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Ye T, Li H, Hai D, Zhaxi Z, Duan J, Lin Y, Xie J, Cheng J, Li B, Chen T, Yu X, Lyu X, Xiao X, Fu Y, Jiang D. A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms. Int J Mol Sci 2025; 26:3853. [PMID: 40332509 PMCID: PMC12027680 DOI: 10.3390/ijms26083853] [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: 02/21/2025] [Revised: 04/09/2025] [Accepted: 04/16/2025] [Indexed: 05/08/2025] Open
Abstract
Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.
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Affiliation(s)
- Ting Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
- National Biopesticide Engineering Research Centre, Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Han Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Zhima Zhaxi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Jie Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.Y.); (H.L.); (D.H.); (Z.Z.); (J.D.); (J.X.); (J.C.); (B.L.); (T.C.); (X.Y.); (X.L.); (X.X.)
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (Y.F.)
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Wang Z, Wen H. A review of the recombination events, mechanisms and consequences of Coxsackievirus A6. INFECTIOUS MEDICINE 2024; 3:100115. [PMID: 38974347 PMCID: PMC11225671 DOI: 10.1016/j.imj.2024.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/25/2024] [Accepted: 04/22/2024] [Indexed: 07/09/2024]
Abstract
Hand, foot, and mouth disease (HFMD) is one of the most common class C infectious diseases, posing a serious threat to public health worldwide. Enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) have been regarded as the major pathogenic agents of HFMD; however, since an outbreak caused by coxsackievirus A6 (CV-A6) in France in 2008, CV-A6 has gradually become the predominant pathogen in many regions. CV-A6 infects not only children but also adults, and causes atypical clinical symptoms such as a more generalized rash, eczema herpeticum, high fever, and onychomadesis, which are different from the symptoms associated with EV-A71 and CV-A16. Importantly, the rate of genetic recombination of CV-A6 is high, which can lead to changes in virulence and the rapid evolution of other characteristics, thus posing a serious threat to public health. To date, no specific vaccines or therapeutics have been approved for CV-A6 prevention or treatment, hence it is essential to fully understand the relationship between recombination and evolution of this virus. Here, we systematically review the genetic recombination events of CV-A6 that have occurred worldwide and explore how these events have promoted virus evolution, thus providing important information regarding future HFMD surveillance and prevention.
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Affiliation(s)
- Zequn Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases, Biosafety in Universities of Shandong, Jinan 250012, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases, Biosafety in Universities of Shandong, Jinan 250012, China
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Divekar G, Colmant AMG, Furlong MJ, Etebari K. Transcriptome Analysis Reveals a Diverse Range of Novel Viruses in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2024; 16:516. [PMID: 38675859 PMCID: PMC11054854 DOI: 10.3390/v16040516] [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: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
In Australia, Soldier flies (Inopus spp.) are economically significant pests of sugarcane that currently lack a viable management strategy. Despite various research efforts, the mechanisms underlying the damage caused by soldier fly larvae remain poorly understood. Our study aims to explore whether this damage is associated with the transmission of plant viruses during larval feeding. We also explore the larval transcriptome to identify any entomopathogenic viruses with the potential to be used as biocontrol agents in future pest management programs. Seven novel virus sequences are identified and characterised using de novo assembly of RNA-Seq data obtained from salivary glands of larvae. The novel virus sequences belong to different virus families and are tentatively named SF-associated anphevirus (SFaAV), SF-associated orthomyxo-like virus (SFaOV), SF-associated narna-like virus (SFaNV), SF-associated partiti-like virus (SFaPV), SF-associated toti-like virus (SFaTV-1 and SFaTV-2) and SF-associated densovirus (SFaDV). These newly identified viruses are more likely insect-associated viruses, as phylogenetic analyses show that they cluster with other insect-specific viruses. Small RNA analysis indicates prominent peaks at both 21 nt and 26-29 nt, suggesting the activation of host siRNA and piwiRNA pathways. Our study helps to improve understanding of the virome of soldier flies and could identify insect viruses for deployment in novel pest management strategies.
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Affiliation(s)
- Gayatri Divekar
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
| | - Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), 13005 Marseille, France
| | - Michael J. Furlong
- School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Kayvan Etebari
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
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Urayama SI, Fukudome A, Hirai M, Okumura T, Nishimura Y, Takaki Y, Kurosawa N, Koonin EV, Krupovic M, Nunoura T. Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan. Nat Microbiol 2024; 9:514-523. [PMID: 38233646 PMCID: PMC10847044 DOI: 10.1038/s41564-023-01579-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota, or even kingdom within the realm Riboviria. We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae. The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.
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Affiliation(s)
- Syun-Ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
| | - Akihito Fukudome
- Howard Hughes Medical Institute, Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoyo Okumura
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Yosuke Nishimura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Norio Kurosawa
- Faculty of Science and Engineering, Soka University, Hachioji, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, Yokosuka, Japan
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Bannur Nanjunda S, Seshadri VN, Krishnan C, Rath S, Arunagiri S, Bao Q, Helmerson K, Zhang H, Jain R, Sundarrajan A, Srinivasan B. Emerging nanophotonic biosensor technologies for virus detection. NANOPHOTONICS (BERLIN, GERMANY) 2022; 11:5041-5059. [PMID: 39634299 PMCID: PMC11501160 DOI: 10.1515/nanoph-2022-0571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/09/2022] [Accepted: 11/13/2022] [Indexed: 12/07/2024]
Abstract
Highly infectious viral diseases are a serious threat to mankind as they can spread rapidly among the community, possibly even leading to the loss of many lives. Early diagnosis of a viral disease not only increases the chance of quick recovery, but also helps prevent the spread of infections. There is thus an urgent need for accurate, ultrasensitive, rapid, and affordable diagnostic techniques to test large volumes of the population to track and thereby control the spread of viral diseases, as evidenced during the COVID-19 and other viral pandemics. This review paper critically and comprehensively reviews various emerging nanophotonic biosensor mechanisms and biosensor technologies for virus detection, with a particular focus on detection of the SARS-CoV-2 (COVID-19) virus. The photonic biosensing mechanisms and technologies that we have focused on include: (a) plasmonic field enhancement via localized surface plasmon resonances, (b) surface enhanced Raman scattering, (c) nano-Fourier transform infrared (nano-FTIR) near-field spectroscopy, (d) fiber Bragg gratings, and (e) microresonators (whispering gallery modes), with a particular emphasis on the emerging impact of nanomaterials and two-dimensional materials in these photonic sensing technologies. This review also discusses several quantitative issues related to optical sensing with these biosensing and transduction techniques, notably quantitative factors that affect the limit of detection (LoD), sensitivity, specificity, and response times of the above optical biosensing diagnostic technologies for virus detection. We also review and analyze future prospects of cost-effective, lab-on-a-chip virus sensing solutions that promise ultrahigh sensitivities, rapid detection speeds, and mass manufacturability.
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Affiliation(s)
- Shivananju Bannur Nanjunda
- Department of Electrical Engineering, Centre of Excellence in Biochemical Sensing and Imaging (CenBioSIm), Indian Institute of Technology Madras, Chennai, India
| | - Venkatesh N. Seshadri
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, India
- Department of Life Science, Indian Academy, Bangalore, India
| | - Chitra Krishnan
- School of Electronics Engineering, Vellore Institute of Technology, Chennai, India
| | - Sweta Rath
- Department of Electrical Engineering, Centre of Excellence in Biochemical Sensing and Imaging (CenBioSIm), Indian Institute of Technology Madras, Chennai, India
| | | | - Qiaoliang Bao
- Department of Materials Science and Engineering, and ARC Centre of Excellence in Future Low Energy Electronics Technologies (FLEET), Monash University, Clayton, VIC, Australia
| | - Kristian Helmerson
- School of Physics and Astronomy, ARC Centre of Excellence in Future Low-Energy Electronics Technologies (FLEET), Monash University, Clayton, VIC3800, Australia
| | - Han Zhang
- International Collaborative Laboratory of 2D Materials for Optoelectronics Science, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen518060, China
| | - Ravi Jain
- Optical Science and Engineering Program, Center for High Technology Materials, Departments of ECE, Physics Astronomy, and Nanoscience Microsystems, University of New Mexico, Albuquerque, NM87106, USA
| | - Asokan Sundarrajan
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, India
| | - Balaji Srinivasan
- Department of Electrical Engineering, Centre of Excellence in Biochemical Sensing and Imaging (CenBioSIm), Indian Institute of Technology Madras, Chennai, India
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Jácome R, Campillo-Balderas JA, Becerra A, Lazcano A. Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited. J Mol Evol 2022; 90:283-295. [PMID: 35639164 PMCID: PMC9153872 DOI: 10.1007/s00239-022-10059-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
In the past few years, our understanding of the RNA virosphere has changed dramatically due to the growth and spurt of metagenomics, exponentially increasing the number of RNA viral sequences, and providing a better understanding of their range of potential hosts. As of today, the only conserved protein among RNA viruses appears to be the monomeric RNA-dependent RNA polymerase. This enzyme belongs to the right-hand DNA-and RNA polymerases, which also includes reverse transcriptases and eukaryotic replicative DNA polymerases. The ubiquity of this protein in RNA viruses makes it a unique evolutionary marker and an appealing broad-spectrum antiviral target. In this work pairwise structural comparisons of viral RdRps and RTs were performed, including tertiary structures that have been obtained in the last few years. The resulting phylogenetic tree shows that the RdRps from (+)ss- and dsRNA viruses might have been recruited several times throughout the evolution of mobile genetic elements. RTs also display multiple evolutionary routes. We have identified a structural core comprising the entire palm, a large moiety of the fingers and the N-terminal helices of the thumb domain, comprising over 300 conserved residues, including two regions that we have named the “knuckles” and the “hypothenar eminence”. The conservation of an helix bundle in the region preceding the polymerase domain confirms that (−)ss and dsRNA Reoviruses’ polymerases share a recent ancestor. Finally, the inclusion of DNA polymerases into our structural analyses suggests that monomeric RNA-dependent polymerases might have diverged from B-family polymerases.
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Affiliation(s)
- Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico
| | | | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico.
- Miembro de El Colegio Nacional, Mexico, Mexico.
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Roossinck MJ. The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind. Annu Rev Virol 2022; 9:19-38. [PMID: 35512631 DOI: 10.1146/annurev-virology-100520-013446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, USA;
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Monaco AP. The selfish environment meets the selfish gene: Coevolution and inheritance of RNA and DNA pools: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools. Bioessays 2022; 44:e2100239. [PMID: 34985131 DOI: 10.1002/bies.202100239] [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: 10/09/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/07/2022]
Abstract
Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS-CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against viral attack through innate immunity and regulation of host-derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ''missing heritability'' of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations.
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Affiliation(s)
- Anthony P Monaco
- Office of the President, Ballou Hall, Tufts University, Medford, Massachusetts, USA
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