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Prazsák I, Tombácz D, Fülöp Á, Torma G, Gulyás G, Dörmő Á, Kakuk B, McKenzie Spires L, Toth Z, Boldogkői Z. KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing. mSystems 2024; 9:e0100723. [PMID: 38206015 PMCID: PMC10878076 DOI: 10.1128/msystems.01007-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing data set of the lytic and latent KSHV transcriptome using native RNA and direct cDNA-sequencing methods. This was supplemented with Cap Analysis of Gene Expression sequencing based on a short-read platform. We also utilized data sets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the transcriptomic architecture of the KSHV genome. We also evaluated the coding capability of transcripts previously thought to be non-coding by integrating our data on the viral transcripts with translatomic information from other publications.IMPORTANCEDeciphering the viral transcriptome of Kaposi's sarcoma-associated herpesvirus is of great importance because we can gain insight into the molecular mechanism of viral replication and pathogenesis, which can help develop potential targets for antiviral interventions. Specifically, the identification of substantial transcriptional overlaps by this work suggests the existence of a genome-wide interference between transcriptional machineries. This finding indicates the presence of a novel regulatory layer, potentially controlling the expression of viral genes.
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Affiliation(s)
- István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
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2
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Torma G, Tombácz D, Csabai Z, Almsarrhad IAA, Nagy GÁ, Kakuk B, Gulyás G, Spires LM, Gupta I, Fülöp Á, Dörmő Á, Prazsák I, Mizik M, Dani VÉ, Csányi V, Harangozó Á, Zádori Z, Toth Z, Boldogkői Z. Identification of herpesvirus transcripts from genomic regions around the replication origins. Sci Rep 2023; 13:16395. [PMID: 37773348 PMCID: PMC10541914 DOI: 10.1038/s41598-023-43344-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023] Open
Abstract
Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a 'super regulatory center' in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Islam A A Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gergely Ármin Nagy
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Virág Éva Dani
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Viktor Csányi
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Harangozó
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Zoltán Zádori
- HUN-REN Veterinary Medical Research Institute HU, Budapest, Hungary
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary.
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary.
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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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Prazsák I, Tombácz D, Fülöp Á, Torma G, Gulyás G, Dörmő Á, Kakuk B, Spires LM, Toth Z, Boldogkői Z. KSHV 3.0: A State-of-the-Art Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558842. [PMID: 37790386 PMCID: PMC10542539 DOI: 10.1101/2023.09.21.558842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing dataset of the lytic and latent KSHV transcriptome using native RNA and direct cDNA sequencing methods. This was supplemented with CAGE sequencing based on a short-read platform. We also utilized datasets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the transcriptomic architecture of the KSHV genome. We also evaluated the coding capability of transcripts previously thought to be non-coding, by integrating our data on the viral transcripts with translatomic information from other publications.
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Affiliation(s)
- István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
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Tombácz D, Torma G, Gulyás G, Fülöp Á, Dörmő Á, Prazsák I, Csabai Z, Mizik M, Hornyák Á, Zádori Z, Kakuk B, Boldogkői Z. Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1. Heliyon 2023; 9:e17716. [PMID: 37449092 PMCID: PMC10336594 DOI: 10.1016/j.heliyon.2023.e17716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
This study employed both short-read sequencing (SRS, Illumina) and long-read sequencing (LRS Oxford Nanopore Technologies) platforms to conduct a comprehensive analysis of the equid alphaherpesvirus 1 (EHV-1) transcriptome. The study involved the annotation of canonical mRNAs and their transcript variants, encompassing transcription start site (TSS) and transcription end site (TES) isoforms, in addition to alternative splicing forms. Furthermore, the study revealed the presence of numerous non-coding RNA (ncRNA) molecules, including intergenic and antisense transcripts, produced by EHV-1. An intriguing finding was the abundant production of chimeric transcripts, some of which potentially encode fusion polypeptides. Moreover, EHV-1 exhibited a greater incidence of transcriptional overlaps and splicing compared to related viruses. It is noteworthy that many genes have their unique TESs along with the co-terminal transcription ends, a characteristic scarcely seen in other alphaherpesviruses. The study also identified transcripts that overlap the replication origins of the virus. Moreover, a novel ncRNA, referred to as NOIR, was found to intersect with the 5'-ends of longer transcript isoform specified by the major transactivator genes ORF64 and ORF65, surrounding the OriL. These findings together imply the existence of a key regulatory mechanism that governs both transcription and replication through, among others, a process that involves interference between the DNA and RNA synthesis machineries.
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Affiliation(s)
- Dóra Tombácz
- 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
| | - Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Hornyák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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Isolation and Characterization of Two Pseudorabies Virus and Evaluation of Their Effects on Host Natural Immune Responses and Pathogenicity. Viruses 2022; 14:v14040712. [PMID: 35458442 PMCID: PMC9032386 DOI: 10.3390/v14040712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/26/2022] [Accepted: 03/26/2022] [Indexed: 02/01/2023] Open
Abstract
Pseudorabies, caused by the pseudorabies virus (PRV), is an acute fatal disease, which can infect rodents, mammals, and other livestock and wild animals across species. Recently, the emergence of PRV virulent isolates indicates a high risk of a variant PRV epidemic and the need for continuous surveillance. In this study, PRV-GD and PRV-JM, two fatal PRV variants, were isolated and their pathogenicity as well as their effects on host natural immune responses were assessed. PRV-GD and PRV-JM were genetically closest to PRV variants currently circulating in Heilongjiang (HLJ8) and Jiangxi (JX/CH/2016), which belong to genotype 2.2. Consistently, antisera from sows immunized with PRV-Ea classical vaccination showed much lower neutralization ability to PRV-GD and PRV-JM. However, the antisera from the pigs infected with PRV-JM had an extremely higher neutralization ability to PRV-TJ (as a positive control), PRV-GD and PRV-JM. In vivo, PRV-GD and PRV-JM infections caused 100% death in mice and piglets and induced extensive tissue damage, cell death, and inflammatory cytokine release. Our analysis of the emergence of PRV variants indicate that pigs immunized with the classical PRV vaccine are incapable of providing sufficient protection against these PRV isolates, and there is a risk of continuous evolution and virulence enhancement. Efforts are still needed to conduct epidemiological monitoring for the PRV and to develop novel vaccines against this emerging and reemerging infectious disease.
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Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus. Sci Rep 2022; 12:1291. [PMID: 35079129 PMCID: PMC8789824 DOI: 10.1038/s41598-022-05457-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcript species, of which 759 were novel and 116 were annotated previously. These RNA molecules include 41 novel putative protein coding transcripts [each containing 5'-truncated in-frame open reading frames (ORFs), 14 monocistronic transcripts, 99 polygenic RNAs, 101 non-coding RNAs, and 504 untranslated region isoforms. This work also identified novel replication origin-associated transcripts, upstream ORFs, cis-regulatory sequences and poly(A) sites. We also detected RNA methylation in 99 viral genes and RNA hyper-editing in the longer 5'-UTR transcript isoform of the canonical ORF 19 transcript.
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Klupp BG. Pseudorabies Virus Infections. Pathogens 2021; 10:pathogens10060719. [PMID: 34201049 PMCID: PMC8226705 DOI: 10.3390/pathogens10060719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Suid alphaherpesvirus 1 (SuHV-1), better known as Pseudorabies virus (PrV), an alphaherpesvirus of swine, is the causative agent of Aujeszky's Disease [...].
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Affiliation(s)
- Barbara G Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
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