies, which implied post-infection time points, we demonstrate that DNA exit that DNA packaging machinery in viruses containing an occurs in phagosome-enclosed viral particles through a inner membrane layer is fundamentally different from the massive opening of five icosahedral faces of the capsid. This vertex-portal apparatus of herpesviruses and bacteriophages large-scale capsid reorganization, which occurs at a unique, [12–14]. Specifically, inner membrane–containing viruses were shown to contain putative DNA-packaging ATPases that, in addition to the regular Walker A and B motifs, carry a Academic Editor: Bill Sugden, University of Wisconsin, Madison, United States of conserved motif that might act as a membrane anchor [12– America 14]. The structural aspects that underlie genome trans- Received December 4, 2007; Accepted March 25, 2008; Published May 13, 2008 location mechanisms deployed by these viruses remain, Copyright: Ó 2008 Zauberman et al. This is an open-access article distributed however, largely unknown [15]. under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the The amoeba-infecting virus Acanthamoeba polyphaga mimivi- original author and source are credited. rus is a member of the nucleocytoplasmic large DNA viruses Abbreviations: cryo-SEM, cryogenic scanning electron microscopy; dsDNA, (NCLDV) clade that comprises several eukaryote-infecting double-stranded DNA; NCLDV, nucleocytoplasmic large DNA virus; TEM, trans- viral families such as the Phycodnaviridae, Iridoviridae, and mission electron microscopy Asfarviridae [16]. As in all members of NCLDVs, the Mimivirus * To whom correspondence should be addressed. E-mail: avi.minsky@weizmann. is composed of a core containing a dsDNA genome, which is ac.il PLoS Biology | www.plosbiology.org1104 May 2008 | Volume 6 | Issue 5 | e114 Mimivirus: A Tale of Two Portals Author Summary vertex (Figure 1A). Geometric considerations of an icosahe- dron structure modified along five icosahedral edges that is Two fundamental events in viral life cycles are the delivery of viral randomly sliced indicate that if all viral particles include such genomes into host cells and the packaging of these genomes into a massive assembly, parts of this structure should be viral protein capsids. In bacteriophages and herpesviruses, these discerned in 75%–80% of the sections used for TEM analysis, processes occur linearly along the genome, base pair after base pair, depending on the thickness (70–80 nm) of the sections. In through a single portal located at a unique site in the viral capsid. ;500 extracellular viruses examined, the 5-fold assembly or We have addressed the question of whether such a linear translocation through a single portal also takes place for viruses parts thereof were detected in ;400 particles (80%), thus harboring very large genomes, by studying genome delivery and demonstrating that all viral particles contain this structure. packaging in the amoeba-infecting virus Acanthamoeba polyphaga None of the examined extracellular viral particles or of the mimivirus. With 1.2 million base pairs, this double-stranded DNA intracellular particles (see below) revealed more than one genome is the largest documented viral genome. By using electron star-shaped structure per particle, a finding fully consistent tomography and cryo-scanning electron microscopy, we identified a with single-particle cryo-TEM studies in which a single large tunnel in the Mimivirus capsid that is formed shortly after modified vertex was detected [18]. infection, following a large-scale opening of the capsid. The tunnel The presence of the star-shaped assembly was further allows the whole viral genome to exit in a rapid, one-step process. DNA encapsidation is mediated by a transient aperture in the capsid confirmed by cryo-TEM studies conducted on whole extra- that, we suggest, may promote concomitant entry of multiple cellular Mimivirus particles that were vitrified in their segments of the viral DNA molecule. These unprecedented modes hydrated state. Due to the interference of the extremely of viral genome translocation imply that Mimivirus—and potentially dense fiber layer that surrounds the viral capsids [18], the 5- other large viruses—evolved mechanisms that allow them to cope fold structure could not be detected in mature particles, but effectively with the exit and entry of particularly large genomes. was clearly and consistently discerned in immature, fiber-less viruses that constitute a small yet significant (;10%) population of the viruses that are released upon lysis of the structurally modified icosahedral vertex, allows for the fusion amoeba cells at the completion of the infection cycle (Figure of the internal viral membrane with the membrane of the 1B). host phagosome. The fusion leads, in turn, to the formation To ascertain that the 5-fold assembly represents a general of a massive membrane conduit through which DNA delivery and genuine feature, .500 extracellular Mimivirus particles occurs. In conjunction with single-particle reconstruction were analyzed by cryo-scanning electron microscopy (cryo- studies that indicated the presence of two successive SEM). These studies corroborate the presence of a massive 5- membrane layers underlying the Mimivirus protein shell fold structure at a unique vertex of the particle. The assembly [18], these observations raise the possibility that the Mim- is detected in fiber-covered Mimivirus where it appears as ivirus genome is released into the host cytoplasm and is crevices, but is particularly