Cytoplasmic polyhedrosis virus structure at 8 A by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation

The Role of Plant Latex in Virus Biology

At least 20,000 plant species produce latex, a capacity that appears to have evolved independently on numerous occasions. With a few exceptions, latex is stored under pressure in specialized cells known as laticifers and is exuded upon injury, leading to the assumption that it has a role in securing the plant after mechanical injury. In addition, a defensive effect against insect herbivores and fungal infections has been well established. Latex also appears to have effects on viruses, and laticifers are a hostile environment for virus colonization. Only one example of successful colonization has been reported: papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2) in Carica papaya. In this review, a summary of studies that support both the pro- and anti-viral effects of plant latex compounds is provided. The latex components represent a promising natural source for the discovery of new pro- and anti-viral molecules in the fields of agriculture and medicine.

Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein

Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells.

Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly

L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 Å. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA.

A 2.9 Å resolution structure of the L-BC virus provides insight into the contacts between capsid proteins and the mechanism of capsid assembly.

Viral Capsid and Polymerase in Reoviridae

The members of the family Reoviridae (reoviruses) consist of 9-12 discrete double-stranded RNA (dsRNA) segments enclosed by single, double, or triple capsid layers. The outer capsid proteins of reoviruses exhibit the highest diversity in both sequence and structural organization. By contrast, the conserved RNA-dependent RNA polymerase (RdRp) structure in the conserved innermost shell in all reoviruses suggests that they share common transcriptional regulatory mechanisms. After reoviruses are delivered into the cytoplasm of a host cell, their inner capsid particles (ICPs) remain intact and serve as a stable nanoscale machine for RNA transcription and capping performed using enzymes in ICPs. Advances in cryo-electron microscopy have enabled the reconstruction at near-atomic resolution of not only the icosahedral capsid, including capping enzymes, but also the nonicosahedrally distributed complexes of RdRps within the capsid at different transcriptional stages. These near-atomic resolution structures allow us to visualize highly coordinated structural changes in the related enzymes, genomic RNA, and capsid protein during reovirus transcription. In addition, reoviruses encode their own enzymes for nascent RNA capping before RNA releasing from their ICPs.

Atomic Structure of the Trichomonas vaginalis Double-Stranded RNA Virus 2

Trichomonas vaginalis viruses (TVVs) are double-stranded RNA (dsRNA) viruses that cohabitate in Trichomonas vaginalis, the causative pathogen of trichomoniasis, the most common nonviral sexually transmitted disease worldwide. Featuring an unsegmented dsRNA genome encoding a single capsid shell protein (CSP), TVVs contrast with multisegmented dsRNA viruses, such as the diarrhea-causing rotavirus, whose larger genome is split into 10 dsRNA segments encoding 5 unique capsid proteins.

Trichomonas vaginalis, the causative pathogen for the most common nonviral sexually transmitted infection worldwide, is itself frequently infected with one or more of the four types of small double-stranded RNA (dsRNA) Trichomonas vaginalis viruses (TVV1 to 4, genus Trichomonasvirus, family Totiviridae). Each TVV encloses a nonsegmented genome within a single-layered capsid and replicates entirely intracellularly, like many dsRNA viruses, and unlike those in the Reoviridae family. Here, we have determined the structure of TVV2 by cryo-electron microscopy (cryoEM) at 3.6 Å resolution and derived an atomic model of its capsid. TVV2 has an icosahedral, T = 2*, capsid comprised of 60 copies of the icosahedral asymmetric unit (a dimer of the two capsid shell protein [CSP] conformers, CSP-A and CSP-B), typical of icosahedral dsRNA virus capsids. However, unlike the robust CSP-interlocking interactions such as the use of auxiliary “clamping” proteins among Reoviridae, only lateral CSP interactions are observed in TVV2, consistent with an assembly strategy optimized for TVVs’ intracellular-only replication cycles within their protozoan host. The atomic model reveals both a mostly negatively charged capsid interior, which is conducive to movement of the loosely packed genome, and channels at the 5-fold vertices, which we suggest as routes of mRNA release during transcription. Structural comparison of TVV2 to the Saccharomyces cerevisiae L-A virus reveals a conserved helix-rich fold within the CSP and putative guanylyltransferase domain along the capsid exterior, suggesting conserved mRNA maintenance strategies among Totiviridae. This first atomic structure of a TVV provides a framework to guide future biochemical investigations into the interplay between Trichomonas vaginalis and its viruses.

Alkaline phosphatase can promote the replication of Bombyx mori cypovirus 1 by interaction with its turret protein

Bombyx mori cypovirus 1 (BmCPV1) is a member of the Reoviridae family which is characterized by its single-layered capsid. Similar with other turreted viruses in the Reoviridae, transcription of BmCPV1 occurs inside the capsid, and the nascent mRNA is released to the turret which consists of five turret proteins (TPs) and located at the 5-fold axis of the outer capsid, then the capping enzyme TP will guanylate and methylate the nascent viral mRNA to produce a matured mRNA. However, during these processes, how the BmCPV1 draws other cellular proteins to facilitate its replication is still lesser-known. Here we used an ELISA to investigate the interaction between ALP and BmCPV1. A co-immunoprecipitation technique was employed to detect the interaction of ALP with the Methylase domain of TP. We further studied whether ALP affects the replication of BmCPV1 inside the cell, results show that reducing the expression of ALP through RNAi reduced the transcription level of the BmCPV1 VP1 gene, which was increased by overexpression of ALP. In summary, our data demonstrate an interaction between ALP and BmCPV1 and that ALP promoted the replication of BmCPV1, and support our hypothesis of the ALP is an RTPase to facilitate the capping process of BmCPV1.

Molecular insights into RNA-binding properties of Escherichia coli-expressed RNA-dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus

Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) is responsible for morbidity of the Indian non-mulberry silkworm, A. mylitta. AmCPV belongs to the family Reoviridae and has 11 double-stranded (ds) RNA genome segments (S1-S11). Segment 2 (S2) encodes a 123-kDa polypeptide with RNA-dependent RNA polymerase (RdRp) activity. To examine the RNA-binding properties of the viral polymerase, the full-length RdRp and its three domains (N-terminal, polymerase and C-terminal domains) were expressed in Escherichia coli BL21 (DE3) cells with hexahistidine and trigger factor tag fused consecutively at its amino terminus, and the soluble fusion proteins were purified. The purified full-length polymerase specifically bound to the 3' untranslated region (3'-UTR) of a viral plus-sense (+) strand RNA with strong affinity regardless of the salt concentrations, but the isolated polymerase domain of the enzyme exhibited poor RNA-binding ability. Further, the RdRp recognition signals were found to be different from the cis-acting signals that promote minus-sense (-) strand RNA synthesis, because different internal regions of the 3'-UTR of the (+) strand RNA did not effectively compete out the binding of RdRp to the intact 3'-UTR of the (+) strand RNA, but all of these RNA molecules could serve as templates for (-) strand RNA synthesis by the polymerase.

Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus

Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.

A putative ATPase mediates RNA transcription and capping in a dsRNA virus

mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus.

Functional insights from molecular modeling, docking, and dynamics study of a cypoviral RNA dependent RNA polymerase

Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) contains 11 double stranded RNA genome segments and infects tasar silkworm A. mylitta. RNA-dependent RNA polymerase (RdRp) is reported as a key enzyme responsible for propagation of the virus in the host cell but its structure function relationship still remains elusive. Here a computational approach has been taken to compare sequence and secondary structure of AmCPV RdRp with other viral RdRps to identify consensus motifs. Then a reliable pairwise sequence alignment of AmCPV RdRp with its closest sequence structure homologue λ3 RdRp is done to predict three dimensional structure of AmCPV RdRp. After comparing with other structurally known viral RdRps, important sequence and/or structural features involved in substrate entry or binding, polymerase reaction and the product release events have been identified. A conserved RNA pentanucleotide (5'-AGAGC-3') at the 3'-end of virus genome is predicted as cis-acting signal for RNA synthesis and its docking and simulation study along with the model of AmCPV RdRp has allowed to predict mode of template binding by the viral polymerase. It is found that template RNA enters into the catalytic center through nine sequence-independent and two sequence-dependent interactions with the specific amino acid residues. However, number of sequence dependent interactions remains almost same during 10 nano-second simulation time while total number of interactions decreases. Further, docking of N(7)-methyl-GpppG (mRNA cap) on the model as well as prediction of RNA secondary structure has shown the template entry process in the active site. These findings have led to postulate the mechanism of RNA-dependent RNA polymerization process by AmCPV RdRp. To our knowledge, this is the first report to evaluate structure function relationship of a cypoviral RdRp.

Transmission electron microscopy and the molecular structure of icosahedral viruses

The field of structural virology developed in parallel with methodological advances in X-ray crystallography and cryo-electron microscopy. At the end of the 1970s, crystallography yielded the first high resolution structure of an icosahedral virus, the T=3 tomato bushy stunt virus at 2.9Å. It took longer to reach near-atomic resolution in three-dimensional virus maps derived from electron microscopy data, but this was finally achieved, with the solution of complex icosahedral capsids such as the T=25 human adenovirus at ∼3.5Å. Both techniques now work hand-in-hand to determine those aspects of virus assembly and biology that remain unclear. This review examines the trajectory followed by EM imaging techniques in showing the molecular structure of icosahedral viruses, from the first two-dimensional negative staining images of capsids to the latest sophisticated techniques that provide high resolution three-dimensional data, or snapshots of the conformational changes necessary to complete the infectious cycle.

Identification of mud crab reovirus VP12 and its interaction with the voltage-dependent anion-selective channel protein of mud crab Scylla paramamosain

Mud crab reovirus (MCRV) is the causative agent of a severe disease in cultured mud crab (Scylla paramamosain), which has caused huge economic losses in China. MCRV is a double-stranded RNA virus with 12 genomic segments. In this paper, SDS-PAGE, mass spectrometry and Western blot analyses revealed that the VP12 protein encoded by S12 gene is a structural protein of MCRV. Immune electron microscopy assay indicated that MCRV VP12 is a component of MCRV outer shell capsid. Yeast two hybrid cDNA library of mud crab was constructed and mud crab voltage-dependent anion-selective channel (mcVDAC) was obtained by MCRV VP12 screening. The full length of mcVDAC was 1180 bp with an open reading frame (ORF) of 849 bp encoding a 282 amino acid protein. The mcVDAC had a constitutive expression pattern in different tissues of mud crab. The interaction between MCRV VP12 and mcVDAC was determined by co-immunoprecipitation assay. The results of this study have provided an insight on the mechanisms of MCRV infection and the interactions between the virus and mud crab.

A newly isolated reovirus has the simplest genomic and structural organization of any reovirus

A total of 2,691 mosquitoes representing 17 species was collected from eight locations in southwest Cameroon and screened for pathogenic viruses. Ten isolates of a novel reovirus (genus Dinovernavirus) were detected by culturing mosquito pools on Aedes albopictus (C6/36) cell cultures. A virus that caused overt cytopathic effects was isolated, but it did not infect vertebrate cells or produce detectable disease in infant mice after intracerebral inoculation. The virus, tentatively designated Fako virus (FAKV), represents the first 9-segment, double-stranded RNA (dsRNA) virus to be isolated in nature. FAKV appears to have a broad mosquito host range, and its detection in male specimens suggests mosquito-to-mosquito transmission in nature. The structure of the T=1 FAKV virion, determined to subnanometer resolution by cryoelectron microscopy (cryo-EM), showed only four proteins per icosahedral asymmetric unit: a dimer of the major capsid protein, one turret protein, and one clamp protein. While all other turreted reoviruses of known structures have at least two copies of the clamp protein per asymmetric unit, FAKV's clamp protein bound at only one conformer of the major capsid protein. The FAKV capsid architecture and genome organization represent the most simplified reovirus described to date, and phylogenetic analysis suggests that it arose from a more complex ancestor by serial loss-of-function events.

IMPORTANCE

We describe the detection, genetic, phenotypic, and structural characteristics of a novel Dinovernavirus species isolated from mosquitoes collected in Cameroon. The virus, tentatively designated Fako virus (FAKV), is related to both single-shelled and partially double-shelled viruses. The only other described virus in this genus was isolated from cultured mosquito cells. It was previously unclear whether the phenotypic characteristics of that virus were reflective of this genus in nature or were altered during serial passaging in the chronically infected cell line. FAKV is a naturally occurring single-shelled reovirus with a unique virion architecture that lacks several key structural elements thought to stabilize a single-shelled reovirus virion, suggesting what may be the minimal number of proteins needed to form a viable reovirus particle. FAKV evolved from more complex ancestors by losing a genome segment and several virion proteins.

Genome segment 4 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes RNA triphosphatase and methyltransferases

Cloning and sequencing of Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) genome segment S4 showed that it consists of 3410 nt with a single ORF of 1110 aa which could encode a protein of ~127 kDa (p127). Bioinformatics analysis showed the presence of a 5' RNA triphosphatase (RTPase) domain (LRDR), a S-adenosyl-l-methionine (SAM)-binding (GxGxG) motif and the KDKE tetrad of 2'-O-methyltransferase (MTase), which suggested that S4 may encode RTPase and MTase. The ORF of S4 was expressed in Escherichia coli as a His-tagged fusion protein and purified by nickel-nitrilotriacetic acid affinity chromatography. Biochemical analysis of recombinant p127 showed its RTPase as well as SAM-dependent guanine N(7)-and ribose 2'-O-MTase activities. A MTase assay using in vitro transcribed AmCPV S2 RNA having a 5' G*pppG end showed that guanine N(7) methylation occurred prior to the ribose 2'-O methylation to yield a m(7)GpppG/m(7)GpppGm RNA cap. Mutagenesis of the SAM-binding (GxGxG) motif (G831A) completely abolished N(7)- and 2'-O-MTase activities, indicating the importance of these residues for capping. From the kinetic analysis, the Km values of N(7)-MTase for SAM and RNA were calculated as 4.41 and 0.39 µM, respectively. These results suggested that AmCPV S4-encoded p127 catalyses RTPase and two cap methylation reactions for capping the 5' end of viral RNA.

Interactions among Dendrolimus punctatus cypovirus proteins and identification of the genomic segment encoding its A-spike

Revealing the interactions among cypovirus proteins would facilitate our understanding of the replication and assembly of this virus. In the present study, interactions among proteins encoded by the 10 segments of Dendrolimus punctatus cypovirus (DpCPV) were identified using yeast two-hybrid (Y2H) and far-Western blotting assays. In total, 24 pairs of interactions were detected. Twelve pairs of one-direction interactions, four pairs of binary interactions and four pairs of self-associations were identified in the Y2H assays. Another four pairs of interactions were identified by far-Western blotting. The interactions between the methyltransferase domain of the turret protein (VP3) and VP4 as well as between polyhedrin and VP4 were further confirmed by far-Western blotting and pull-down assays, respectively. In addition, immunogold labelling showed that the A-spike of DpCPV is formed by VP4. In conclusion, we obtained a protein-protein interaction network of DpCPV and showed that its A-spike is formed by VP4 encoded by genomic segment 6.

Genome segment 5 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes a bona fide guanylyltransferase

BACKGROUND

Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV), a cypovirus of Reoviridae family, infects non mulberry Indian silk worm, Antheraea mylitta, and contains eleven segmented double stranded RNA in its genome (S1-S11). Some of its genome segments (S1-S3, and S6-S11) have been previously characterized but genome segment encoding the viral guanylyltransferase which helps in RNA capping has not been characterized.

RESULTS

In this study genome segment 5 (S5) of AmCPV was converted to cDNA, cloned and sequenced. S5 consisted of 2180 nucleotides, with one long ORF of 1818 nucleotides and could encode a protein of 606 amino acids with molecular mass of ~65 kDa (p65). Bioinformatics analysis showed presence of KLRS and HxnH motifs as observed in some other reoviral guanylyltransferase and suggests that S5 may encodes viral guanylyltransferase. The ORF of S5 was expressed in E. coli as 65 kDa his tagged fusion protein, purified through Ni-NTA chromatography and polyclonal antibody was raised. Immunoblot analysis of virion particles with the purified antibody showed specific immunoreactive band and suggests p65 as a viral structural protein. Functional analysis showed that recombinant p65 possesses guanylyltransferase activity, and transfers GMP moiety to the 5' diphosphate (A/G) ended viral RNA after the formation of p65-GMP complex for capping. Kinetic analysis showed K(m) of this enzyme for GTP and RNA was 34.24 uM and 98.35 nM, respectively. Site directed mutagenesis at K21A in KLRS motif, and H93A or H105A in HxnH motif completely abolished the autoguanylylation activity and indicates importance of these residues at these sites. Thermodynamic analysis showed p65-GTP interaction was primarily driven by enthalpy (ΔH = -399.1 ± 4.1 kJ/mol) whereas the p65-RNA interaction by favorable entropy (0.043 ± 0.0049 kJ/ mol).

CONCLUSION

Viral capping enzymes play a critical role in the post transcriptional or post replication modification in case of RNA virus. Our results of cloning, sequencing and functional analysis of AmCPV S5 indicates that S5 encoded p65 through its guanylyltransferase activity can transfer guanine residue to the 5' end of viral RNA for capping. Further studies will help to understand complete capping process of cypoviral RNA during viral replication within the viral capsid.

A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing

For double-stranded RNA (dsRNA) viruses in the family Reoviridae, their inner capsids function as the machinery for viral RNA (vRNA) replication. Unlike other multishelled reoviruses, cypovirus has a single-layered capsid, thereby representing a simplified model for studying vRNA replication of reoviruses. VP5 is one of the three major cypovirus capsid proteins and functions as a clamp protein to stabilize cypovirus capsid. Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. Our further characterization of VP5 revealed that its helix-destabilizing activity is RNA specific, lacks directionality and could be inhibited by divalent ions, such as Mg(2+), Mn(2+), Ca(2+) or Zn(2+), to varying degrees. Furthermore, we found that HaCPV-5 VP5 facilitates the replication initiation of an alternative polymerase (i.e. reverse transcriptase) through a panhandle-structured RNA template, which mimics the 5'-3' cyclization of cypoviral positive-stranded RNA. Given that the replication of negative-stranded vRNA on the positive-stranded vRNA template necessitates the dissociation of the 5'-3' panhandle, the RNA chaperone activity of VP5 may play a direct role in the initiation of reoviral dsRNA synthesis.

Molecular characterization of protein p50 of Dendrolimus punctatus cytoplasmic polyhedrosis virus

Genome segment 7 of the 10-segmented RNA genomes of Dendrolimus punctatus cytoplasmic polyhedrosis virus (DpCPV) comprises 1502 nucleotides with one ORF of 1347 bp. This ORF was predicted to encode a protein of 448 amino acids with a molecular mass of 49,756 Da (p50). Antisera against both p50 and an antigen domain (AD) near the N-terminus of p50 specifically bound to a viral structural protein of ca. 33 kDa (V5), indicating that V5 was an N-terminal product of p50. Immunoblotting analysis with anti-p50 antibodies detected p50 and V5 molecules in the host midguts three days and five days post infection, respectively. The intracellular localization of p50 protein was examined by expressing truncations of p50 fused with GFP in recombinant baculovirus-infected Sf9 cells. The p50 protein was present in the cytoplasm of the cells, and the N-terminal portion (67-135 aa) of the protein played a key role in this localization.

Cryo-EM structure of a transcribing cypovirus

Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transcription and capping process is facilitated by viral capsid proteins is still unknown. Cypovirus provides a good model system for studying the mRNA transcription and capping mechanism of viruses in the family Reoviridae. Here, we report a full backbone model of a transcribing cypovirus built from a near-atomic-resolution density map by cryoelectron microscopy. Compared with the structure of a nontranscribing cypovirus, the major capsid proteins of transcribing cypovirus undergo a series of conformational changes, giving rise to structural changes in the capsid shell: (i) an enlarged capsid chamber, which provides genomic RNA with more flexibility to move within the densely packed capsid, and (ii) a widened peripentonal channel in the capsid shell, which we confirmed to be a pathway for nascent mRNA. A rod-like structure attributable to a partially resolved nascent mRNA was observed in this channel. In addition, conformational change in the turret protein results in a relatively open turret at each fivefold axis. A GMP moiety, which is transferred to 5'-diphosphorylated mRNA during the mRNA capping reaction, was identified in the pocket-like guanylyltransferase domain of the turret protein.

Structural insights into the classification of Mud Crab Reovirus

Cryo-electron microscopy was applied to analyze mud crab reovirus (MCRV), which causes 'sleeping disease' in mud crab, Scylla serrata, a marine species cultured in China. We present here the three dimensional structure of MCRV at 13.8Å resolution. The outer capsid shell is composed of 260 trimers with complete T=13 icosahedral symmetry. A major difference between MCRV and previously reported aquareoviruses is that it lacks a pentameric turret structure. These results together with recently published molecular biological evidence (Deng et al., 2012) indicate that, from a structural perspective, MCRV should be classified as a new member of the family Reoviridae.

Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses

Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we report a 3.1 Å resolution cryo electron microscopy structure of CPV and derive its atomic model, consisting of 60 turret proteins (TPs), 120 each of capsid shell proteins (CSPs) and large protrusion proteins (LPPs). Two unique segments of CSP contribute to CPV's stability: an inserted protrusion domain interacting with neighboring proteins, and an N-anchor tying up CSPs together through strong interactions such as β sheet augmentation. Without the need to interact with outer shell proteins, LPP retains only the N-terminal two-third region containing a conserved helix-barrel core and interacts exclusively with CSP. TP is also simplified, containing only domains involved in RNA capping. Our results illustrate how CPV proteins have evolved in a coordinative manner to economically carry out their conserved functions.

Electron tomography reveals polyhedrin binding and existence of both empty and full cytoplasmic polyhedrosis virus particles inside infectious polyhedra

Previous studies have described the structure of purified cytoplasmic polyhedrosis virus (CPV) and that of polyhedrin protein. However, how polyhedrin molecules embed CPV particles inside infectious polyhedra is not known. By using electron tomography, we show that CPV particles are occluded within the polyhedrin crystalline lattice with a random spatial distribution and interact with the polyhedrin protein through the A-spike rather than as previously thought through the B-spike. Furthermore, both full (with RNA) and empty (no RNA) capsids were found inside polyhedra, suggesting a spontaneous RNA encapsidating process for CPV assembly in vivo.

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-N-methyltransferase, and 2'-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7.

Atomic resolution cryo electron microscopy of macromolecular complexes

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their "native," noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.

Molecular characterization of genome segments 1 and 3 encoding two capsid proteins of Antheraea mylitta cytoplasmic polyhedrosis virus

Background

Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV), a cypovirus of Reoviridae family, infects Indian non-mulberry silkworm, Antheraea mylitta, and contains 11 segmented double stranded RNA (S1-S11) in its genome. Some of its genome segments (S2 and S6-S11) have been previously characterized but genome segments encoding viral capsid have not been characterized.

Results

In this study genome segments 1 (S1) and 3 (S3) of AmCPV were converted to cDNA, cloned and sequenced. S1 consisted of 3852 nucleotides, with one long ORF of 3735 nucleotides and could encode a protein of 1245 amino acids with molecular mass of ~141 kDa. Similarly, S3 consisted of 3784 nucleotides having a long ORF of 3630 nucleotides and could encode a protein of 1210 amino acids with molecular mass of ~137 kDa. BLAST analysis showed 20-22% homology of S1 and S3 sequence with spike and capsid proteins, respectively, of other closely related cypoviruses like Bombyx mori CPV (BmCPV), Lymantria dispar CPV (LdCPV), and Dendrolimus punctatus CPV (DpCPV). The ORFs of S1 and S3 were expressed as 141 kDa and 137 kDa insoluble His-tagged fusion proteins, respectively, in Escherichia coli M15 cells via pQE-30 vector, purified through Ni-NTA chromatography and polyclonal antibodies were raised. Immunoblot analysis of purified polyhedra, virion particles and virus infected mid-gut cells with the raised anti-p137 and anti-p141 antibodies showed specific immunoreactive bands and suggest that S1 and S3 may code for viral structural proteins. Expression of S1 and S3 ORFs in insect cells via baculovirus recombinants showed to produce viral like particles (VLPs) by transmission electron microscopy. Immunogold staining showed that S3 encoded proteins self assembled to form viral outer capsid and VLPs maintained their stability at different pH in presence of S1 encoded protein.

Conclusion

Our results of cloning, sequencing and functional analysis of AmCPV S1 and S3 indicate that S3 encoded viral structural proteins can self assemble to form viral outer capsid and S1 encoded protein remains associated with it as inner capsid to maintain the stability. Further studies will help to understand the molecular mechanism of capsid formation during cypovirus replication.

Microarray analysis of the gene expression profile in the midgut of silkworm infected with cytoplasmic polyhedrosis virus

In order to obtain an overall view on silkworm response to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection, a microarray system comprising 22,987 oligonucluotide 70-mer probes was employed to compare differentially expressed genes in the midguts of BmCPV-infected and normal silkworm larvae. At 72 h post-inoculation, 258 genes exhibited at least 2.0-fold differences in expression level. Out of these, 135 genes were up-regulated, while 123 genes were down-regulated. According to gene ontology (GO), 140 genes were classified into GO categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates that 35 genes were involved in 10 significant (P<0.05) KEGG pathways. The expressions of genes related to valine, leucine, and isoleucine degradation, retinol metabolism, and vitamin B6 metabolism were all down-regulated. The expressions of genes involved in ribosome and proteasome pathway were all up-regulated. Quantitative real-time polymerase chain reaction was performed to validate the expression patterns of 13 selected genes of interest. The results suggest that BmCPV infection resulted in the disturbance of protein and amino acid metabolism and a series of major physiological and pathological changes in silkworm. Our results provide new insights into the molecular mechanism of BmCPV infection and host cell response.

Application of symmetry adapted function method for three-dimensional reconstruction of octahedral biological macromolecules

A method for three-dimensional (3D) reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs) method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein Degp₂₄ and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N) = 0.1, 0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.

Structural evolution of reoviridae revealed by oryzavirus in acquiring the second capsid shell

The conservation of the core structure and diversification of the external features among the turreted reoviruses appear to be relevant to structural evolution in facilitating the infection of diverse host species. The structure of Rice ragged stunt virus (RRSV), in the genus Oryzavirus of the family Reoviridae, is determined to show a core composed of capsid shell, clamps, and long turrets. The RRSV core structure is equivalent to the core structure of Orthoreovirus and the virion structure of Cytoplasmic polyhedrosis virus (CPV). In RRSV, five peripheral trimers surround each long turret and sit at the Q trimer position in the T=13l icosahedral symmetry, a structural feature unique to turreted reoviruses. That is, the core of RRSV is partially covered by 60 copies of the peripheral trimer. In contrast, the core of Orthoreovirus is covered by 200 copies of the trimer that sit at the Q, R, S, and T trimer positions. Our results suggest that among the three viruses, RRSV has a structure intermediate between that of Orthoreovirus and the CPV virion. This conclusion coincides with the results of the phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerases.

Molecular characterisation of a cypovirus isolated from the western spruce budworm Choristoneura occidentalis

A novel cypovirus, assigned CoCPV, was isolated from natural populations of the western spruce budworm, Choristoneura occidentalis. The complete nucleotide sequences of genomic segments S2-S5 and S7-S10 were determined. Each segment contained a single open reading frame. Conserved motifs 5' (AGUUU......UUUGUGC) 3' were found at the ends of each segment. Analysis of S2, which encoded a putative RNA-dependent RNA polymerase protein, confirmed CoCPV belonged to the genus Cypovirus within the family Reoviridae. Further phylogenetic analysis using S10 (the polyhedrin gene) aligned this virus with species type-16, closely related to a cypovirus isolated from C. fumiferana.

Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers

Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged in icosahedral capsids containing 120 coat-protein subunits. We used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structure of Penicillium stoloniferum virus S at 7.3 A resolution. The capsid, approximately 350 A in outer diameter, contains 12 pentons, each of which is topped by five arched protrusions. Each of these protrusions is, in turn, formed by a quasisymmetric dimer of coat protein, for a total of 60 such dimers per particle. The density map shows numerous tubular features, characteristic of alpha helices and consistent with secondary structure predictions for the coat protein. This three-dimensional structure of a virus from the family Partitiviridae exhibits both similarities to and differences from the so-called "T = 2" capsids of other dsRNA viruses.

Subnanometer-resolution structures of the grass carp reovirus core and virion

Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We report the first subnanometer-resolution three-dimensional structures of both GCRV core and virion by cryoelectron microscopy. These structures have allowed the delineation of interactions among the over 1000 molecules in this enormous macromolecular machine and a detailed comparison with other dsRNA viruses at the secondary-structure level. The GCRV core structure shows that the inner proteins have strong structural similarities with those of orthoreoviruses even at the level of secondary-structure elements, indicating that the structures involved in viral dsRNA interaction and transcription are highly conserved. In contrast, the level of similarity in structures decreases in the proteins situated in the outer layers of the virion. The proteins involved in host recognition and attachment exhibit the least similarities to other members of Reoviridae. Furthermore, in GCRV, the RNA-translocating turrets are in an open state and lack a counterpart for the sigma1 protein situated on top of the close turrets observed in mammalian orthoreovirus. Interestingly, the distribution and the organization of GCRV core proteins resemble those of the cytoplasmic polyhedrosis virus, a cypovirus and the structurally simplest member of the Reoviridae family. Our results suggest that GCRV occupies a unique structure niche between the simpler cypoviruses and the considerably more complex mammalian orthoreovirus, thus providing an important model for understanding the structural and functional conservation and diversity of this enormous family of dsRNA viruses.

3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy

Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.

Towards atomic resolution structural determination by single-particle cryo-electron microscopy

Recent advances in cryo-electron microscopy and single-particle reconstruction (collectively referred to as 'cryoEM') have made it possible to determine the three-dimensional (3D) structures of several macromolecular complexes at near-atomic resolution ( approximately 3.8-4.5A). These achievements were accomplished by overcoming the challenges in sample handling, instrumentation, image processing, and model building. At near-atomic resolution, many detailed structural features can be resolved, such as the turns and deep grooves of helices, strand separation in beta sheets, and densities for loops and bulky amino acid side chains. Such structural data of the cytoplasmic polyhedrosis virus (CPV), the Epsilon 15 bacteriophage and the GroEL complex have provided valuable constraints for atomic model building using integrative tools, thus significantly enhancing the value of the cryoEM structures. The CPV structure revealed a drastic conformational change from a helix to a beta hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain. These latest advances in single-particle cryoEM provide exciting opportunities for the 3D structural determination of viruses and macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR) methods.

The complete nucleotide sequence of the type 5 Helicoverpa armigera cytoplasmic polyhedrosis virus genome

The S1-6, S8, and S9 segments of the type 5 Helicoverpa armigera cytoplasmic polyhedrosis virus (HaCPV-5, Chinese strain) were cloned and sequenced, completing the HaCPV-5 genome. We found that each HaCPV-5 segment exhibits the conserved terminal sequences AGUU and UUGC located at the 5' and 3' ends, respectively. We also analyzed the translation initiation codon of the HaCPV-5 genome and compared it with the available cypovirus sequences in GenBank. We postulated that the conserved purine at the -3 position in relation to the AUG codon is probably the most important nucleotide for efficient translation initiation in cypovirus. Although the nucleotide sequences of the HaCPV-5 segments S1-10 exhibit no significant similarity to other viruses, blast searches did reveal some similarities between predicted HaCPV-5 amino acid sequences and those of other viruses.

Structures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains

Dihydrolipoyl acetyltransferase (E2) is the central component of pyruvate dehydrogenase complex (PDC), which converts pyruvate to acetyl-CoA. Structural comparison by cryo-electron microscopy (cryo-EM) of the human full-length and truncated E2 (tE2) cores revealed flexible linkers emanating from the edges of trimers of the internal catalytic domains. Using the secondary structure constraints revealed in our 8 A cryo-EM reconstruction and the prokaryotic tE2 atomic structure as a template, we derived a pseudo atomic model of human tE2. The active sites are conserved between prokaryotic tE2 and human tE2. However, marked structural differences are apparent in the hairpin domain and in the N-terminal helix connected to the flexible linker. These permutations away from the catalytic center likely impart structures needed to integrate a second component into the inner core and provide a sturdy base for the linker that holds the pyruvate dehydrogenase for access by the E2-bound regulatory kinase/phosphatase components in humans.

Structural studies on orbivirus proteins and particles

X-ray and electron microscopy analysis of Bluetongue virus (BTV), the type species of the Orbivirus genus within the family Reoviridae, have revealed various aspects of the organisation and structure of the proteins that form the viral capsid. Orbiviruses have a segmented dsRNA genome, which imposes constraints on their structure and life cycle. The atomic structure of the BTV core particle, the key viral component which transcribes the viral mRNA within the cell cytoplasm, revealed the architecture and assembly of the major core proteins VP7 and VP3. In addition, these studies formed the basis for a plausible model for the organisation of the dsRNA viral genome and the arrangement of the viral transcriptase complex (composed of the RNA-dependent RNA polymerase, the viral capping enzyme and RNA helicase) that resides within the core particle. Electron cryo-microscopy of the viral particle has shown how the two viral proteins VP2 and VP5 are arranged to form the outer capsid, with distinct packing arrangements between them and the core protein VP7. By comparison of the outer capsid proteins of orbiviruses with those of other nonturreted members of the family Reoviridae, we are able to propose a more detailed model of these structures and possible mechanisms for cell entry. Further structural results are also discussed including the atomic structure of an N-terminal domain of nonstructural protein NS2, a protein involved in virus genome assembly and morphogenesis.

Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging

Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to expansion of the polymerase complex, minus and plus strand RNA synthesis, and assembly of the nucleocapsid. The phi6 in vitro assembly and packaging system is a valuable model for dsRNA virus replication. The structure of the nucleocapsid at 7.5 A resolution presented here reveals the secondary structure of the two major capsid proteins. Asymmetric P1 dimers organize as an inner T = 1 shell, and P8 trimers organize as an outer T = 13 laevo shell. The organization of the P1 molecules in the unexpanded and expanded polymerase complex suggests that the expansion is accomplished by rigid body movements of the P1 monomers. This leads to exposure of new potential RNA binding surfaces to control the sequential packaging of the genome segments.

Identification and genome characterization of Heliothis armigera cypovirus types 5 and 14 and Heliothis assulta cypovirus type 14

Genomic characterization of Heliothis armigera cypovirus (HaCPV) isolated from China showed that insects were co-infected with several cypoviruses (CPVs). One of the CPVs (HaCPV-5) could be separated from the others by changing the rearing conditions of the Heliothis armigera larvae. This finding was further confirmed by nucleotide sequencing analysis. Genomic sequences of segments S10-S7 from HaCPV-14, S10 and S7 from HaCPV-5, and S10 from Heliothis assulta CPV-14 were compared. Results from database searches showed that the nucleotide sequences and deduced amino acid sequences of the newly identified CPVs had high levels of identity with those of reported CPVs of the same type, but not with CPVs of different types. Putative amino acid sequences of HaCPV-5 S7 were similar to that of the protein from Rice ragged stunt virus (genus Oryzavirus, family Reoviridae), suggesting that CPVs and oryzaviruses are related more closely than other genera of the family Reoviridae. Conserved motifs were also identified at the ends of each RNA segment of the same virus type: type 14, 5'-AGAAUUU...CAGCU-3'; and type 5, 5'-AGUU...UUGC-3'. Our results are consistent with classification of CPV types based on the electrophoretic patterns of CPV double-stranded RNA.

Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction

Among members of the genus Orthoreovirus, family Reoviridae, a group of non-enveloped viruses with genomes comprising ten segments of double-stranded RNA, only the "non-fusogenic" mammalian orthoreoviruses (MRVs) have been studied to date by electron cryomicroscopy and three-dimensional image reconstruction. In addition to MRVs, this genus comprises other species that induce syncytium formation in cultured cells, a property shared with members of the related genus Aquareovirus. To augment studies of these "fusogenic" orthoreoviruses, we used electron cryomicroscopy and image reconstruction to analyze the virions of a fusogenic avian orthoreovirus (ARV). The structure of the ARV virion, determined from data at an effective resolution of 14.6 A, showed strong similarities to that of MRVs. Of particular note, the ARV virion has its pentameric lambda-class core turret protein in a closed conformation as in MRVs, not in a more open conformation as reported for aquareovirus. Similarly, the ARV virion contains 150 copies of its monomeric sigma-class core-nodule protein as in MRVs, not 120 copies as reported for aquareovirus. On the other hand, unlike that of MRVs, the ARV virion lacks "hub-and-spokes" complexes within the solvent channels at sites of local sixfold symmetry in the incomplete T=13l outer capsid. In MRVs, these complexes are formed by C-terminal sequences in the trimeric mu-class outer-capsid protein, sequences that are genetically missing from the homologous protein of ARVs. The channel structures and C-terminal sequences of the homologous outer-capsid protein are also genetically missing from aquareoviruses. Overall, the results place ARVs between MRVs and aquareoviruses with respect to the highlighted features.

Parvovirus uncoating in vitro reveals a mechanism of DNA release without capsid disassembly and striking differences in encapsidated DNA stability

The uncoating mechanism of parvoviruses is unknown. Their capsid robustness and increasing experimental data would suggest an uncoating mechanism without capsid disassembly. We have developed an in vitro system to detect and quantify viral DNA externalization and applied the assay on two parvoviruses with important differences in capsid structure, human B19 and minute virus of mice (MVM). Upon briefly treating the capsids to increasing temperatures, the viral genome became accessible in its full-length in a growing proportion of virions. Capsid disassembly started at temperatures above 60 degrees C for B19 and 70 degrees C for MVM. For both viruses, the externalization followed an all-or-nothing mechanism, without transitions exposing only a particular genomic region. However, the heat-induced DNA accessibility was remarkably more pronounced in B19 than in MVM. This difference was also evident under conditions mimicking endosomal acidification (pH 6.5 to 5), which triggered the externalization of B19-DNA but not of MVM-DNA. The externalized ssDNA was a suitable template for the full second-strand synthesis. Immunoprecipitation with antibodies against conformational epitopes and quantitative PCR revealed that the DNA externalized by heat was mostly dissociated from its capsid, however, the low pH-induced DNA externalization of B19 was predominantly capsid-associated. These results provide new insights into parvovirus uncoating suggesting a mechanism by which the full-length viral genome is released without capsid disassembly. The remarkable instability of the encapsidated B19 DNA, which is easily released from its capsid, would also explain the faster heat inactivation of B19 when compared to other parvoviruses.

Electron cryomicroscopy of single particles at subnanometer resolution

Electron cryomicroscopy and single-particle reconstruction have advanced substantially over the past two decades. There are now numerous examples of structures that have been solved using this technique to better than 10 A resolution. At such resolutions, direct identification of alpha helices is possible and, often, beta-sheet-containing regions can be identified. The most numerous subnanometer resolution structures are the icosahedral viruses, as higher resolution is easier to achieve with higher symmetry. Important non-icosahedral structures solved to subnanometer resolution include several ribosome structures, clathrin assemblies and, most recently, the Ca2+ release channel. There is now hope that, in the next few years, this technique will achieve resolutions approaching 4 A, permitting a complete trace of the protein backbone without reference to a crystal structure.

The structural basis of recognition and removal of cellular mRNA 7-methyl G 'caps' by a viral capsid protein: a unique viral response to host defense

The single segment, double-stranded RNA genome of the L-A virus (L-A) of yeast encodes two proteins: the major coat protein Gag (76 kDa) and the Gag-Pol fusion protein (180 kDa). The icosahedral L-A capsid is formed by 120 copies of Gag and has architecture similar to that seen in the reovirus, blue tongue virus and rice dwarf virus inner protein shells. Gag chemically removes the m7GMP caps from host cellular mRNAs. Previously we identified a trench on the outer surface of Gag that included His154, to which caps are covalently attached. Here we report the refined L-A coordinates at 3.4 angstroms resolution with additional structural features and the structure of L-A with bound m7GDP at 6.5 angstroms resolution, which shows the conformational change of the virus upon ligand binding. Based on site-directed mutations, residues in or adjacent to the trench that are essential (or dispensable) for the decapping reaction are described here. Along with His154, the reaction requires a cluster of positive charge adjoining the trench and residues Tyr 452, Tyr150 and either Tyr or Phe at position 538. A tentative mechanism for decapping is proposed.

Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs

A new generation of electron microscopes equipped with field emission gun electron sources and the ability to image molecules in their native environment at liquid nitrogen or helium temperatures has enabled the analysis of macromolecular structures at medium resolution (approximately 10 angstroms) and in different conformational states. The amalgamation of electron microscopy and X-ray crystallographic approaches makes it possible to solve structures in the 100-1000 angstroms size range, advancing our understanding of the function of complex assemblies. Many new structures have been solved during the past two years, including one of the smallest complexes to be determined by single-particle cryo-electron microscopy, the transferrin receptor-transferrin complex. Other notable results include the near atomic level resolution structure of the nicotinic acetylcholine receptor in helical arrays and an icosahedral virus structure with an asymmetric polymerase resolved.

A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope

Sub-nanometer resolution structure determination is becoming a common practice in electron cryomicroscopy of macromolecular assemblies. The data for these studies have until now been collected on photographic film. Using cytoplasmic polyhedrosis virus (CPV), a previously determined structure, as a test specimen, we show the feasibility of obtaining a 9 angstroms structure from images acquired from a 4 k x 4 k Gatan CCD on a 200 kV electron cryomicroscope. The match of the alpha-helices in the protein components of the CPV with the previous structure of the same virus validates the suitability of this type of camera as the recording media targeted for single particle reconstructions at sub-nanometer resolution.

Web portal to an image database for high-resolution three-dimensional reconstruction

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.