The Experts below are selected from a list of 30 Experts worldwide ranked by ideXlab platform
John Ziebuhr - One of the best experts on this subject based on the ideXlab platform.
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Characterization of a Bafinivirus exoribonuclease activity
Journal of General Virology, 2018Co-Authors: Izabela Durzynska, Marc Sauerwald, Nadja Karl, Ramakanth Madhugiri, John ZiebuhrAbstract:White bream virus (WBV), a poorly characterized plus-strand RNA virus infecting freshwater fish of the Cyprinidae family, is the prototype species of the genus Bafinivirus in the subfamily Torovirinae (family Coronaviridae, order Nidovirales). In common with other nidoviruses featuring >20 kilobase genomes, Bafiniviruses have been predicted to encode an exoribonuclease (ExoN) in their replicase gene. Here, we used information on the substrate specificity of Bafinivirus 3C-like proteases to express WBV ExoN in an active form in Escherichia coli. The 374-residue protein displayed robust 3′-to-5′ exoribonuclease activity in the presence of Mg2+ ions and, unlike its coronavirus homologues, did not require a protein cofactor for activity. Characterization of mutant forms of ExoN provided support for predictions on putative active-site and conserved zinc-binding residues. WBV ExoN was revealed to be most active on double-stranded RNA substrates containing one or two non-paired 3′-terminal nucleotides, supporting its presumed role in increasing the fidelity of the Bafinivirus RNA-dependent RNA polymerase.
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characterization of Bafinivirus main protease autoprocessing activities
Journal of Virology, 2011Co-Authors: Rachel Ulferts, John Ziebuhr, Thomas C MettenleiterAbstract:The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (Mpro) of the type species, White bream virus (WBV), of the newly established genus Bafinivirus (order Nidovirales, family Coronaviridae, subfamily Torovirinae). Comparative sequence analysis and mutagenesis data confirmed that the WBV Mpro is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-β-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV Mpro autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in trans. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln↓(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of Mpro, resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative Mpro autoprocessing sites has not been described previously for other nidovirus Mpro domains. The data presented in this study lend further support to our previous conclusion that Bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order Nidovirales.
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Coronavirus replicative proteins
Nidoviruses, 2008Co-Authors: John ZiebuhrAbstract:Over the past few years, impressive progress into the functions and structures of coronavirus replicative proteins has been made. Nevertheless, our understanding of the molecular mechanisms that coronaviruses have evolved to synthesize, express, and maintain their unusually large RNA genomes is still far from being complete. Coronaviruses form one genus in the family Coronaviridae, which also contains the genus Torovirus and the tentative genus Bafinivirus. The family Coronaviridae has been grouped with the families Arteriviridae and Roniviridae in the virus order Nidovirales. Apart from similar genome structures and expression strategies, the phylogenetic relationship of corona-, toro-, bafini-, roni-, and arteriviruses is evident from the conserved array of replicase gene-encoded protein functions, which includes (i) a chymotrypsin-like protease (3CLpro/Mpro) that is flanked by membrane-spanning domains, (ii) a superfamily 1 RNA-dependent RNA polymerase (RdRp), (iii) a superfamily 1 helicase that has an amino-terminal Zn-binding domain (ZBD), and (iv) a uridylate-specific endoribonuclease (NendoU). Furthermore, coronaviruses encode 3’-to-5’ exoribonuclease (ExoN), putative ribose-2’-O-methyltransferase (MT), PLpro, and ADP-ribose 1’’-phosphatase (ADRP) activities, whereas putative cyclic nucleotide phosphodiesterase domains have been identified only in group 2a coronaviruses. A second, “noncanonical” polymerase activity has recently been identified in coronaviruses, which may act as a primase, thus further adding to the amazing complexity of the enzymology involved in coronavirus RNA synthesis. The functional domains and enzymatic activities associated with coronavirus nsp1 to nsp16 are summarized in this chapter.
Rachel Ulferts - One of the best experts on this subject based on the ideXlab platform.
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characterization of Bafinivirus main protease autoprocessing activities
Journal of Virology, 2011Co-Authors: Rachel Ulferts, John Ziebuhr, Thomas C MettenleiterAbstract:The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (Mpro) of the type species, White bream virus (WBV), of the newly established genus Bafinivirus (order Nidovirales, family Coronaviridae, subfamily Torovirinae). Comparative sequence analysis and mutagenesis data confirmed that the WBV Mpro is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-β-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV Mpro autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in trans. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln↓(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of Mpro, resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative Mpro autoprocessing sites has not been described previously for other nidovirus Mpro domains. The data presented in this study lend further support to our previous conclusion that Bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order Nidovirales.
Thomas C Mettenleiter - One of the best experts on this subject based on the ideXlab platform.
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characterization of Bafinivirus main protease autoprocessing activities
Journal of Virology, 2011Co-Authors: Rachel Ulferts, John Ziebuhr, Thomas C MettenleiterAbstract:The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (Mpro) of the type species, White bream virus (WBV), of the newly established genus Bafinivirus (order Nidovirales, family Coronaviridae, subfamily Torovirinae). Comparative sequence analysis and mutagenesis data confirmed that the WBV Mpro is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-β-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV Mpro autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in trans. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln↓(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of Mpro, resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative Mpro autoprocessing sites has not been described previously for other nidovirus Mpro domains. The data presented in this study lend further support to our previous conclusion that Bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order Nidovirales.
James R. Winton - One of the best experts on this subject based on the ideXlab platform.
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Genetic analysis of a novel nidovirus from fathead minnows.
Journal of General Virology, 2012Co-Authors: William N. Batts, Andrew E. Goodwin, James R. WintonAbstract:A bacilliform virus was isolated from diseased fathead minnows (Pimephales promelas). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream (Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales. In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus. A PCR assay was developed for the identification of future FHMNV-like isolates.
William N. Batts - One of the best experts on this subject based on the ideXlab platform.
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Genetic analysis of a novel nidovirus from fathead minnows.
Journal of General Virology, 2012Co-Authors: William N. Batts, Andrew E. Goodwin, James R. WintonAbstract:A bacilliform virus was isolated from diseased fathead minnows (Pimephales promelas). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream (Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales. In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus. A PCR assay was developed for the identification of future FHMNV-like isolates.
