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5. The origins of SARS-CoV-2: A critical review

Author

Holmes, EC, Goldstein, SA, Rasmussen, AL, Robertson, DL, Crits-Christoph, A, Wertheim, JO, Anthony, SJ, Barclay, WS, Boni, MF, Doherty, PC, Farrar, J, Geoghegan, JL, Jiang, X, Leibowitz, JL, Neil, SJD, Skern, T, Weiss, SR, Worobey, M, Andersen, KG, Garry, RF, Rambaut, A, Holmes, EC, Goldstein, SA, Rasmussen, AL, Robertson, DL, Crits-Christoph, A, Wertheim, JO, Anthony, SJ, Barclay, WS, Boni, MF, Doherty, PC, Farrar, J, Geoghegan, JL, Jiang, X, Leibowitz, JL, Neil, SJD, Skern, T, Weiss, SR, Worobey, M, Andersen, KG, Garry, RF, and Rambaut, A

Abstract

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

Published
2021

11. Purification of two picornaviral 2A proteinases: interaction with eIF-4-gamma and influence on in vitro translation

Author

Liebig, H.-D., Yan, R., Ziegler, E., Hartmuth, K., Klump, H., Kowalski, H., Blaas, D., Sommergruber, W., Frasel, L., Lamphear, B., Rhoads, R., Kuechler, E., and Skern, T.

Subjects
Proteases -- Research, Rhinoviruses -- Research, Messenger RNA -- Research, Biological sciences, Chemistry
Abstract

The capability of translating capped mRNA is reduced by the human rhinovirus and the mammalian enterovirus. The infection allows translation of uncapped viral RNA. The cleavage of the eukaryotic initiation factor 4-gamma is induced by the viral proteinase 2A. The soluble form of Escherichia coli provides an expression for the nature proteinases 2A of human rhinovirus 2 and coxsackievirus B4.

Published
1993

12. ICTV Virus Taxonomy Profile: Picornaviridae

Author

Zell, R., Delwart, E., Gorbalenya, A.E., Hovi, T., King, A.M.Q., Knowles, N.J., Lindberg, A.M., Pallansch, M.A., Palmenberg, A.C., Reuter, G., Simmonds, P., Skern, T., Stanway, G., Yamashita, T., and ICTV Report Consortium

Subjects
0301 basic medicine, viruses, Picornaviridae, medicine.disease_cause, Virus Replication, Genome, Microbiology, Amphibians, Birds, 03 medical and health sciences, ICTV, taxonomy, Virology, medicine, Animals, Humans, Virus classification, Mammals, Picornaviridae Infections, biology, poliovirus, Animal, foot-and-mouth disease virus, enterovirus, Poliovirus, Fishes, Reptiles, biology.organism_classification, 3. Good health, ICTV Virus Taxonomy Profiles, 030104 developmental biology, rhinovirus, Viral replication, Enterovirus, Foot-and-mouth disease virus, Rhinovirus, Positive-strand RNA Viruses
Abstract

The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.

Published
2017

13. Vaccinia virus immunomodulator A46: A lipid and protein-binding scaffold for sequestering host TIR-domain proteins

Author

Fedosyuk, S, Bezerra, GA, Radakovics, K, Smith, TK, Sammito, M, Bobik, N, Round, A, Ten Eyck, LF, Djinović-Carugo, K, Usón, I, Skern, T, and Fremont, DH

Abstract

Vaccinia virus interferes with early events of the activation pathway of the transcriptional factor NF-kB by binding to numerous host TIR-domain containing adaptor proteins. We have previously determined the X-ray structure of the A46 C-terminal domain; however, the structure and function of the A46 N-terminal domain and its relationship to the C-terminal domain have remained unclear. Here, we biophysically characterize residues 1-83 of the N-terminal domain of A46 and present the X-ray structure at 1.55 Å. Crystallographic phases were obtained by a recently developed ab initio method entitled ARCIMBOLDO_BORGES that employs tertiary structure libraries extracted from the Protein Data Bank; data analysis revealed an all β-sheet structure. This is the first such structure solved by this method which should be applicable to any protein composed entirely of β-sheets. The A46(1-83) structure itself is a β-sandwich containing a co-purified molecule of myristic acid inside a hydrophobic pocket and represents a previously unknown lipid-binding fold. Mass spectrometry analysis confirmed the presence of long-chain fatty acids in both N-terminal and full-length A46; mutation of the hydrophobic pocket reduced the lipid content. Using a combination of high resolution X-ray structures of the N- and C-terminal domains and SAXS analysis of full-length protein A46(1-240), we present here a structural model of A46 in a tetrameric assembly. Integrating affinity measurements and structural data, we propose how A46 simultaneously interferes with several TIR-domain containing proteins to inhibit NF-κB activation and postulate that A46 employs a bipartite binding arrangement to sequester the host immune adaptors TRAM and MyD88.

Published
2016

18. Family - Picornaviridae

Author

Knowles, N J, Hovi, T, Hyypiä, T, King, A M Q, Lindberg, A. Michael, Pallansch, M A, Palmenberg, A C, Simmonds, P, Skern, T, Stanway, G, Yamashita, T, Zell, R, Knowles, N J, Hovi, T, Hyypiä, T, King, A M Q, Lindberg, A. Michael, Pallansch, M A, Palmenberg, A C, Simmonds, P, Skern, T, Stanway, G, Yamashita, T, and Zell, R

Abstract

This chapter focuses on Picornaviridae family whose member genuses includeEnterovirus, Cardiovirus, Aphthovirus, Hepatovirus, and Parechovirus. The virions of this family consist of a capsid with no envelope and surrounds a core of ssRNA. Hydrated native particles are 30 nm in diameter, but vary from 22 to 30 nm in electron micrographs due to drying and flattening during preparation. The virions contain one molecule of positive sense, ssRNA, and possess a single long ORF. The UTRs at both termini contain regions of secondary structure, which are essential to genome function. In addition to the major CPs, 1A, 1B, 1C and 1D, and 3B (VPg), small amounts of 1AB (VP0) are commonly seen in lieu of one or more copies of 1A and 1B. Protein 1A is small in hepatoviruses, and 1AB is uncleaved in avihepatoviruses, kobuviruses, parechoviruses, and a number of unclassified picornaviruses. Some picornaviruses carry a sphingosine-like molecule in a cavity located inside 1D, and protein 1A generally has a molecule of myristic acid covalently attached to the amino terminal glycine. The virion RNA is infectious and serves as both the genome and the viral mRNA. Infection is generally cytolytic, but persistent infections are common with some species and reported with others. Poliovirus infected cells undergo extensive vacuolation as membranes are reorganized into viral replication complexes.

Published
2012
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19. A proposal to change existing virus species names to non-Latinized binomials

Author

van Regenmortel, M. H. V., Burke, D. S., Calisher, C. H., Dietzgen, R. G., Fauquet, C. M., Ghabrial, S. A., Jahrling, P. B., Johnson, K. M., Holbrook, M. R., Horzinek, M. C., Keil, G. M., Kuhn, J. H., Mahy, B. W. J., Martelli, G. P., Pringle, C., Rybicki, E. P., Skern, T., Tesh, R. B., Wahl-Jensen, V., Walker, P. J., Weaver, S. C., van Regenmortel, M. H. V., Burke, D. S., Calisher, C. H., Dietzgen, R. G., Fauquet, C. M., Ghabrial, S. A., Jahrling, P. B., Johnson, K. M., Holbrook, M. R., Horzinek, M. C., Keil, G. M., Kuhn, J. H., Mahy, B. W. J., Martelli, G. P., Pringle, C., Rybicki, E. P., Skern, T., Tesh, R. B., Wahl-Jensen, V., Walker, P. J., and Weaver, S. C.

Abstract

A proposal has been posted on the ICTV website (2011. 001aG. N. v1. binomial_sp_names) to replace virus species names by non-Latinized binomial names consisting of the current italicized species name with the terminal word "virus" replaced by the italicized and non-capitalized genus name to which the species belongs. If implemented, the current italicized species name Measles virus, for instance, would become Measles morbillivirus while the current virus name measles virus and its abbreviation MeV would remain unchanged. The rationale for the proposed change is presented. © 2010 Springer-Verlag.

Published
2010

20. A proposal to change existing virus species names to non-Latinized binomials

Author

van Regenmortel, MHV, Burke, DS, Calisher, CH, Dietzgen, RG, Fauquet, CM, Ghabrial, SA, Jahrling, PB, Johnson, KM, Holbrook, MR, Horzinek, MC, Keil, GM, Kuhn, JH, Mahy, BWJ, Martelli, GP, Pringle, C, Rybicki, EP, Skern, T, Tesh, RB, Wahl-Jensen, V, Walker, PJ, Weaver, SC, van Regenmortel, MHV, Burke, DS, Calisher, CH, Dietzgen, RG, Fauquet, CM, Ghabrial, SA, Jahrling, PB, Johnson, KM, Holbrook, MR, Horzinek, MC, Keil, GM, Kuhn, JH, Mahy, BWJ, Martelli, GP, Pringle, C, Rybicki, EP, Skern, T, Tesh, RB, Wahl-Jensen, V, Walker, PJ, and Weaver, SC

Abstract

A proposal has been posted on the ICTV website (2011. 001aG. N. v1. binomial_sp_names) to replace virus species names by non-Latinized binomial names consisting of the current italicized species name with the terminal word "virus" replaced by the italicized and non-capitalized genus name to which the species belongs. If implemented, the current italicized species name Measles virus, for instance, would become Measles morbillivirus while the current virus name measles virus and its abbreviation MeV would remain unchanged. The rationale for the proposed change is presented. © 2010 Springer-Verlag.

Published
2010

23. Foot-and-mouth disease virus leader proteinase Purification of the Lb form and determination of its cleavage site on eIF-4γ

Author

Kirchweger, R., Ziegler, E., Lamphear, B. J., Waters, D., Liebig -, H. D., Sommergruber, W., Francisco Sobrino, Hohenadl, C., Blaas, D., Rhoads, R. E., and Skern, T.

Subjects
viruses
Abstract

Many picornaviruses cause a dramatic decrease in the translation of cellular mRNAs in the infected cell, without affecting the translation of their own RNA. Specific proteolysis of protein synthesis initiation factor eIF-4γ occurs during infection with rhinoviruses, enteroviruses, and aphthoviruses, apparently leading to an inability of the ribosomes to bind capped mRNAs. Cleavage of eIF-4γ in human rhinoviruses and enteroviruses is carried out by the viral 2A proteinase; in aphthoviruses (i.e.;foot-and- mouth disease viruses), the leader proteinase is responsible for this reaction. We describe here the purification to homogeneity of the Lb form of the leader proteinase expressed in Escherichia coli. The primary cleavage products of eIF-4γ obtained in vitro with purified leader or 2A proteinase are electrophoretically indistinguishable from those found during infection in vivo. However, additional proteolysis products of eIF-4γ are observed with the leader proteinase and the human rhinovirus type 2 2A proteinase in vitro. The cleavage site of the leader proteinase in eIF-4γ from rabbit reticulocyte was determined by sequencing the purified C-terminal cleavage product by automated Edman degradation. The cleavage site is between Gly-479 and Arg-480 and thus differs from that of rhinovirus and enterovirus 2A proteinases, which cleave between Arg-486 and Gly-487.

Published
1994

24. New ways of initiating translation in eukaryotes.

Author

Schneider, Renate, Agol, V I, Andino, R, Bayard, F, Cavener, D R, Chappell, S A, Chen, J J, Darlix, J L, Dasgupta, ARUNDHATI, Donzé, O, Duncan, R, Elroy-Stein, O, Farabaugh, P J, Filipowicz, W, Gale, M, Gehrke, L, Goldman, E., Groner, Y, Harford, J B, Hatzglou, M, He, B, Hellen, C U, Hentze, M W, Hershey, J, Hershey, P, Hohn, T, Holcik, M, Hunter, C P, Igarashi, K, Jackson, R, Jagus, R, Jefferson, L S, Joshi, B, Kaempfer, R, Katze, M, Kaufman, Randal J, Kiledjian, M, Kimball, S R, Kimchi, A, Kirkegaard, K, Koromilas, A E, Krug, R M, Kruys, Véronique, Lamphear, B J, Lemon, S, Lloyd, R E, Maquat, L E, Martinez-Salas, E, Mathews, M B, Mauro, V P, Miyamoto, S, Mohr, I, Morris, D R, Moss, E G, Nakashima, N, Palmenberg, A, Parkin, N T, Pe'ery, T, Pelletier, J, Peltz, S, Pestova, T V, Pilipenko, E V, Prats, A C, Racaniello, V, Read, G S, Rhoads, R E, Richter, J D, Rivera-Pomar, R, Rouault, T, Sachs, A, Sarnow, P, Scheper, G C, Schiff, L, Schoenberg, D R, Semler, B L, Siddiqui, A, Skern, T, Sonenberg, N, Sossin, W, Standart, N, Tahara, S M, Thomas, A A, Toulmé, J J, Wilusz, J, Wimmer, E, Witherell, G, Wormington, M, Schneider, Renate, Agol, V I, Andino, R, Bayard, F, Cavener, D R, Chappell, S A, Chen, J J, Darlix, J L, Dasgupta, ARUNDHATI, Donzé, O, Duncan, R, Elroy-Stein, O, Farabaugh, P J, Filipowicz, W, Gale, M, Gehrke, L, Goldman, E., Groner, Y, Harford, J B, Hatzglou, M, He, B, Hellen, C U, Hentze, M W, Hershey, J, Hershey, P, Hohn, T, Holcik, M, Hunter, C P, Igarashi, K, Jackson, R, Jagus, R, Jefferson, L S, Joshi, B, Kaempfer, R, Katze, M, Kaufman, Randal J, Kiledjian, M, Kimball, S R, Kimchi, A, Kirkegaard, K, Koromilas, A E, Krug, R M, Kruys, Véronique, Lamphear, B J, Lemon, S, Lloyd, R E, Maquat, L E, Martinez-Salas, E, Mathews, M B, Mauro, V P, Miyamoto, S, Mohr, I, Morris, D R, Moss, E G, Nakashima, N, Palmenberg, A, Parkin, N T, Pe'ery, T, Pelletier, J, Peltz, S, Pestova, T V, Pilipenko, E V, Prats, A C, Racaniello, V, Read, G S, Rhoads, R E, Richter, J D, Rivera-Pomar, R, Rouault, T, Sachs, A, Sarnow, P, Scheper, G C, Schiff, L, Schoenberg, D R, Semler, B L, Siddiqui, A, Skern, T, Sonenberg, N, Sossin, W, Standart, N, Tahara, S M, Thomas, A A, Toulmé, J J, Wilusz, J, Wimmer, E, Witherell, G, and Wormington, M

Abstract

Comment, Letter, info:eu-repo/semantics/published

Published
2001

25. Leader Protease

Author

Cencic, R., primary, Mayer, C., additional, Juliano, M.A., additional, Juliano, L., additional, Konrat, R., additional, Kontaxis, G., additional, and Skern, T., additional

Published
2007
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45. PCR cloning of a protein-coding part of the thioredoxin gene from Streptomyces aureofaciens.

Author

Labudová, O., Némethová, M., Kollárová, M., Skern, T., and Küchler, E.

Abstract

The method of two-stage half-specific amplification was described and successfully used in the isolation of the protein-coding part of the thioredoxin gene from Streptomyces aureofaciens BMK. The efficiency of a new PCR modification for the specific amplification of the target DNA fragments (genes) with unknown sequences is compared with the used half-specific PCR. The determined target sequence demonstrates the highest homology with the thioredoxin genes from Corynebacterium nephridii C-1 and Anabaena 7119. [ABSTRACT FROM AUTHOR]

Published
1994
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46. New ways of initiating translation in eukaryotes.

Author

Schneider, R, Agol, V I, Andino, R, Bayard, F, Cavener, D R, Chappell, S A, Chen, J J, Darlix, J L, Dasgupta, A, Donzé, O, Duncan, R, Elroy-Stein, O, Farabaugh, P J, Filipowicz, W, Gale, M, Gehrke, L, Goldman, E, Groner, Y, Harford, J B, Hatzglou, M, He, B, Hellen, C U, Hentze, M W, Hershey, J, Hershey, P, Hohn, T, Holcik, M, Hunter, C P, Igarashi, K, Jackson, R, Jagus, R, Jefferson, L S, Joshi, B, Kaempfer, R, Katze, M, Kaufman, R J, Kiledjian, M, Kimball, S R, Kimchi, A, Kirkegaard, K, Koromilas, A E, Krug, R M, Kruys, V, Lamphear, B J, Lemon, S, Lloyd, R E, Maquat, L E, Martinez-Salas, E, Mathews, M B, Mauro, V P, Miyamoto, S, Mohr, I, Morris, D R, Moss, E G, Nakashima, N, Palmenberg, A, Parkin, N T, Pe'ery, T, Pelletier, J, Peltz, S, Pestova, T V, Pilipenko, E V, Prats, A C, Racaniello, V, Read, G S, Rhoads, R E, Richter, J D, Rivera-Pomar, R, Rouault, T, Sachs, A, Sarnow, P, Scheper, G C, Schiff, L, Schoenberg, D R, Semler, B L, Siddiqui, A, Skern, T, Sonenberg, N, Tahara, S M, Thomas, A A, Toulmé, J J, Wilusz, J, Wimmer, E, Witherell, G, and Wormington, M

Published
2001

48. Characterization of the translation-dependent step during iron-regulated decay of transferrin receptor mRNA.

Author

Posch, M, Sutterluety, H, Skern, T, and Seiser, C

Abstract

Iron regulates the stability of the mRNA encoding the transferrin receptor (TfR). When iron is scarce, iron regulatory proteins (IRPs) stabilize TfR mRNA by binding to the 3'-untranslated region. High levels of iron induce degradation of TfR mRNA; the translation inhibitor cycloheximide prevents this. To distinguish between cotranslational mRNA decay and a trans effect of translation inhibitors, we designed a reporter system exploiting the properties of the selectable marker gene thymidine kinase (TK). The 3'-untranslated region of human transferrin receptor, which contains all elements necessary for iron-dependent regulation of mRNA stability, was fused to the TK cDNA. In stably transfected mouse fibroblasts, the expression of the reporter gene was perfectly regulated by iron. Introduction of stop codons in the TK coding sequence or insertion of stable stem-loop structures in the leader sequence did not affect on the iron-dependent regulation of the reporter mRNA. This implies that global translation inhibitors stabilize TfR mRNA in trans. Cycloheximide prevented the destabilization of TfR mRNA only in the presence of active IRPs. Inhibition of IRP inactivation by cycloheximide or by the specific proteasome inhibitor MG132 correlated with the stabilization of TfR mRNA. These observations suggest that inhibition of translation by cycloheximide interferes with the rate-limiting step of iron-induced TfR mRNA decay in a trans-acting mechanism by blocking IRP inactivation.

Published
1999

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