1
|
Wu H, Li W, Fan J, Jiang S, Li J, Hu P, Yu Z, Li Y, Pang R, Wu H. The hidden RNA viruses in Blattodea (cockroaches and termites). Microb Genom 2024; 10:001265. [PMID: 39037207 PMCID: PMC11316551 DOI: 10.1099/mgen.0.001265] [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: 02/12/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024] Open
Abstract
The insect order Blattodea (cockroaches and termites) has drawn substantial research attention for their dietary habits and lifestyle of living with or around humans. In the present study, we focused on the discovery of RNA viruses hidden in Blattodea insects using the publicly available RNA sequencing datasets. Overall, 136 distinctive RNA viruses were identified from 36 Blattodea species, of which more than 70 % were most closely related to the invertebrate-associated viral groups within Picornavirales, Sobelivirales, Bunyaviricetes, Jingchuvirales, Durnavirales, Lispiviridae, Orthomyxoviridae, Permutotetraviridae, Flaviviridae and Muvirales. Several viruses were associated with pathogens of vertebrates (Paramyxoviridae), plants (Tymovirales), protozoa (Totiviridae), fungi (Narnaviridae) and bacteria (Norzivirales). Collectively, 93 complete or near-complete viral genomes were retrieved from the datasets, and several viruses appeared to have remarkable temporal and spatial distributions. Interestingly, the newly identified Periplaneta americana dicistrovirus displayed a remarkable distinct bicistronic genome arrangement from the well-recognized dicistroviruses with the translocated structural and non-structural polyprotein encoding open reading frames over the genome. These results significantly enhance our knowledge of RNA virosphere in Blattodea insects, and the novel genome architectures in dicistroviruses and other RNA viruses may break our stereotypes in the understanding of the genomic evolution and the emergence of potential novel viral species.
Collapse
Affiliation(s)
- Haoming Wu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Wenxin Li
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Jingyan Fan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Shengsheng Jiang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Jiaxin Li
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Peng Hu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Zejun Yu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Yang Li
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430024, PR China
| | - Rui Pang
- College of Plant Protection, South China Agricultural University, Guangzhou 510651, PR China
| | - Huan Wu
- Department of Laboratory Medicine, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430019, PR China
| |
Collapse
|
2
|
Bayandina SV, Mukha DV. Saccharomyces cerevisiae as a Model for Studying Human Neurodegenerative Disorders: Viral Capsid Protein Expression. Int J Mol Sci 2023; 24:17213. [PMID: 38139041 PMCID: PMC10743263 DOI: 10.3390/ijms242417213] [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: 11/05/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In this article, we briefly describe human neurodegenerative diseases (NDs) and the experimental models used to study them. The main focus is the yeast Saccharomyces cerevisiae as an experimental model used to study neurodegenerative processes. We review recent experimental data on the aggregation of human neurodegenerative disease-related proteins in yeast cells. In addition, we describe the results of studies that were designed to investigate the molecular mechanisms that underlie the aggregation of reporter proteins. The advantages and disadvantages of the experimental approaches that are currently used to study the formation of protein aggregates are described. Special attention is given to the similarity between aggregates that form as a result of protein misfolding and viral factories-special structural formations in which viral particles are formed inside virus-infected cells. A separate part of the review is devoted to our previously published study on the formation of aggregates upon expression of the insect densovirus capsid protein in yeast cells. Based on the reviewed results of studies on NDs and related protein aggregation, as well as viral protein aggregation, a new experimental model system for the study of human NDs is proposed. The core of the proposed system is a comparative transcriptomic analysis of changes in signaling pathways during the expression of viral capsid proteins in yeast cells.
Collapse
Affiliation(s)
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
3
|
Armién AG, Polon R, Rejmanek D, Moeller RB, Crossley BM. Outbreak of densovirus with high mortality in a commercial mealworm ( Tenebrio molitor) farm: A molecular, bright-field, and electron microscopic characterization. Vet Pathol 2023; 60:689-703. [PMID: 37341069 PMCID: PMC10469485 DOI: 10.1177/03009858231180488] [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] [Indexed: 06/22/2023]
Abstract
Mealworms are one of the most economically important insects in large-scale production for human and animal nutrition. Densoviruses are highly pathogenic for invertebrates and exhibit an extraordinary level of diversity which rivals that of their hosts. Molecular, clinical, histological, and electron microscopic characterization of novel densovirus infections is of utmost economic and ecological importance. Here, we describe an outbreak of densovirus with high mortality in a commercial mealworm (Tenebrio molitor) farm. Clinical signs included inability to prehend food, asymmetric locomotion evolving to nonambulation, dehydration, dark discoloration, and death. Upon gross examination, infected mealworms displayed underdevelopment, dark discoloration, larvae body curvature, and organ/tissue softness. Histologically, there was massive epithelial cell death, and cytomegaly and karyomegaly with intranuclear inclusion (InI) bodies in the epidermis, pharynx, esophagus, rectum, tracheae, and tracheoles. Ultrastructurally, these InIs represented a densovirus replication and assembly complex composed of virus particles ranging from 23.79 to 26.99 nm in diameter, as detected on transmission electron microscopy. Whole-genome sequencing identified a 5579-nucleotide-long densovirus containing 5 open reading frames. A phylogenetic analysis of the mealworm densovirus showed it to be closely related to several bird- and bat-associated densoviruses, sharing 97% to 98% identity. Meanwhile, the nucleotide similarity to a mosquito, cockroach, and cricket densovirus was 55%, 52%, and 41%, respectively. As this is the first described whole-genome characterization of a mealworm densovirus, we propose the name Tenebrio molitor densovirus (TmDNV). In contrast to polytropic densoviruses, this TmDNV is epitheliotropic, primarily affecting cuticle-producing cells.
Collapse
|
4
|
Laugel M, Lecomte E, Ayuso E, Adjali O, Mével M, Penaud-Budloo M. The Diversity of Parvovirus Telomeres. Vet Med Sci 2022. [DOI: 10.5772/intechopen.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Parvoviridae are small viruses composed of a 4–6 kb linear single-stranded DNA protected by an icosahedral capsid. The viral genes coding non-structural (NS), capsid, and accessory proteins are flanked by intriguing sequences, namely the telomeres. Telomeres are essential for parvovirus genome replication, encapsidation, and integration. Similar (homotelomeric) or different (heterotelomeric) at the two ends, they all contain imperfect palindromes that fold into hairpin structures. Up to 550 nucleotides in length, they harbor a wide variety of motifs and structures known to be recognized by host cell factors. Our study aims to comprehensively analyze parvovirus ends to better understand the role of these particular sequences in the virus life cycle. Forty Parvoviridae terminal repeats (TR) were publicly available in databases. The folding and specific DNA secondary structures, such as G4 and triplex, were systematically analyzed. A principal component analysis was carried out from the prediction data to determine variables signing parvovirus groups. A special focus will be put on adeno-associated virus (AAV) inverted terminal repeats (ITR), a member of the genus Dependoparvovirus used as vectors for gene therapy. This chapter highlights the diversity of the Parvoviridae telomeres regarding shape and secondary structures, providing information that could be relevant for virus-host interactions studies.
Collapse
|
5
|
Lay CL, Shi M, Buček A, Bourguignon T, Lo N, Holmes EC. Unmapped RNA Virus Diversity in Termites and their Symbionts. Viruses 2020; 12:v12101145. [PMID: 33050289 PMCID: PMC7650761 DOI: 10.3390/v12101145] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.
Collapse
Affiliation(s)
- Callum Le Lay
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Aleš Buček
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
- Correspondence:
| |
Collapse
|
6
|
Intracellular Localization of Blattella germanica Densovirus (BgDV1) Capsid Proteins. Viruses 2018; 10:v10070370. [PMID: 30011943 PMCID: PMC6071259 DOI: 10.3390/v10070370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 01/16/2023] Open
Abstract
Densovirus genome replication and capsid assembly take place in the nucleus of the infected cells. However, the mechanisms underlying such processes as the delivery of virus proteins to the nucleus and the export of progeny virus from the nucleus remain elusive. It is evident that nuclear transport signals should be involved in these processes. We performed an in silico search for the putative nuclear localization signal (NLS) and nuclear export signal (NES) motifs in the capsid proteins of the Blattella germanica Densovirus 1 (BgDV1) densovirus. A high probability NLS motif was found in the common C-terminal of capsid proteins together with a NES motif in the unique N-terminal of VP2. We also performed a global search for the nuclear traffic signals in the densoviruses belonging to five Densovirinae genera, which revealed high diversity in the patterns of NLSs and NESs. Using a heterologous system, the HeLa mammalian cell line expressing GFP-fused BgDV1 capsid proteins, we demonstrated that both signals are functionally active. We suggest that the NLS shared by all three BgDV1 capsid proteins drives the trafficking of the newly-synthesized proteins into the nucleus, while the NES may play a role in the export of the newly-assembled BgDV1 particles into the cytoplasm through nuclear pore complexes.
Collapse
|
7
|
Zhou C, Liu S, Song W, Luo S, Meng G, Yang C, Yang H, Ma J, Wang L, Gao S, Wang J, Yang H, Zhao Y, Wang H, Zhou X. Characterization of viral RNA splicing using whole-transcriptome datasets from host species. Sci Rep 2018; 8:3273. [PMID: 29459752 PMCID: PMC5818608 DOI: 10.1038/s41598-018-21190-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/31/2018] [Indexed: 01/16/2023] Open
Abstract
RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses.
Collapse
Affiliation(s)
- Chengran Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Wenhui Song
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shiqi Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chentao Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hua Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Liang Wang
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Shan Gao
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Hui Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,The Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China. .,National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
8
|
Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Reprint of: Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2017; 147:23-36. [PMID: 32781498 DOI: 10.1016/j.jip.2017.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
Collapse
Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| |
Collapse
|
9
|
Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2016; 140:83-96. [PMID: 27663091 DOI: 10.1016/j.jip.2016.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
Collapse
Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| |
Collapse
|
10
|
Yang WT, Shi SH, Jiang YL, Zhao L, Chen HL, Huang KY, Yang GL, Wang CF. Genetic characterization of a densovirus isolated from great tit (Parus major) in China. INFECTION GENETICS AND EVOLUTION 2016; 41:107-112. [PMID: 27051046 DOI: 10.1016/j.meegid.2016.03.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
During a study of ornithophilous viruses in China, a new densovirus (DNV) was isolated from the lung tissue of Parus major (PmDNV-JL). The complete genome of PmDNV-JL was cloned and sequenced. Five open reading frames (ORFs) were identified in the 5166nt sequence, on the basis of deduced amino acids. It was further shown that this virus caused cytopathic effects (CPE) in Feline kidney cells. The NS1 gene sequence of PmDNV-JL shares 70-99% nucleotide sequence identity with isolates of the Blattella germanica densovirus (BgDNV) and BgDNV-like virus. Phylogenetic analysis indicated that the predicted amino acid sequences of capsid (VP) and non-structural domain (NS1) of PmDNV-JL clustered with the BgDNV and were similar to BgDNV-HB within the genus Densovirus.
Collapse
Affiliation(s)
- Wen-Tao Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Shao-Hua Shi
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Yan-Long Jiang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Liang Zhao
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Hong-Liang Chen
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Ke-Yan Huang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Gui-Lian Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Chun-Feng Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal probiotics, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| |
Collapse
|
11
|
Kozlov EN, Martynova EU, Roshina NV, Karakozova MV, Mukha DV. Expression of cDNA of the gene for the capsid protein VP2 of German cockroach densovirus in the transgenic strain of Drosophila melanogaster. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
First complete genome of an Ambidensovirus; Cherax quadricarinatus densovirus, from freshwater crayfish Cherax quadricarinatus. Mar Genomics 2015; 24 Pt 3:305-12. [DOI: 10.1016/j.margen.2015.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022]
|
13
|
Martynova EU, Schal C, Mukha DV. Effects of recombination on densovirus phylogeny. Arch Virol 2015; 161:63-75. [PMID: 26475154 DOI: 10.1007/s00705-015-2642-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023]
Abstract
Densoviruses are a group of arthropod-infecting viruses with a small single-stranded linear DNA genome. These viruses constitute the subfamily Densovirinae of the family Parvoviridae. While recombination in between vertebrate-infecting parvoviruses has been investigated, to date, no systematic analysis of recombination has been carried out for densoviruses. The aim of the present work was to study possible recombination events in the evolutionary history of densoviruses and to assess possible effects of recombination on phylogenies inferred using amino acid sequences of nonstructural (NS) and capsid (viral protein, VP) proteins. For this purpose, the complete or nearly complete genome nucleotide sequences of 40 densoviruses from the GenBank database were used to construct a phylogenetic cladogram. The viruses under study clustered into five distinct groups corresponding to the five currently accepted genera. Recombination within each group was studied independently. The RDP4 software revealed three statistically highly credible recombination events, two of which involved viruses of the genus Ambidensovirus, and the other, viruses from the genus Iteradensovirus. These recombination events led to mismatches between phylogenetic trees constructed using comparison of amino acid sequences of proteins encoded by genome regions of recombinant and non-recombinant origin (regulatory NS1 and NS3 proteins and capsid VP protein).
Collapse
Affiliation(s)
- Elena U Martynova
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Coby Schal
- North Carolina State University, Raleigh, North Carolina, 27695-7613, USA
| | - Dmitry V Mukha
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia.
| |
Collapse
|
14
|
Kozlov EN, Mukha DV. Mammalian cell culture as a model for studying the intracellular traffic of densovirus proteins. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415020118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Martynova EU, Kapelinskaya TV, Schal C, Mukha DV. Intracellular localization of regulatory proteins of the German cockroach Blattella germanica densovirus. Mol Biol 2014. [DOI: 10.1134/s0026893314020113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Swevers L, Vanden Broeck J, Smagghe G. The possible impact of persistent virus infection on the function of the RNAi machinery in insects: a hypothesis. Front Physiol 2013; 4:319. [PMID: 24204347 PMCID: PMC3817476 DOI: 10.3389/fphys.2013.00319] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/15/2013] [Indexed: 11/13/2022] Open
Abstract
RNAi experiments in insects are characterized by great variability in efficiency; for instance beetles and locusts are very amenable to dsRNA-mediated gene silencing, while other insect groups, most notably lepidopterans, are more refractory to RNAi. Several factors can be forwarded that could affect the efficiency of RNAi, such as the composition and function of the intracellular RNAi machinery, the mechanism of dsRNA uptake, the presence of dsRNA- and siRNA-degrading enzymes and non-specific activation of the innate immune response. In this essay, we investigate the evidence whether persistent infection with RNA viruses could be a major factor that affects the response to exogenous dsRNA in insects. The occurrence of RNA viruses in different insect groups will be discussed, as well as several mechanisms by which viruses could interfere with the process of RNAi. Finally, the impact of RNA virus infection on the design of dsRNA-based insect control strategies will be considered.
Collapse
Affiliation(s)
- Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," Athens, Greece
| | | | | |
Collapse
|
17
|
Ito K, Kidokoro K, Shimura S, Katsuma S, Kadono-Okuda K. Detailed investigation of the sequential pathological changes in silkworm larvae infected with Bombyx densovirus type 1. J Invertebr Pathol 2013; 112:213-8. [DOI: 10.1016/j.jip.2012.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
|
18
|
Rubio M, de Horna A, Belles X. MicroRNAs in metamorphic and non-metamorphic transitions in hemimetabolan insect metamorphosis. BMC Genomics 2012; 13:386. [PMID: 22882747 PMCID: PMC3462697 DOI: 10.1186/1471-2164-13-386] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/26/2012] [Indexed: 11/28/2022] Open
Abstract
Background Previous work showed that miRNAs play key roles in the regulation of metamorphosis in the hemimetabolan species Blattella germanica. To gain insight about which miRNAs might be important, we have constructed two miRNA libraries, one of the penultimate, pre-metamorphic nymphal instar (N5) and the other of the last, metamorphic nymphal instar (N6). Results High throughput sequencing gave 61 canonical miRNAs present in the N5 and N6 libraries, although at different proportions in each. Comparison of both libraries led to the identification of three and 37 miRNAs significantly more expressed in N5 and N6 respectively. Twelve of these 40 miRNAs were then investigated further by qRT-PCR and results indicated that miR-252-3p was well expressed in N5 but not in N6, whereas let-7-5p, miR-100-5p and miR-125-5p showed the reverse pattern. 20-Hydroxyecdysone (20E) tended to stimulate miRNA expression, whereas juvenile hormone (JH) inhibited the 20E stimulatory effect. Expression of let-7, miR-100 and miR-125 was increased by 20E, which has also been observed in D. melanogaster. The only miRNA that was inhibited by 20E was miR-252-3p. The involvement of let-7, miR-100 and miR-125 in metamorphosis has been demonstrated in other insects. Depletion of miR-252-3p caused growth and developmental delays, which suggests that this miRNA is involved in regulating these processes prior to metamorphosis. Conclusions The comparative analysis of miRNA libraries from pre-metamorphic (N5) and metamorphic stages (N6) of B. germanica proved to be a useful tool to identify miRNAs with roles in hemimetabolan metamorphosis. Three miRNAs emerged as important factors in the metamorphic stage (N6): let-7-5p, miR-100-5p and miR-125-5p, whereas miR-252-3p appears to be important in the pre-metamorphic stage (N5).
Collapse
Affiliation(s)
- Mercedes Rubio
- Institute of Evolutionary Biology, CSIC-UPF, Passeig Marítim 39, 08003 Barcelona, Spain
| | | | | |
Collapse
|
19
|
Super-induction of Dicer-2 expression by alien double-stranded RNAs: an evolutionary ancient response to viral infection? Dev Genes Evol 2012; 222:229-35. [DOI: 10.1007/s00427-012-0404-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/25/2012] [Indexed: 12/15/2022]
|
20
|
Kapelinskaya TV, Martynova EU, Schal C, Mukha DV. Expression strategy of densonucleosis virus from the German cockroach, Blattella germanica. J Virol 2011; 85:11855-70. [PMID: 21900160 PMCID: PMC3209303 DOI: 10.1128/jvi.05523-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 09/08/2011] [Indexed: 11/20/2022] Open
Abstract
Blattella germanica densovirus (BgDNV) is an autonomous parvovirus that infects the German cockroach. BgDNV possesses three mRNAs for NS proteins, two of which are splice variants of the unspliced transcript. The unspliced variant encodes open reading frame 5 (ORF5) (NS3), while NSspl1 encodes ORF3 (NS1) and ORF4 (NS2) and NSspl2 encodes the C-proximal half of NS1. BgDNV possesses three VP transcripts, one of which (VP) is unspliced, while the other two (VPspl1 and VPspl2) are generated by alternative splicing. The unspliced VP transcript contains both ORF1 and ORF2, while in VPspl1, ORF1 and ORF2 are joined in frame. The transcription of NS genes begins at an earlier stage of the virus life cycle than the transcription of VP genes. NS and VP transcripts overlap by 48 nucleotides (nt). BgDNV is characterized by two additional NS transcripts overlapping by more than 1,650 nt with VP-coding transcripts. Four different bands (97, 85, 80, and 57 kDa) corresponding to three BgDNV capsid proteins were detected on SDS-PAGE. Mass spectrometry analysis showed that the amino acid composition of the 85-kDa and 80-kDa proteins is the same. Moreover, both of these proteins are ubiquitinated. The BgDNV PLA(2) domain, which is critical for cellular uptake of the virus, is located in ORF2 and is present only in VP1. In contrast to all of the parvoviruses studied in this respect, VP2 has a unique N terminus that is not contained within VP1 and VP3. In situ recognition with NS1- and VP-specific antibodies revealed an uneven pattern of NS1 expression resembling a halo within the nuclear membrane.
Collapse
Affiliation(s)
- Tatiana V. Kapelinskaya
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin 3, Moscow 119991, Russia
| | - Elena U. Martynova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin 3, Moscow 119991, Russia
| | - Coby Schal
- Department of Entomology and W. M. Keck Center for Behavioral Biology, Box 7613, North Carolina State University, Raleigh, North Carolina 27695-7613
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin 3, Moscow 119991, Russia
| |
Collapse
|
21
|
The Acheta domesticus densovirus, isolated from the European house cricket, has evolved an expression strategy unique among parvoviruses. J Virol 2011; 85:10069-78. [PMID: 21775445 DOI: 10.1128/jvi.00625-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Acheta domesticus densovirus (AdDNV), isolated from crickets, has been endemic in Europe for at least 35 years. Severe epizootics have also been observed in American commercial rearings since 2009 and 2010. The AdDNV genome was cloned and sequenced for this study. The transcription map showed that splicing occurred in both the nonstructural (NS) and capsid protein (VP) multicistronic RNAs. The splicing pattern of NS mRNA predicted 3 nonstructural proteins (NS1 [576 codons], NS2 [286 codons], and NS3 [213 codons]). The VP gene cassette contained two VP open reading frames (ORFs), of 597 (ORF-A) and 268 (ORF-B) codons. The VP2 sequence was shown by N-terminal Edman degradation and mass spectrometry to correspond with ORF-A. Mass spectrometry, sequencing, and Western blotting of baculovirus-expressed VPs versus native structural proteins demonstrated that the VP1 structural protein was generated by joining ORF-A and -B via splicing (splice II), eliminating the N terminus of VP2. This splice resulted in a nested set of VP1 (816 codons), VP3 (467 codons), and VP4 (429 codons) structural proteins. In contrast, the two splices within ORF-B (Ia and Ib) removed the donor site of intron II and resulted in VP2, VP3, and VP4 expression. ORF-B may also code for several nonstructural proteins, of 268, 233, and 158 codons. The small ORF-B contains the coding sequence for a phospholipase A2 motif found in VP1, which was shown previously to be critical for cellular uptake of the virus. These splicing features are unique among parvoviruses and define a new genus of ambisense densoviruses.
Collapse
|
22
|
Structure and expression strategy of the genome of Culex pipiens densovirus, a mosquito densovirus with an ambisense organization. J Virol 2009; 83:6863-73. [PMID: 19386710 DOI: 10.1128/jvi.00524-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of all densoviruses (DNVs) so far isolated from mosquitoes or mosquito cell lines consists of a 4-kb single-stranded DNA molecule with a monosense organization (genus Brevidensovirus, subfamily Densovirinae). We previously reported the isolation of a Culex pipiens DNV (CpDNV) that differs significantly from brevidensoviruses by (i) having a approximately 6-kb genome, (ii) lacking sequence homology, and (iii) lacking antigenic cross-reactivity with Brevidensovirus capsid polypeptides. We report here the sequence organization and transcription map of this virus. The cloned genome of CpDNV is 5,759 nucleotides (nt) long, and it possesses an inverted terminal repeat (ITR) of 285 nt and an ambisense organization of its genes. The nonstructural (NS) proteins NS-1, NS-2, and NS-3 are located in the 5' half of one strand and are organized into five open reading frames (ORFs) due to the split of both NS-1 and NS-2 into two ORFs. The ORF encoding capsid polypeptides is located in the 5' half of the complementary strand. The expression of NS proteins is controlled by two promoters, P7 and P17, driving the transcription of a 2.4-kb mRNA encoding NS-3 and of a 1.8-kb mRNA encoding NS-1 and NS-2, respectively. The two NS mRNAs species are spliced off a 53-nt sequence. Capsid proteins are translated from an unspliced 2.3-kb mRNA driven by the P88 promoter. CpDNV thus appears as a new type of mosquito DNV, and based on the overall organization and expression modalities of its genome, it may represent the prototype of a new genus of DNV.
Collapse
|
23
|
Kapelinskaya TV, Martynova EU, Korolev AL, Schal C, Mukha DV. Transcription of the German cockroach densovirus BgDNV genome: alternative processing of viral RNAs. DOKL BIOCHEM BIOPHYS 2008; 421:176-80. [PMID: 18853766 DOI: 10.1134/s1607672908040042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- T V Kapelinskaya
- Vavilov Institute of General Genetics, Russian Academy of Sciences, ul. Gubkina 3, Moscow, 119991 Russia
| | | | | | | | | |
Collapse
|