Mutational Analysis of the Binding Pockets of the Diketo Acid Inhibitor L-742,001 in the Influenza Virus PA Endonuclease

The influenza virus PA endonuclease, which cleaves capped host pre-mRNAs to initiate synthesis of viral mRNA, is a prime target for antiviral therapy. The diketo acid compound L-742,001 was previously identified as a potent inhibitor of the influenza virus endonuclease reaction, but information on its precise binding mode to PA or potential resistance profile is limited. Computer-assisted docking of L-742,001 into the crystal structure of inhibitor-free N-terminal PA (PA-Nter) indicated a binding orientation distinct from that seen in a recent crystallographic study with L-742,001-bound PA-Nter (R. M. DuBois et al., PLoS Pathog. 8:e1002830, 2012). A comprehensive mutational analysis was performed to determine which amino acid changes within the catalytic center of PA or its surrounding hydrophobic pockets alter the antiviral sensitivity to L-742,001 in cell culture. Marked (up to 20-fold) resistance to L-742,001 was observed for the H41A, I120T, and G81F/V/T mutant forms of PA. Two- to 3-fold resistance was seen for the T20A, L42T, and V122T mutants, and the R124Q and Y130A mutants were 3-fold more sensitive to L-742,001. Several mutations situated at noncatalytic sites in PA had no or only marginal impact on the enzymatic functionality of viral ribonucleoprotein complexes reconstituted in cell culture, consistent with the less conserved nature of these PA residues. Our data provide relevant insights into the binding mode of L-742,001 in the PA endonuclease active site. In addition, we predict some potential resistance sites that should be taken into account during optimization of PA endonuclease inhibitors toward tight binding in any of the hydrophobic pockets surrounding the catalytic center of the enzyme.     

Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease

Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral replication. Translation of viral mRNAs by the host ribosome requires mRNA capping for recognition and binding, and the necessary mRNA caps are cleaved or “snatched” from host pre-mRNAs by the PA endonuclease. The structure-based development of inhibitors that target PA endonuclease is now possible with the recent crystal structure of the PA catalytic domain. In this study, we sought to understand the molecular mechanism of inhibition by several compounds that are known or predicted to block endonuclease-dependent polymerase activity. Using an in vitro endonuclease activity assay, we show that these compounds block the enzymatic activity of the isolated PA endonuclease domain. Using X-ray crystallography, we show how these inhibitors coordinate the two-metal endonuclease active site and engage the active site residues. Two structures also reveal an induced-fit mode of inhibitor binding. The structures allow a molecular understanding of the structure-activity relationship of several known influenza inhibitors and the mechanism of drug resistance by a PA mutation. Taken together, our data reveal new strategies for structure-based design and optimization of PA endonuclease inhibitors.     

A Mutational Analysis of DNA Binding and Cleavage by the Homing Endonuclease PI-SceI

We have carried out an extensive mutational analysis of PI-SceI, the best studied intein-like homing endonuclease of the LAGLIDADG family, to find out which amino acid residues are involved in substrate binding and processing. Our analysis was focused on domain I, in which two regions were shown to be in contact with DNA, and on domain II, in which the amino acid residues making up catalytic centers I and II were identified and their role in catalysis investigated. As a result of our comprehensive mutational analysis a model is presented for DNA binding and cleavage by PI-SceI.     

Association of the Influenza Virus RNA Polymerase Subunit PB2 with the Host Chaperonin CCT

The RNA polymerase of influenza A virus is a host range determinant and virulence factor. In particular, the PB2 subunit of the RNA polymerase has been implicated as a crucial factor that affects cell tropism as well as virulence in animal models. These findings suggest that host factors associating with the PB2 protein may play an important role during viral replication. In order to identify host factors that associate with the PB2 protein, we purified recombinant PB2 from transiently transfected mammalian cells and identified copurifying host proteins by mass spectrometry. We found that the PB2 protein associates with the cytosolic chaperonin containing TCP-1 (CCT), stress-induced phosphoprotein 1 (STIP1), FK506 binding protein 5 (FKBP5), α- and β-tubulin, Hsp60, and mitochondrial protein p32. Some of these binding partners associate with each other, suggesting that PB2 might interact with these proteins in multimeric complexes. More detailed analysis of the interaction of the PB2 protein with CCT revealed that PB2 associates with CCT as a monomer and that the CCT binding site is located in a central region of the PB2 protein. PB2 proteins from various influenza virus subtypes and origins can associate with CCT. Silencing of CCT resulted in reduced viral replication and reduced PB2 protein and viral RNA accumulation in a ribonucleoprotein reconstitution assay, suggesting an important function for CCT during the influenza virus life cycle. We propose that CCT might be acting as a chaperone for PB2 to aid its folding and possibly its incorporation into the trimeric RNA polymerase complex.Influenza A viruses, members of the family of Orthomyxoviridae, contain a segmented RNA genome of negative polarity. The genomic RNA segments together with the three subunits of the viral RNA-dependent RNA polymerase (PB1, PB2, and PA protein) and the nucleoprotein (NP) form viral ribonucleoprotein complexes (vRNPs). The PB1 subunit is the polymerase itself, while the PB2 and PA subunits are involved in the generation of 5′ capped RNA primers through binding to and endonucleolytic cleavage of host pre-mRNAs (8, 10, 11, 41, 61). After the virus enters the cell via endocytosis, vRNPs are released into the cytoplasm and transported into the nucleus. In the nucleus, vRNPs catalyze the synthesis of viral mRNAs and complementary RNAs (cRNA) which, in turn, are used as templates for the synthesis of vRNAs. The newly formed vRNPs in association with other viral proteins (M1 and nonstructural protein 2/nuclear export factor [NS2/NEP]) are transported into the cytoplasm and subsequently to the cell membrane, where the assembly process takes place, followed by the release of progeny virions by budding (44).The PB1, PB2, and PA proteins are synthesized in the cytoplasm whereupon PB1 and PA form a dimeric complex that is transported into the nucleus. In the nucleus the dimer assembles with the PB2 subunit, which is transported separately (7, 14). RanBP5 was identified as a factor that is involved in the import of the PB1-PA dimer into the nucleus (6), while PB2 uses the classical importin-α/β pathway for nuclear import (57). Recently, further support for this transport and assembly model was provided by using fluorescence cross-correlation spectroscopy (25). An alternative pathway proposed for the import of the RNA polymerase subunits into the nucleus involves the heat shock protein 90 (Hsp90) that was shown to interact with the PB1 and PB2 proteins (39). Heat shock protein 70 (Hsp70) was also found to interact with the influenza virus polymerase subunits and vRNPs, and it was implicated in blocking the nuclear export of vRNPs (22).The RNA polymerase has been implicated as a host range determinant and pathogenicity factor of influenza viruses. In particular, amino acid residue 627 in the PB2 subunit was shown to determine the ability of certain influenza viruses to replicate in avian and mammalian cells (34, 54). A lysine at position 627, characteristic of most human influenza virus strains, appears to enhance replication in mammalian cells, while a glutamic acid, found in most avian isolates, attenuates virus replication in mammalian cells. The presence of a lysine was also shown to enhance virulence in mammalian models and has been associated with the lethality of H5N1 viruses in humans (20). It has been proposed that a negative factor, present in mammalian cells, specifically reduces the activity of a polymerase containing a glutamic acid (38). However, the identity of this factor remains to be determined. Interestingly, the 2009 H1N1 pandemic influenza virus encodes a glutamic acid at this position, and a second-site suppressor mutation has been identified in PB2 that promotes activity in mammalian cells (37). Introduction of a lysine at residue 627 in the 2009 H1N1 pandemic virus did not result in enhanced virulence (21, 62). Several other amino acid residues in the PB2 protein were also implicated in host range determination and virulence, suggesting that multiple amino acid substitutions are involved (15, 48). Collectively, these results suggest that the PB2 protein interacts with host factors and that these interactions have implications for host range and virulence.Therefore, we set up a biochemical copurification assay followed by mass spectrometry to identify host factors that associate with the PB2 protein in mammalian cells. We confirmed the interaction with several previously identified host factors, e.g., Hsp70 and Hsp90, and identified novel host proteins that interact with the PB2 protein. Among these, we have identified the oligomeric chaperonin containing TCP-1 (CCT) (also known as TRiC [TCP-1 ring complex]) and investigated the significance of this interaction in more detail. We found that CCT interacts with the PB2 protein but not with the PB1 or PA protein. However, PB2 in association with PB1 or PB1 and PA did not interact with CCT. We also found that PB2 proteins of different influenza virus strains of different origins, hosts, and subtypes interact with CCT. Growth of influenza virus, as well as the accumulation of the PB2 protein and viral RNAs in a ribonucleoprotein reconstitution assay, was reduced in CCT-silenced cells compared to that in control cells. These results suggest a role for CCT in the influenza A virus life cycle, possibly acting as a chaperone for the PB2 protein.     

The N-Terminal Domain of PA from Bat-Derived Influenza-Like Virus H17N10 Has Endonuclease Activity

Influenza imposes a great burden on society, not only in its seasonal appearance that affects both humans and domesticated animals but also through the constant threat of potential pandemics. Migratory birds are considered to be the reservoir hosts for influenza viruses, but other animals must also be considered. The recently identified influenza-like virus genome, from H17N10 in bats, was shown to be markedly different from genomes of other known influenza viruses, as both its surface glycoproteins hemagglutinin (HA) and neuraminidase (NA) do not have canonical functions. However, no studies on other individual proteins from this particular virus have been reported until now. Here, we describe the structure of the N-terminal domain of PA from H17N10 influenza-like virus at 2.7-Å resolution and show that it has a fold similar to those of homologous PA domains present in more familiar influenza A virus strains. Moreover, we demonstrate that it possesses endonuclease activity and that the histidine residue in the active site is essential for this activity. Although this particular influenza virus subtype is probably not infectious for humans (even its virus state has not been confirmed in bats, as only the genome has been sequenced), reassortment of canonical influenza viruses with certain segments from H17N10 cannot be ruled out at this stage. Therefore, further studies are urgently needed for the sake of influenza prevention and control.     

Mutational Analysis of the Putative Fusion Domain of Ebola Virus Glycoprotein

Ebola viruses contain a single glycoprotein (GP) spike, which functions as a receptor binding and membrane fusion protein. It contains a highly conserved hydrophobic region (amino acids 524 to 539) located 24 amino acids downstream of the N terminus of the Ebola virus GP2 subunit. Comparison of this region with the structural features of the transmembrane subunit of avian retroviral GPs suggests that the conserved Ebola virus hydrophobic region may, in fact, serve as the fusion peptide. To test this hypothesis directly, we introduced conservative (alanine) and nonconservative (arginine) amino acid substitutions at eight positions in this region of the GP2 molecule. The effects of these mutations were deduced from the ability of the Ebola virus GP to complement the infectivity of a vesicular stomatitis virus (VSV) lacking the receptor-binding G protein. Some mutations, such as Ile-to-Arg substitutions at positions 532 (I532R), F535R, G536A, and P537R, almost completely abolished the ability of the GP to support VSV infectivity without affecting the transport of GP to the cell surface and its incorporation into virions or the production of virus particles. Other mutations, such as G528R, L529A, L529R, I532A, and F535A, reduced the infectivity of the VSV-Ebola virus pseudotypes by at least one-half. These findings, together with previous reports of liposome association with a peptide corresponding to positions 524 to 539 in the GP molecule, offer compelling support for a fusion peptide role for the conserved hydrophobic region in the Ebola virus GP.     

一种用于流感病毒亚单位疫苗纯度分析的改进方法

目的：在SDS-PAGE方法的基础上建立一种改进方法,用于流感病毒亚单位疫苗中间体的杂质分析。方法：用糖苷酶F对不同亚型的疫苗中间体去糖基化处理后进行SDS-PAGE,与未经去糖基化处理的还原型SDS-PAGE结果进行比较。结果：去糖基化处理消除了血凝素的糖基化对电泳迁移率的影响,从而实现了血凝素亚基和杂质的电泳分离。结论：此方法应用于流感病毒亚单位疫苗中间体的杂质分析,较之常规的还原型SDS-PAGE方法具有更高的分辨力。     

Identification of the N-Terminal Domain of the Influenza Virus PA Responsible for the Suppression of Host Protein Synthesis

Cellular protein synthesis is suppressed during influenza virus infection, allowing for preferential production of viral proteins. To explore the impact of polymerase subunits on protein synthesis, we coexpressed enhanced green fluorescent protein (eGFP) or luciferase together with each polymerase component or NS1 of A/California/04/2009 (Cal) and found that PA has a significant impact on the expression of eGFP and luciferase. Comparison of the suppressive activity on coexpressed proteins between various strains revealed that avian virus or avian-origin PAs have much stronger activity than human-origin PAs, such as the one from A/WSN/33 (WSN). Protein synthesis data suggested that reduced expression of coexpressed proteins is not due to PA''s reported proteolytic activity. A recombinant WSN containing Cal PA showed enhanced host protein synthesis shutoff and induction of apoptosis. Further characterization of the PA fragment indicated that the N-terminal domain (PANt), which includes the endonuclease active site, is sufficient to suppress cotransfected gene expression. By characterizing various chimeric PANts, we found that multiple regions of PA, mainly the helix α4 and the flexible loop of amino acids 51 to 74, affect the activity. The suppressive effect of PANt cDNA was mainly due to PA-X, which was expressed by ribosomal frameshifting. In both Cal and WSN viruses, PA-X showed a stronger effect than the corresponding PANt, suggesting that the unique C-terminal sequences of PA-X also play a role in suppressing cotransfected gene expression. Our data indicate strain variations in PA gene products, which play a major role in suppression of host protein synthesis.     

Synthetic Templates and the RNA Polymerase of Influenza a Virus

Abstract

Polyadenylic acid (poly A) and polyguanylic acid (poly G) have been modified to give polymers containing and Gpm5C termini. Polymers containing methylated (Gpmf C) termini are inactive as templates for the RNA-dependent RNA polymerase of Influenza A virus.     

Limited Compatibility of Polymerase Subunit Interactions in Influenza A and B Viruses

Despite their close phylogenetic relationship, natural intertypic reassortants between influenza A (FluA) and B (FluB) viruses have not been described. Inefficient polymerase assembly of the three polymerase subunits may contribute to this incompatibility, especially because the known protein-protein interaction domains, including the PA-binding domain of PB1, are highly conserved for each virus type. Here we show that substitution of the FluA PA-binding domain (PB1-A_1–25) with that of FluB (PB1-B_1–25) is accompanied by reduced polymerase activity and viral growth of FluA. Consistent with these findings, surface plasmon resonance spectroscopy measurements revealed that PA of FluA exhibits impaired affinity to biotinylated PB1-B_1–25 peptides. PA of FluB showed no detectable affinity to biotinylated PB1-A_1–25 peptides. Consequently, FluB PB1 harboring the PA-binding domain of FluA (PB1-AB) failed to assemble with PA and PB2 into an active polymerase complex. To regain functionality, we used a single amino acid substitution (T6Y) known to confer binding to PA of both virus types, which restored polymerase complex formation but surprisingly not polymerase activity for FluB. Taken together, our results demonstrate that the conserved virus type-specific PA-binding domains differ in their affinity to PA and thus might contribute to intertypic exclusion of reassortants between FluA and FluB viruses.     

Crystal Structure of the Vaccinia Virus DNA Polymerase Holoenzyme Subunit D4 in Complex with the A20 N-Terminal Domain

Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20_1–50). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20_1–50 clearly behaves as a heterodimer. The crystal structure of D4/A20_1–50 solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A20_1–50 binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20_1–50 formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20_1–50 interaction. Finally, we propose a model of D4/A20_1–50 in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.