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Jefferson VA, Bostick H, Oldenburg D, Meyer F. Evidence of a Protein-Coding Gene Antisense to the U L5 Gene in Bovine Herpesvirus I. Viruses 2023; 15:1977. [PMID: 37896756 PMCID: PMC10610667 DOI: 10.3390/v15101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Bovine herpesvirus type 1 (BoHV-1) is an important agricultural pathogen that infects cattle and other ruminants worldwide. Though it was first sequenced and annotated over twenty years ago, the Cooper strain, used in this study, was sequenced as recently as 2012 and is currently said to encode 72 unique proteins. However, tandem mass spectrometry has identified several peptides produced during active infection that align with the BoHV-1 genome in unannotated regions. One of these abundant peptides, "ORF M", aligned antisense to the DNA helicase/primase protein UL5. This study characterizes the novel transcript and its protein product and provides evidence to support the existence of homolog protein-coding genes in other Herpesviruses.
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Affiliation(s)
- Victoria A. Jefferson
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
| | - Hannah Bostick
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
| | - Darby Oldenburg
- Gundersen Medical Foundation, 1900 South Ave., La Crosse, WI 54601, USA;
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (H.B.)
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2
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Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. Microbiol Spectr 2021; 9:e0049021. [PMID: 34523988 PMCID: PMC8557916 DOI: 10.1128/spectrum.00490-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cyanobacteria, capable of oxygenic photosynthesis, play a vital role in nitrogen and carbon cycles. Nostoc sp. PCC 7120 (Nostoc 7120) is a model cyanobacterium commonly used to study cell differentiation and nitrogen metabolism. Although its genome was released in 2002, a high-quality genome annotation remains unavailable for this model cyanobacterium. Therefore, in this study, we performed an in-depth proteogenomic analysis based on high-resolution mass spectrometry (MS) data to refine the genome annotation of Nostoc 7120. We unambiguously identified 5,519 predicted protein-coding genes and revealed 26 novel genes, 75 revised genes, and 27 different kinds of posttranslational modifications in Nostoc 7120. A subset of these novel proteins were further validated at both the mRNA and peptide levels. Functional analysis suggested that many newly annotated proteins may participate in nitrogen or cadmium/mercury metabolism in Nostoc 7120. Moreover, we constructed an updated Nostoc 7120 database based on our proteogenomic results and presented examples of how the updated database could be used to improve the annotation of proteomic data. Our study provides the most comprehensive annotation of the Nostoc 7120 genome thus far and will serve as a valuable resource for the study of nitrogen metabolism in Nostoc 7120. IMPORTANCE Cyanobacteria are a large group of prokaryotes capable of oxygenic photosynthesis and play a vital role in nitrogen and carbon cycles on Earth. Nostoc 7120 is a commonly used model cyanobacterium for studying cell differentiation and nitrogen metabolism. In this study, we presented the first comprehensive draft map of the Nostoc 7120 proteome and a wide range of posttranslational modifications. In addition, we constructed an updated database of Nostoc 7120 based on our proteogenomic results and presented examples of how the updated database could be used for system-level studies of Nostoc 7120. Our study provides the most comprehensive annotation of Nostoc 7120 genome and a valuable resource for the study of nitrogen metabolism in this model cyanobacterium.
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Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
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Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Tombácz D, Moldován N, Torma G, Nagy T, Hornyák Á, Csabai Z, Gulyás G, Boldogkői M, Jefferson VA, Zádori Z, Meyer F, Boldogkői Z. Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach. Front Genet 2021; 12:619056. [PMID: 33897757 PMCID: PMC8059770 DOI: 10.3389/fgene.2021.619056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ákos Hornyák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Miklós Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Victoria A Jefferson
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Florencia Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing. Sci Rep 2020; 10:20496. [PMID: 33235226 PMCID: PMC7686369 DOI: 10.1038/s41598-020-77520-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps.
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Marin M, Burucúa M, Rensetti D, Rosales JJ, Odeón A, Pérez S. Distinctive features of bovine alphaherpesvirus types 1 and 5 and the virus-host interactions that might influence clinical outcomes. Arch Virol 2019; 165:285-301. [PMID: 31845150 DOI: 10.1007/s00705-019-04494-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/09/2019] [Indexed: 12/14/2022]
Abstract
Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) are two closely related alphaherpesviruses. BoHV-1 causes several syndromes in cattle, including respiratory disease and sporadic cases of encephalitis, whereas BoHV-5 is responsible for meningoencephalitis in calves. Although both viruses are neurotropic, they differ in their neuropathogenic potential. This review summarizes the findings on the specific mechanisms and pathways known to modulate the pathogenesis of BoHV-1 and BoHV-5, particularly in relation to respiratory and neurological syndromes, which characterize BoHV-1 and BoHV-5 infections, respectively.
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Affiliation(s)
- Maia Marin
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Balcarce, Ruta 226 Km 73.5, Balcarce, 7620, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Mercedes Burucúa
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Balcarce, Ruta 226 Km 73.5, Balcarce, 7620, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Daniel Rensetti
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, 7000, Tandil, Argentina
| | - Juan José Rosales
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, 7000, Tandil, Argentina.,Centro de Investigación Veterinaria de Tandil (CIVETAN)-CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, 7000, Tandil, Argentina
| | - Anselmo Odeón
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Balcarce, Ruta 226 Km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Sandra Pérez
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, 7000, Tandil, Argentina. .,Centro de Investigación Veterinaria de Tandil (CIVETAN)-CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, 7000, Tandil, Argentina.
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