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Nibert ML, Xie Y, Xiao J, Gao Y, Liu D, Yang G, Tao J. Transcriptome mining of RNA viruses (family Totiviridae ) in Eimeria necatrix and Eimeria stiedai. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541574. [PMID: 37292684 PMCID: PMC10245732 DOI: 10.1101/2023.05.20.541574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Coccidian protozoa from the genus Eimeria are widespread parasites of vertebrates, causing serious disease (coccidiosis) and economic loss most notably in poultry. Several species of Eimeria are themselves infected with small RNA viruses assigned to the family Totiviridae . In this study, the sequences of two such viruses were newly determined, one of which represents the first complete protein-coding sequence of a virus from E. necatrix , an important pathogen of chickens, and the other of which is from E. stiedai , an important pathogen of rabbits. Sequence features of the newly identified viruses, compared with those of ones reported previously, provide several insights. Phylogenetic analyses suggest that these eimerian viruses constitute a well-demarcated clade, probably deserving of recognition as a distinct genus.
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Zhao Y, Du H, Liu Y, Zhong R, Guan Z, Wang G, Zhang Y, Wei C, Wang M, Wan X, Zang R, Wen C, Meng H. Molecular characterization of a novel victorivirus isolated from the phytopathogenic fungus Phaeobotryon rhois. Arch Virol 2023; 168:15. [PMID: 36593368 DOI: 10.1007/s00705-022-05678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 01/03/2023]
Abstract
Phaeobotryon rhois is an important pathogenic fungus that causes dieback and canker disease of woody hosts. A novel mycovirus, tentatively named "Phaeobotryon rhois victorivirus 1" (PrVV1), was identified in P. rhois strain SX8-4. The PrVV1 has a double-stranded RNA (dsRNA) genome that is 5,224 base pairs long and contains two open reading frames (ORF1 and ORF2), which overlap at a AUGA sequence. ORF1 encodes a polypeptide of 786 amino acids (aa) that contains the conserved coat protein (CP) domain of victoriviruses, while ORF2, encodes a large polypeptide of 826 aa that contains the conserved RNA-dependent RNA polymerase (RdRp) domain of victoriviruses. Our analysis of genomic structure, homology, and phylogeny indicated that PrVV1 is a novel member of the genus Victorivirus in the family Totiviridae. This is the first report of the complete genome sequence of a victorivirus that infects P. rhois.
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Affiliation(s)
- Ying Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuanyuan Liu
- Yinchuan City Center for Disease Control and Prevention, Yinchuan, China
| | - Rongrong Zhong
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhengzhe Guan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ganlin Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuanyuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Chenxing Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengjiao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinru Wan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Rui Zang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haoguang Meng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
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Complete genome sequence of a novel victorivirus infecting cicada flower (Cordyceps chanhua). Arch Virol 2023; 168:4. [DOI: 10.1007/s00705-022-05640-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023]
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4
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Yuan Z, Geng Y, Dai Y, Li J, Lv M, Liao Q, Xie L, Zhang H. A fijiviral nonstructural protein triggers cell death in plant and bacterial cells via its transmembrane domain. MOLECULAR PLANT PATHOLOGY 2023; 24:59-70. [PMID: 36305370 PMCID: PMC9742498 DOI: 10.1111/mpp.13277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 05/10/2023]
Abstract
Southern rice black-streaked dwarf virus (SRBSDV; Fijivirus, Reoviridae) has become a threat to cereal production in East Asia in recent years. Our previous cytopathologic studies have suggested that SRBSDV induces a process resembling programmed cell death in infected tissues that results in distinctive growth abnormalities. The viral product responsible for the cell death, however, remains unknown. Here P9-2 protein, but not its RNA, was shown to induce cell death in Escherichia coli and plant cells when expressed either locally with a transient expression vector or systemically using a heterologous virus. Both computer prediction and fluorescent assays indicated that the viral nonstructural protein was targeted to the plasma membrane (PM) and further modification of its subcellular localization abolished its ability to induce cell death, indicating that its PM localization was required for the cell death induction. P9-2 was predicted to harbour two transmembrane helices within its central hydrophobic domain. A series of mutation assays further showed that its central transmembrane hydrophobic domain was crucial for cell death induction and that its conserved F90, Y101, and L103 amino acid residues could play synergistic roles in maintaining its ability to induce cell death. Its homologues in other fijiviruses also induced cell death in plant and bacterial cells, implying that the fijiviral nonstructural protein may trigger cell death by targeting conserved cellular factors or via a highly conserved mechanism.
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Affiliation(s)
- Zhengjie Yuan
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yanfei Geng
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yuanxing Dai
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
- College of Chemistry and Life ScienceZhejiang Normal UniversityJinhuaChina
| | - Jing Li
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Mingfang Lv
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Qiansheng Liao
- College of Life ScienceZhejiang Sci‐Tech UniversityHangzhouChina
| | - Li Xie
- Analysis Center of Agrobiology and Environmental SciencesZhejiang UniversityHangzhouChina
| | - Heng‐Mu Zhang
- Laboratory of Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
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Yang M, Wang G, Mu W, Guo J, Xi J, Hu L, Liang K, Xu Q, Hu Z, Song J. A novel victorivirus isolated from the tobacco spot blight fungus Stagonosporopsis cucurbitacearum in China. Arch Virol 2022; 167:2845-2850. [PMID: 36214899 DOI: 10.1007/s00705-022-05618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Stagonosporopsis cucurbitacearum is an important plant-pathogenic fungus that causes stem and leaf blight diseases in a variety of crops. Here, we report the characterization of a novel victorivirus, tentatively named "Stagonosporopsis cucurbitacearum victorivirus 1" (ScVV-1), isolated from the S. cucurbitacearum isolate M-7. The ScVV-1 genome is 5,165 bp in length with a predicted GC content of 60.1% and contains two large open reading frames (ORF 1 and ORF2) encoding putative proteins that share significant sequence similarity with coat proteins (CPs) and RNA-dependent RNA polymerases (RdRps) of mycoviruses of the family Totiviridae. The ScVV-1 RdRp appears to be translated using a stop-initiation pentanucleotide UAAUG sequence. Phylogenetic analysis based on CP and RdRp amino acid (aa) sequences both indicated that ScVV-1 belongs to the genus Victorivirus in the family Totiviridae. To our knowledge, this is the first full-length genome sequence of a victorivirus infecting S. cucurbitacearum.
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Affiliation(s)
- Mengmeng Yang
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Guiyao Wang
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Wenjun Mu
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Jianhua Guo
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Jiaqin Xi
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Liwei Hu
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Kexin Liang
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China
| | - Qiang Xu
- China Tobacco Jiangsu Industry Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Zongyu Hu
- China Tobacco Jiangsu Industry Co., Ltd, Nanjing, 210000, Jiangsu, China.
| | - Jizhen Song
- Key Laboratory of Eco-environment and Leaf Tobacco Quality, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, Henan, China.
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Zhong J, Sui WW, Li P, Tang QJ, Liu TB, Xiao YS. Characterization of a novel victorivirus from Nigrospora chinensis, a fungus isolated from tobacco. Arch Virol 2022; 167:2851-2855. [PMID: 36255526 DOI: 10.1007/s00705-022-05619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Here, we characterized a new mycovirus from the fungus Nigrospora chinensis, which was named "Nigrospora chinensis victorivirus 1" (NcVV1). The NcVV1 genome is 5283 bp in length, containing two continuous open reading frames (ORFs), ORF1 and ORF2. ORF1 and ORF2 were predicted to encode a putative coat protein (CP) and an RNA-dependent RNA polymerase (RdRp), respectively. The stop codon of ORF1 overlaps with the start codon of ORF2 by the tetranucleotide sequence AUGA. Phylogenetic analysis based on amino acid sequences of RdRp and CP indicated that NcVV1 clustered with members of the genus Victorivirus in the family Totiviridae. To our knowledge, this was the first report of a mycovirus infecting N. chinensis.
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Affiliation(s)
- Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
| | - Wen Wen Sui
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Ping Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Qian Jun Tang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Tian Bo Liu
- Tobacco Research Institute of Hunan Province, Changsha, 410004, Hunan, People's Republic of China.
| | - Yan Song Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, 423000, Hunan, People's Republic of China.
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Zhong J, Li P, Gao BD, Zhong SY, Li XG, Hu Z, Zhu JZ. Novel and diverse mycoviruses co-infecting a single strain of the phytopathogenic fungus Alternaria dianthicola. Front Cell Infect Microbiol 2022; 12:980970. [PMID: 36237429 PMCID: PMC9552818 DOI: 10.3389/fcimb.2022.980970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Alternaria dianthicola is a pathogenic fungus that causes serious leaf or flower blight on some medicinal plants worldwide. In this study, multiple dsRNA bands in the range of 1.2-10 kbp were found in a Alternaria dianthus strain HNSZ-1, and eleven full-length cDNA sequences of these dsRNA were obtained by high-throughput sequencing, RT-PCR detection and conventional Sanger sequencing. Homology search and phylogenetic analyses indicated that the strain HNSZ-1 was infected by at least nine mycoviruses. Among the nine, five viruses were confirmed to represent novel viruses in the families Hypoviridae, Totiviridae, Mymonaviridae and a provisional family Ambiguiviridae. Virus elimination and horizontal transmission indicated that the (-) ssRNA virus, AdNSRV1, might be associated with the slow growth and irregular colony phenotype of the host fungus. As far as we know, this is the first report for virome characterization of A. dianthus, which might provide important insights for screening of mycovirus for biological control and for studying of the interactions between viruses or viruses and their host.
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Affiliation(s)
- Jie Zhong
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha City, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
| | - Ping Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
| | - Bi Da Gao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
| | - Shuang Yu Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
| | - Xiao Gang Li
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha City, China
- *Correspondence: Jun Zi Zhu, ; Zhao Hu, ; Xiao Gang Li,
| | - Zhao Hu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
- *Correspondence: Jun Zi Zhu, ; Zhao Hu, ; Xiao Gang Li,
| | - Jun Zi Zhu
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha City, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha City, China
- *Correspondence: Jun Zi Zhu, ; Zhao Hu, ; Xiao Gang Li,
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Molecular characterization of a novel victorivirus isolated from Botryosphaeria dothidea, the causal agent of longan leaf spot disease. Arch Virol 2022; 167:2417-2422. [PMID: 35962824 DOI: 10.1007/s00705-022-05573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/03/2022] [Indexed: 11/02/2022]
Abstract
Mycoviruses are widespread in all major taxonomic groups of filamentous fungi. Previous research has indicated that mycoviruses are associated with the phytopathogenic fungus Botryosphaeria dothidea. In this study, three distinct double-stranded RNA viruses were detected in B. dothidea strain YCLYY11 isolated from a leaf spot of longan (Dimocarpus longana). The results of BLAST analysis revealed that the predicted amino acid sequences of those viruses were similar to those of Botryosphaeria dothidea chrysovirus 1, Botryosphaeria dothidea partitivirus 1, and an apparent novel victorivirus. Sequencing and analysis of the complete genome of the novel victorivirus indicated it is 5218 bp in length and contains two open reading frames (ORFs) that overlap at the tetranucleotide AUGA. BLASTp analysis of the proteins encoded by ORF1 and ORF2 showed that they were most similar to the coat protein and RNA-dependent RNA polymerase of Sphaeropsis sapinea RNA virus 2 (81.37% and 74.09% identical, respectively). A phylogenetic tree showed that the novel virus clustered together with victoriviruses and was separate from members of the other four genera of the family Totiviridae. Based on its genome structure and the results of phylogenetic analysis, we propose that this novel victorivirus should be named "Botryosphaeria dothidea victorivirus 3". This is also the first report of these three mycoviruses coinfecting a strain of B. dothidea.
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Complete genome sequence of a novel victorivirus infecting Aspergillus niger. Arch Virol 2022; 167:1475-1479. [PMID: 35449474 DOI: 10.1007/s00705-022-05441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/04/2022] [Indexed: 11/02/2022]
Abstract
Aspergillus niger is an important filamentous phytopathogenic fungus with a broad host range. A novel double-stranded (ds) RNA mycovirus, named Aspergillus niger victorivirus 1 (AnV1), isolated from A. niger strain baiyun3.23-4, was sequenced and analyzed. The AnV1 genome is 5317 nucleotides long with a GC content of 56%. AnV1 contains two open reading frames (ORF1 and 2), overlapping at a tetranucleotide sequence (AUGA). ORF1 encodes a putative capsid protein (CP) of 778 amino acids (aa), while ORF2 potentially encodes a putative RNA-dependent RNA polymerase (RdRp) of 826 aa. Phylogenetic analysis indicated that AnV1 is a new member of the genus Victorivirus in the family Totiviridae. As far as we know, this is the first report of the complete genome sequence of a victorivirus infecting A. niger.
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Wang X, Lai J, Hu H, Yang J, Zang K, Zhao F, Zeng G, Liao Q, Gu Z, Du Z. Infection of Nigrospora nonsegmented RNA Virus 1 Has Important Biological Impacts on a Fungal Host. Viruses 2022; 14:v14040795. [PMID: 35458525 PMCID: PMC9029208 DOI: 10.3390/v14040795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Nigrospora nonsegmented RNA virus 1 (NoNRV1) has been reported previously in the fungus Nigrospora oryzae, but its biological effects on its host are unknown. In this work, we isolated a strain 9-1 of N. oryzae from a chrysanthemum leaf and identified NoNRV1 infection in the isolated strain. The genome sequence of NoNRV1 identified here is highly homologous to that of the isolate HN-21 of NoNRV1 previously reported; thus, we tentatively designated the newly identified NoNRV1 as NoNRV1-ZJ. Drug treatment with Ribavirin successfully removed NoNRV1-ZJ from the strain 9-1, which provided us with an ideal control to determine the biological impacts of NoNRV1 infection on host fungi. By comparing the virus-carrying (9-1) and virus-cured (9-1C) strains, our results indicated that infection with NoNRV1 promoted the pigmentation of the host cells, while it had no discernable effects on host growth on potato dextrose agar plates when subjected to osmotic or oxidative stress. Interestingly, we observed inhibitory impacts of virus infection on the thermotolerance of N. oryzae and the pathogenicity of the host fungus in cotton leaves. Collectively, our work provides clear evidence of the biological relevance of NoNRV1 infection in N. oryzae, including pigmentation, hypovirulence, and thermotolerance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhouhang Gu
- Correspondence: (Z.G.); (Z.D.); Tel.: +86-571-8684-3195 (Z.D.)
| | - Zhiyou Du
- Correspondence: (Z.G.); (Z.D.); Tel.: +86-571-8684-3195 (Z.D.)
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Khan HA, Sato Y, Kondo H, Jamal A, Bhatti MF, Suzuki N. A novel victorivirus from the phytopathogenic fungus Neofusicoccum parvum. Arch Virol 2022; 167:923-929. [PMID: 35112205 DOI: 10.1007/s00705-021-05304-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 11/02/2022]
Abstract
Neofusicoccum parvum is an important plant-pathogenic ascomycetous fungus that causes trunk diseases in a variety of plants. A limited number of reports on mycoviruses from this fungus are available. Here, we report the characterization of a novel victorivirus, Neofusicoccum parvum victorivirus 3 (NpVV3). An agarose gel dsRNA profile of a Pakistani strain of N. parvum, NFN, showed a band of ~5 kbp that was not detectable in Japanese strains of N. parvum. Taking a high-throughput and Sanger sequencing approach, the complete genome sequence of NpVV3 was determined to be 5226 bp in length with two open reading frames (ORF1 and ORF2) that encode a capsid protein (CP) and an RNA-dependent RNA polymerase (RdRP). The RdRP appears to be translated by a stop/restart mechanism facilitated by the junction sequence AUGucUGA, as is found in some other victoriviruses. BLASTp searches showed that NpVV3 CP and RdRP share the highest amino acid sequence identity (80.5% and 72.4%, respectively) with the corresponding proteins of NpVV1 isolated from a French strain of N. parvum. However, NpVV3 was found to be different from NpVV1 in its terminal sequences and the stop/restart facilitator sequence. NpVV3 particles ~35 nm in diameter were partially purified and used to infect an antiviral-RNA-silencing-deficient strain (∆dcl2) of an experimental ascomycetous fungal host, Cryphonectria parasitica. NpVV3 showed symptomless infection in the new host strain.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Abstract
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
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Kartali T, Nyilasi I, Kocsubé S, Patai R, Polgár TF, Zsindely N, Nagy G, Bodai L, Lipinszki Z, Vágvölgyi C, Papp T. Characterization of Four Novel dsRNA Viruses Isolated from Mucor hiemalis Strains. Viruses 2021; 13:v13112319. [PMID: 34835124 PMCID: PMC8625083 DOI: 10.3390/v13112319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
We previously screened the total nucleic acid extracts of 123 Mucor strains for the presence of dsRNA molecules without further molecular analyses. Here, we characterized five novel dsRNA genomes isolated from four different Mucor hiemalis strains with next-generation sequencing (NGS), namely Mucor hiemalis virus 1a (MhV1a) from WRL CN(M) 122; Mucor hiemalis virus 1b (MhV1b) from NRRL 3624; Mucor hiemalis virus 2 (MhV2) from NRRL 3616; and Mucor hiemalis virus 3 (MhV3) and Mucor hiemalis virus (MhV4) from NRRL 3617 strains. Genomes contain two open reading frames (ORF), which encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In MhV1a and MhV1b, it is predicted to be translated as a fusion protein via -1 ribosomal frameshift, while in MhV4 via a rare +1 (or-2) ribosomal frameshift. In MhV2 and MhV3, the presence of specific UAAUG pentanucleotide motif points to the fact for coupled translation termination and reinitialization. MhV1a, MhV2, and MhV3 are part of the clade representing the genus Victorivirus, while MhV4 is seated in Totivirus genus clade. The detected VLPs in Mucor strains were from 33 to 36 nm in diameter. Hybridization analysis revealed that the dsRNA molecules of MhV1a-MhV4 hybridized to the corresponding molecules.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- Correspondence: (T.K.); (T.P.)
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Roland Patai
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
| | - Tamás F. Polgár
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
- Theoretical Medicine Doctoral School, University of Szeged, 6722 Szeged, Hungary
| | - Nóra Zsindely
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary;
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences and Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
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14
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Mizutani Y, Uesaka K, Ota A, Calassanzio M, Ratti C, Suzuki T, Fujimori F, Chiba S. De novo Sequencing of Novel Mycoviruses From Fusarium sambucinum: An Attempt on Direct RNA Sequencing of Viral dsRNAs. Front Microbiol 2021; 12:641484. [PMID: 33927702 PMCID: PMC8076516 DOI: 10.3389/fmicb.2021.641484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
An increasing number of viruses are continuously being found in a wide range of organisms, including fungi. Recent studies have revealed a wide viral diversity in microbes and a potential importance of these viruses in the natural environment. Although virus exploration has been accelerated by short-read, high-throughput sequencing (HTS), and viral de novo sequencing is still challenging because of several biological/molecular features such as micro-diversity and secondary structure of RNA genomes. This study conducted de novo sequencing of multiple double-stranded (ds) RNA (dsRNA) elements that were obtained from fungal viruses infecting two Fusarium sambucinum strains, FA1837 and FA2242, using conventional HTS and long-read direct RNA sequencing (DRS). De novo assembly of the read data from both technologies generated near-entire genomic sequence of the viruses, and the sequence homology search and phylogenetic analysis suggested that these represented novel species of the Hypoviridae, Totiviridae, and Mitoviridae families. However, the DRS-based consensus sequences contained numerous indel errors that differed from the HTS consensus sequences, and these errors hampered accurate open reading frame (ORF) prediction. Although with its present performance, the use of DRS is premature to determine viral genome sequences, the DRS-mediated sequencing shows great potential as a user-friendly platform for a one-shot, whole-genome sequencing of RNA viruses due to its long-reading ability and relative structure-tolerant nature.
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Affiliation(s)
- Yukiyoshi Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Ayane Ota
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Matteo Calassanzio
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Fumihiro Fujimori
- Graduate School of Humanities and Life Sciences, Tokyo Kasei University, Itabashi, Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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15
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Liu TY, Tsai SH, Chen JW, Wang YC, Hu ST, Chen YY. Mab_3083c Is a Homologue of RNase J and Plays a Role in Colony Morphotype, Aggregation, and Sliding Motility of Mycobacterium abscessus. Microorganisms 2021; 9:microorganisms9040676. [PMID: 33805851 PMCID: PMC8064342 DOI: 10.3390/microorganisms9040676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium abscessus is an opportunistic pathogen causing human diseases, especially in immunocompromised patients. M. abscessus strains with a rough morphotype are more virulent than those with a smooth morphotype. Morphotype switch may occur during a clinical infection. To investigate the genes involved in colony morphotype switching, we performed transposon mutagenesis in a rough clinical strain of M. abscessus. A morphotype switching mutant (smooth) named mab_3083c::Tn was obtained. This mutant was found to have a lower aggregative ability and a higher sliding motility than the wild type strain. However, its glycopeptidolipid (GPL) content remained the same as those of the wild type. Complementation of the mutant with a functional mab_3083c gene reverted its morphotype back to rough, indicating that mab_3083c is associated with colony morphology of M. abscessus. Bioinformatic analyses showed that mab_3083c has a 75.4% identity in amino acid sequence with the well-characterized ribonuclease J (RNase J) of M. smegmatis (RNase JMsmeg). Complementation of the mutant with the RNase J gene of M. smegmatis also switched its colony morphology from smooth back to rough. These results suggest that Mab_3083c is a homologue of RNase J and involved in regulating M. abscessus colony morphotype switching.
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Affiliation(s)
- Ting-Yu Liu
- Institute of Microbiology and Immunology, School of Life Science, National Yang-Ming University, Taipei 112, Taiwan; (T.-Y.L.); (S.-H.T.)
| | - Sheng-Hui Tsai
- Institute of Microbiology and Immunology, School of Life Science, National Yang-Ming University, Taipei 112, Taiwan; (T.-Y.L.); (S.-H.T.)
| | - Jenn-Wei Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan
| | - Yu-Ching Wang
- Department of Biochemical Science and Technology, National Chiayi Univeristy, Chiayi City 600, Taiwan;
| | - Shiau-Ting Hu
- Institute of Microbiology and Immunology, School of Life Science, National Yang-Ming University, Taipei 112, Taiwan; (T.-Y.L.); (S.-H.T.)
- Correspondence: (S.-T.H.); (Y.-Y.C.)
| | - Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi Univeristy, Chiayi City 600, Taiwan;
- Correspondence: (S.-T.H.); (Y.-Y.C.)
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16
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Owashi Y, Aihara M, Moriyama H, Arie T, Teraoka T, Komatsu K. Population Structure of Double-Stranded RNA Mycoviruses That Infect the Rice Blast Fungus Magnaporthe oryzae in Japan. Front Microbiol 2020; 11:593784. [PMID: 33193269 PMCID: PMC7664462 DOI: 10.3389/fmicb.2020.593784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Various viruses infect Magnaporthe oryzae (syn. Pyricularia oryzae), which is a well-studied fungus that causes rice blast disease. Most research has focused on the discovery of new viruses and the hypovirulence-associated traits conferred by them. Therefore, the diversity and prevalence of viruses in wild fungal populations have not been explored. We conducted a comprehensive screening of M. oryzae mycoviruses from various regions in Japan using double-stranded RNA (dsRNA) electrophoresis and RT-PCR assays. We detected three mycoviruses, Magnaporthe oryzae virus 2 (MoV2), Magnaporthe oryzae chrysovirus 1 (MoCV1), and Magnaporthe oryzae partitivirus 1 (MoPV1), among 127 of the 194 M. oryzae strains screened. The most prevalent virus was MoPV1 (58.8%), which often co-infected in a single fungal strain together with MoV2 or MoCV1. MoV2 and MoCV1 were found in 22.7 and 10.8% of strains, respectively, and they were usually distributed in different regions so that mixed-infection with these two mycoviruses was extremely rare. The predominance of MoPV1 in M. oryzae is supported by significant negative values from neutrality tests, which indicate that the population size of MoPV1 tends to increase. Population genetic analyses revealed high nucleotide diversity and the presence of phylogenetically diverse subpopulations among the MoV2 isolates. This was not the case for MoPV1. Furthermore, studies of a virus-cured M. oryzae strain revealed that MoV2 does not cause any abnormalities or symptoms in its host. However, a leaf sheath inoculation assay showed that its presence slightly increased the speed of mycelial growth, compared with virus-free mycelia. These results demonstrate that M. oryzae in Japan harbors diverse dsRNA mycovirus communities with wide variations in their population structures among different viruses.
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Affiliation(s)
- Yuta Owashi
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan.,Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Mitsuhiro Aihara
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Hiromitsu Moriyama
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Tohru Teraoka
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
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17
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Wu R, Yang Y, Duan X, An H, Du Z, Zhang S, Zhang X. Four distinct isolates of Helminthosporium victoriae virus 190S identified from Bipolaris maydis. Virus Res 2020; 285:197941. [PMID: 32387400 DOI: 10.1016/j.virusres.2020.197941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/15/2020] [Accepted: 03/15/2020] [Indexed: 11/27/2022]
Abstract
Helminthosporium victoriae virus 190S (HvV190S) is the type species of the genus Victorivirus under the family Totiviridae. To date, HvV190S has never been found in places outside of the USA and has Helminthosporium victoriae as its only know natural host fungus in the field. Here, we report the identification of 4 double-stranded RNA (dsRNA) viruses from Bipolaris maydis in Hubei province of China. Interestingly, the genomes of the 4 viruses show 81.2 %-85.5 % nucleotide sequence identities to HvV190S. Their capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) share 95.5-97.9 % and 94.6-96.6 % amino acid sequence identities to corresponding proteins of HvV190S. Therefore, the 4 viruses, which show 81.8-87.3 % pairwise genome sequence identities, should be considered as distinct isolates of HvV190S. Our finding suggests that HvV190S is widely distributed in the world and may infect fungal species other than H. victoriae.
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Affiliation(s)
- Ruixue Wu
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Yunyue Yang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaotian Duan
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Hongliu An
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Songbai Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, Hubei, 434025, China.
| | - Xiaoting Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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18
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Chen Y, Wu J, Liang G, Geng G, Zhao F, Yin P, Nowsheen S, Wu C, Li Y, Li L, Kim W, Zhou Q, Huang J, Liu J, Zhang C, Guo G, Deng M, Tu X, Gao X, Liu Z, Chen Y, Lou Z, Luo K, Yuan J. CHK2-FOXK axis promotes transcriptional control of autophagy programs. SCIENCE ADVANCES 2020; 6:eaax5819. [PMID: 31911943 PMCID: PMC6938702 DOI: 10.1126/sciadv.aax5819] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/23/2019] [Indexed: 05/08/2023]
Abstract
Autophagy is an evolutionarily conserved catabolic process, which plays a vital role in removing misfolded proteins and clearing damaged organelles to maintain internal environment homeostasis. Here, we uncovered the checkpoint kinase 2 (CHK2)-FOXK (FOXK1 and FOXK2) axis playing an important role in DNA damage-mediated autophagy at the transcriptional regulation layer. Mechanistically, following DNA damage, CHK2 phosphorylates FOXK and creates a 14-3-3γ binding site, which, in turn, traps FOXK proteins in the cytoplasm. Because FOXK functions as the transcription suppressor of ATGs, DNA damage-mediated FOXKs' cytoplasmic trapping induces autophagy. In addition, we found that a cancer-derived FOXK mutation induces FOXK hyperphosphorylation and enhances autophagy, resulting in chemoresistance. Cotreatment with cisplatin and chloroquine overcomes the chemoresistance caused by FOXK mutation. Overall, our study highlights a mechanism whereby DNA damage triggers autophagy by increasing autophagy genes via CHK2-FOXK-mediated transcriptional control, and misregulation of this pathway contributes to chemoresistance.
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Affiliation(s)
- Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jinhuan Wu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Guang Liang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guohe Geng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Chengming Wu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jiaqi Liu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiumei Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 300193 Tianjin, China
| | - Zhongmin Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yihan Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Corresponding author.
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19
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Wang J, Xiao Y, Liu X, Ni Y, Zhao H, Zhao X, Liu H, Xiao X. Complete genome sequence of a novel victorivirus isolated from the sesame charcoal rot fungus Macrophomina phaseolina. Arch Virol 2019; 165:509-514. [PMID: 31845152 DOI: 10.1007/s00705-019-04497-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/11/2019] [Indexed: 11/27/2022]
Abstract
Macrophomina phaseolina is an important phytopathogenic fungus with a broad host range. Here, the complete genome sequence of a novel victorivirus, tentatively named Macrophomina phaseolina victorivirus 1 (MpV1), was identified from strain 2012-019 of M. phaseolina. The MpV1 genome is 5,128 nucleotides long with a predicted GC content of 62%. Sequence analysis indicated that two open reading frames (ORF 1 and 2) overlap at a tetranucleotide AUGA sequence. Proteins encoded by ORF1 and ORF2 showed significant sequence similarity to coat proteins and the RNA-dependent RNA polymerases, respectively, of members of the family Totiviridae. Analysis of the genomic structure of MpV1, homolog searches of the deduced amino acid sequences, and phylogenetic analysis indicated that MpV1 is a new member of the genus Victorivirus. As far as we know, this is the first report of the full-length nucleotide sequence of the genome of a novel victorivirus that infects M. phaseolina.
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Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Yannong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Xinbei Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
| | - Xueqiong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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20
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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21
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Kartali T, Nyilasi I, Szabó B, Kocsubé S, Patai R, Polgár TF, Nagy G, Vágvölgyi C, Papp T. Detection and Molecular Characterization of Novel dsRNA Viruses Related to the Totiviridae Family in Umbelopsis ramanniana. Front Cell Infect Microbiol 2019; 9:249. [PMID: 31380294 PMCID: PMC6644447 DOI: 10.3389/fcimb.2019.00249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/26/2019] [Indexed: 11/24/2022] Open
Abstract
Umbelopsis ramanniana is an oleaginous fungus belonging to the Mucoromycotina subphylum. Our group had previously detected four double-stranded RNA (dsRNA) bands in the U. ramanniana NRRL 1296 strain by gel electrophoresis. Here we describe the molecular characterization of its dsRNA elements as well as the discovery of four novel dsRNA viruses: Umbelopsis ramanniana virus 1 (UrV1), Umbelopsis ramanniana virus 2 (UrV2), Umbelopsis ramanniana virus 3 (UrV3), and Umbelopsis ramanniana virus 4 (UrV4). Full genomes of UrV1, UrV3, and UrV4 were determined using the full-length amplification of cDNAs (FLAC) technique; they contain two open reading frames (ORF), which putatively encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In case of UrV2, a partial ORF encoding a partial RdRp gene could be determined. Based on the phylogeny inferred from the RdRp sequences, UrV1 and UrV4 belong to the genus Totivirus, while UrV2 may belong to the genus Victorivirus. UrV3 nested to a novel, unclassified group of Totiviridae, which is related to the genus Totivirus. Hybridization analysis revealed that the dsRNA molecules of UrV1 and UrV4 correspond to the same 5.0-kbp electrophoretic band, whilst the probe for the UrV3 hybridized to the largest, 5.3-kbp and the 3.0-kbp bands of the dsRNA pattern of U. ramanniana. Interestingly, the probe for the UrV2 sequence did not hybridized to any dsRNA bands, but it could be amplified from the isolated 3.0-kbp fragment. By transmission electron microscopy, two different isometric virus particles with about 50 and 35 nm in diameter were detected in U. ramanniana NRRL 1296 indicating that this strain harbor multiple viruses. Beside U. ramanniana, dsRNA elements were also detected in other Umbelopsis isolates with different patterns consisting of 2 to 4 discrete and different sized (0.7–5.3-kbp) dsRNA molecules. Based on a hybridization analysis with UrV1 CP and RdRp probes, the bands with the size of around 5.0-kbp, which were present in all tested Umbelopsis strains, are presumed as possible full mycovirus genomes.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boglárka Szabó
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Tamás F Polgár
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Gábor Nagy
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
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22
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Jamal A, Sato Y, Shahi S, Shamsi W, Kondo H, Suzuki N. Novel Victorivirus from a Pakistani Isolate of Alternaria alternata Lacking a Typical Translational Stop/Restart Sequence Signature. Viruses 2019; 11:E577. [PMID: 31242660 PMCID: PMC6631646 DOI: 10.3390/v11060577] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 01/27/2023] Open
Abstract
The family Totiviridae currently contains five genera Totivirus, Victorivirus, Leishmavirus, Trichomonasvirus, and Giardiavirus. Members in this family generally have a set of two-open reading frame (ORF) elements in their genome with the 5'-proximal ORF (ORF1) encoding a capsid protein (CP) and the 3'-proximal one (ORF2) for RNA-dependent RNA polymerase (RdRp). How the downstream open reading frames (ORFs) are expressed is genus-specific. All victoriviruses characterized thus far appear to use the stop/restart translation mechanism, allowing for the expression of two separate protein products from bicitronic genome-sized viral mRNA, while the totiviruses use a -1 ribosomal frame-shifting that leads to a fusion product of CP and RdRp. We report the biological and molecular characterization of a novel victorivirus termed Alternaria alternata victorivirus 1 (AalVV1) isolated from Alternaria alternata in Pakistan. The phylogenetic and molecular analyses showed AalVV1 to be distinct from previously reported victoriviruses. AalVV1 appears to have a sequence signature required for the -1 frame-shifting at the ORF1/2 junction region, rather than a stop/restart key mediator. By contrast, SDS-polyacrylamide gel electrophoresis and peptide mass fingerprinting analyses of purified virion preparations suggested the expression of two protein products, not a CP-RdRp fusion product. How these proteins are expressed is discussed in this study. Possible effects of infection by this virus were tested in two fungal species: A. alternata and RNA silencing proficient and deficient strains of Cryphonectria parasitica, a model filamentous fungus. AalVV1 showed symptomless infection in all of these fungal strains, even in the RNA silencing deficient C. parasitica strain.
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Affiliation(s)
- Atif Jamal
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
- Crop Diseases Research Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan.
| | - Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
| | - Wajeeha Shamsi
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.
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Liu H, Liu R, Li CX, Wang H, Zhu HJ, Gao BD, Zhou Q, Zhong J. A Victorivirus and Two Novel Mitoviruses Co-Infected the Plant Pathogen Nigrospora oryzae. Viruses 2019; 11:E83. [PMID: 30669450 PMCID: PMC6356909 DOI: 10.3390/v11010083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/24/2022] Open
Abstract
Three dsRNAs, in sizes of approximately 2.5⁻5 kbp, were detected in the plant pathogenic fungus Nigrospora oryzae strain CS-7.5-4. Genomic analysis showed that the 5.0 kb dsRNA was a victorivirus named as Nigrospora oryzae victorivirus 2 (NoRV2). The genome of NoRV2 was 5166 bp in length containing two overlapping open reading frames (ORFs), ORF1 and ORF2. ORF1 was deduced to encode a coat protein (CP) showing homology to the CPs of viruses belonging to the Totiviridae family. The stop codon of ORF1 and the start codon of ORF2 were overlapped by the tetranucleotide sequence AUGA. ORF2 was predicted to encode an RNA-dependent RNA polymerase (RdRp), which was highly similar to the RdRps of victoriviruses. Virus-like particle examination demonstrated that the genome of NoRV2 was solely encapsidated by viral particles with a diameter of approximately 35 nm. The other two dsRNAs that were less than 3.0 kb were predicted to be the genomes of two mitoviruses, named as Nigrospora oryzae mitovirus 1 (NoMV1) and Nigrospora oryzae mitovirus 2 (NoMV2). Both NoMV1 and NoMV2 were A-U rich and with lengths of 2865 and 2507 bp, respectively. Mitochondrial codon usage inferred that each of the two mitoviruses contains a major large ORF encoding a mitoviral RdRp. Horizontal transfer experiments showed that the NoMV1 and NoMV2 could be cotransmitted horizontally via hyphal contact to other virus-free N. oryzae strains and causes phenotypic change to the recipient, such as an increase in growth rate. This is the first report of mitoviruses in N. oryzae.
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Affiliation(s)
- Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Rui Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Chang Xin Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Hui Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Hong Jian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Bi Da Gao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
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Abstract
My long career in virology has been a continuous learning exercise with a very modest start. Virology and related pertinent fields have changed significantly during my lifetime. Sometimes I wish that my career had just started and I could apply all available and state of the art technology to solving problems and explaining intriguing observations. I was always convinced that visiting growers' fields is essential for researchers to get firsthand observations and knowledge of virus disease problems under field conditions. I never thought I would pursue so many avenues of research, yet it is true that research never ends. I enjoyed dissecting strain diversity in a very important plant pathogen like bean pod mottle virus (BPMV) and using BPMV-based vectors to address fundamental virology questions. Lastly, solving the enigma of the transmissible disease of Helminthosporium victoriae and attempting to gain an understanding of the molecular basis of disease in a plant pathogenic fungus were thrilling.
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Affiliation(s)
- Said A Ghabrial
- Plant Pathology Department, University of Kentucky, Lexington, Kentucky 40546, USA;
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25
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Velasco L, Arjona-Girona I, Ariza-Fernández MT, Cretazzo E, López-Herrera C. A Novel Hypovirus Species From Xylariaceae Fungi Infecting Avocado. Front Microbiol 2018; 9:778. [PMID: 29867781 PMCID: PMC5952064 DOI: 10.3389/fmicb.2018.00778] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 04/05/2018] [Indexed: 12/22/2022] Open
Abstract
The white rot root disease caused by Rosellinia necatrix is a major concern for avocado cultivation in Spain. Healthy escapes of avocado trees surrounded by diseased trees prompted us to hypothesize the presence of hypovirulent R. necatrix due to mycovirus infections. Recently, we reported the presence of another fungal species, Entoleuca sp., belonging to the Xylariaceae, that was also found in healthy avocado trees and frequently co-infecting the same roots than R. necatrix. We investigated the presence of mycoviruses that might explain the hypovirulence. For that, we performed deep sequencing of dsRNAs from two isolates of Entoleuca sp. that revealed the simultaneous infection of several mycoviruses, not described previously. In this work, we report a new member of the Hypoviridae, tentatively named Entoleuca hypovirus 1 (EnHV1). The complete genome sequence was obtained for two EnHV1 strains, which lengths resulted to be 14,958 and 14,984 nt, respectively, excluding the poly(A) tails. The genome shows two ORFs separated by a 32-nt inter-ORF, and both 5′- and 3′-UTRs longer than any other hypovirus reported to date. The analysis of virus-derived siRNA populations obtained from Entoleuca sp. demonstrated antiviral silencing activity in this fungus. We screened a collection of Entoleuca sp. and R. necatrix isolates and found that EnHV1 was present in both fungal species. A genetic population analysis of EnHV1 strains revealed the presence of two main clades, each of them including members from both Entoleuca sp. and R. necatrix, which suggests intra- and interspecific virus transmission in the field. Several attempts failed to cure Entoleuca sp. from EnHV1. However, all Entoleuca sp. isolates collected from avocado, whether harboring the virus or not, showed hypovirulence. Conversely, all R. necatrix isolates were pathogenic to that crop, regardless of being infected by EnHV1.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Málaga, Spain
| | - Isabel Arjona-Girona
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | | | - Enrico Cretazzo
- Instituto Andaluz de Investigación y Formación Agraria, Málaga, Spain
| | - Carlos López-Herrera
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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26
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Gunišová S, Hronová V, Mohammad MP, Hinnebusch AG, Valášek LS. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes. FEMS Microbiol Rev 2018; 42:165-192. [PMID: 29281028 PMCID: PMC5972666 DOI: 10.1093/femsre/fux059] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein production must be strictly controlled at its beginning and end to synthesize a polypeptide that faithfully copies genetic information carried in the encoding mRNA. In contrast to viruses and prokaryotes, the majority of mRNAs in eukaryotes contain only one coding sequence, resulting in production of a single protein. There are, however, many exceptional mRNAs that either carry short open reading frames upstream of the main coding sequence (uORFs) or even contain multiple long ORFs. A wide variety of mechanisms have evolved in microbes and higher eukaryotes to prevent recycling of some or all translational components upon termination of the first translated ORF in such mRNAs and thereby enable subsequent translation of the next uORF or downstream coding sequence. These specialized reinitiation mechanisms are often regulated to couple translation of the downstream ORF to various stimuli. Here we review all known instances of both short uORF-mediated and long ORF-mediated reinitiation and present our current understanding of the underlying molecular mechanisms of these intriguing modes of translational control.
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Affiliation(s)
- Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
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Picarelli MASC, Gobatto D, Patrício F, Rivas EB, Colariccio A. Vírus que infectam fungos fitopatogênicos. ARQUIVOS DO INSTITUTO BIOLÓGICO 2018. [DOI: 10.1590/1808-1657000162016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO: Micovírus são vírus que infectam todos os taxa de fungos. São geralmente crípticos (latentes), mas podem causar pequenas ou imperceptíveis alterações no hospedeiro. Nos fungos fitopatogênicos, os vírus podem interferir com os sintomas e, em alguns casos, reduzir a virulência de seu hospedeiro; por esta razão, são objeto de estudo, por serem um potencial agente de biocontrole e por serem ferramentas importantes para o conhecimento sobre os mecanismos de patogênese de fungos. A presente revisão teve o objetivo de reunir os dados de literatura relacionados aos aspectos gerais da biologia e do comportamento dos micovírus presentes em alguns fungos fitopatogênicos.
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28
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Reprint of "The victorivirus Helminthosporium victoriae virus 190S is the primary cause of disease/hypovirulence in its natural host and a heterologous host". Virus Res 2017; 219:100-107. [PMID: 27208849 DOI: 10.1016/j.virusres.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 11/20/2022]
Abstract
A transmissible disease of the plant pathogenic fungus Helminthosporium victoriae, the causal agent of Victoria blight of oats, was reported more than 50 years ago. Diseased, but not normal, isolates, of H. victoriae contain two distinct viruses designated according to their sedimentation values as victorivirus Helminthosporium victoriae virus 190S (HvV190S) and chrysovirus Helminthosporium victoriae 145S (HvV145S). Although a viral etiology of the disease was previously proposed, conclusive evidence was lacking. Here we present unequivocal evidence based on transfecting virus-free H. victoriae protoplasts with purified virus particles showing that HvV190S is essential for disease development. Furthermore, we show an expansion of the host range of HvV190S to include Cryphonectria parasitica and we also show similarity in a subset of phenotypic traits between HvV190S-infected RNA silencing deficient mutant (Δdcl-2) of C. parasitica and a strain of H. victoriae. In virulence assays on detached American chestnut branches and Red Delicious apple fruits, HvV190S-infected C. parasitica strain Δdcl-2 was markedly less virulent than wild type and virus-free Δdcl-2 C. parasitica strains. Furthermore, the hypovirulent HvV190S-infected C. parasitica Δdcl-2 strain exhibited strong antifungal activity in dual culture with the plant pathogenic fungus Sclerotinia sclerotiorum. No such inhibitory activity was observed in comparable dual cultures with wild type and virus-free Δdcl-2 C. parasitica strains. The discovery that infection with HvV190S induced a hypovirulent phenotype in a heterologous plant pathogenic host is very significant since it might be possible to convert other economically important plant pathogenic fungi to hypovirulence using HvV190S.
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Mycoviruses in the Plant Pathogen Ustilaginoidea virens Are Not Correlated with the Genetic Backgrounds of Its Hosts. Int J Mol Sci 2017; 18:ijms18050963. [PMID: 28467379 PMCID: PMC5454876 DOI: 10.3390/ijms18050963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 04/26/2017] [Indexed: 11/27/2022] Open
Abstract
Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0.5 to 5.3 kbp. Sequence analysis of its genomic properties indicated that it is a novel victorivirus, named Ustilaginoidea virens RNA virus 5 (UvRV5), that belongs to the family Totiviridae. RT-PCR detection was performed and indicated that not all the dsRNA bands that were 5.3 kbp in size contained UvRV5. Moreover, the genetic relatedness of all the U. virens strains was estimated according to phylogenetic analysis of the partial intergenic spacer region (IGS) sequences. However, concordance was not found between the dsRNA profiles and the IGS-based genetic relatedness of their host fungi.
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30
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Zhong J, Chen D, Zhu HJ, Gao BD, Zhou Q. Hypovirulence of Sclerotium rolfsii Caused by Associated RNA Mycovirus. Front Microbiol 2016; 7:1798. [PMID: 27891121 PMCID: PMC5103162 DOI: 10.3389/fmicb.2016.01798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/26/2016] [Indexed: 11/21/2022] Open
Abstract
Mycoviruses associated with hypovirulence are potential biological control agents and could be useful to study the pathogenesis of fungal host pathogens. Sclerotium rolfsii, a pathogenic fungus, causes southern blight in a wide variety of crops. In this study, we isolated a series of dsRNAs from a debilitated S. rolfsii strain, BLH-1, which had pronounced phenotypic aberrations including reduced pathogenicity, mycelial growth and deficient sclerotia production. Virus-curing and horizontal transmission experiments that eliminated or transmitted, respectively, all dsRNA elements showed that the dsRNAs were involved in the hypovirulent traits of BLH-1. Ultrastructure examination also showed hyphae fracture and cytoplasm or organelle degeneration in BLH-1 hyphal cells compared to the virus-free strain. Three assembled cDNA contigs generated from the cDNA library cloned from the purified dsRNA indicated that strain BLH-1 was infected by at least three novel mycoviruses. One has similarity to the hypovirulence-associated Sclerotinia sclerotiorum hypovirus 2 (SsHV2) in the family Hypoviridae, and the other two are related to two different unclassified dsRNA mycovirus families. To our knowledge, this is the first report of S. rolfsii hypovirulence that was correlated with its associated dsRNA.
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Affiliation(s)
- Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University Changsha, China
| | - Dan Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University Changsha, China
| | - Hong J Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University Changsha, China
| | - Bi D Gao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University Changsha, China
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University Changsha, China
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31
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Characterization of three mycoviruses co-infecting the plant pathogenic fungus Sclerotinia nivalis. Virus Res 2016; 223:28-38. [DOI: 10.1016/j.virusres.2016.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/06/2016] [Accepted: 06/16/2016] [Indexed: 11/21/2022]
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32
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Complete genome sequence and evolution analysis of Eimeria stiedai RNA virus 1, a novel member of the family Totiviridae. Arch Virol 2016; 161:3571-3576. [DOI: 10.1007/s00705-016-3020-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 08/17/2016] [Indexed: 10/21/2022]
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33
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Isolation and characterization of a novel mycovirus from Penicillium digitatum. Virology 2016; 494:15-22. [DOI: 10.1016/j.virol.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/18/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
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34
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Molecular identification of a novel victorivirus from the phytopathogenic fungus Nigrospora oryzae. Virus Genes 2016; 52:156-9. [DOI: 10.1007/s11262-015-1284-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/24/2015] [Indexed: 11/27/2022]
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35
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Xie J, Havens WM, Lin YH, Suzuki N, Ghabrial SA. The victorivirus Helminthosporium victoriae virus 190S is the primary cause of disease/hypovirulence in its natural host and a heterologous host. Virus Res 2015; 213:238-245. [PMID: 26724750 DOI: 10.1016/j.virusres.2015.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022]
Abstract
A transmissible disease of the plant pathogenic fungus Helminthosporium victoriae, the causal agent of Victoria blight of oats, was reported more than 50 years ago. Diseased, but not normal, isolates, of H. victoriae contain two distinct viruses designated according to their sedimentation values as victorivirus Helminthosporium victoriae virus 190S (HvV190S) and chrysovirus Helminthosporium victoriae 145S (HvV145S). Although a viral etiology of the disease was previously proposed, conclusive evidence was lacking. Here we present unequivocal evidence based on transfecting virus-free H. victoriae protoplasts with purified virus particles showing that HvV190S is essential for disease development. Furthermore, we show an expansion of the host range of HvV190S to include Cryphonectria parasitica and we also show similarity in a subset of phenotypic traits between HvV190S-infected RNA silencing deficient mutant (Δdcl-2) of C. parasitica and a strain of H. victoriae. In virulence assays on detached American chestnut branches and Red Delicious apple fruits, HvV190S-infected C. parasitica strain Δdcl-2 was markedly less virulent than wild type and virus-free Δdcl-2 C. parasitica strains. Furthermore, the hypovirulent HvV190S-infected C. parasitica Δdcl-2 strain exhibited strong antifungal activity in dual culture with the plant pathogenic fungus Sclerotinia sclerotiorum. No such inhibitory activity was observed in comparable dual cultures with wild type and virus-free Δdcl-2 C. parasitica strains. The discovery that infection with HvV190S induced a hypovirulent phenotype in a heterologous plant pathogenic host is very significant since it might be possible to convert other economically important plant pathogenic fungi to hypovirulence using HvV190S.
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Affiliation(s)
- Jiatao Xie
- Plant Pathology Department, University of Kentucky, Lexington, KY 40546, USA
| | - Wendy M Havens
- Plant Pathology Department, University of Kentucky, Lexington, KY 40546, USA
| | - Yu-Hsin Lin
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
| | - Said A Ghabrial
- Plant Pathology Department, University of Kentucky, Lexington, KY 40546, USA.
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36
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Characterization of a Novel Megabirnavirus from Sclerotinia sclerotiorum Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus. J Virol 2015; 89:8567-79. [PMID: 26063429 DOI: 10.1128/jvi.00243-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Mycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus, Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1), in an apparently hypovirulent strain (SX466) of Sclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related to Rosellinia necatrix megabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5'-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) of Cryphonectria hypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1. IMPORTANCE Mycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized a novel dsRNA virus (Sclerotinia sclerotiorum megabirnavirus 1 [SsMBV1]) that was isolated from an apparently hypovirulent strain, SX466, of Sclerotinia sclerotiorum. Although SsMBV1 is phylogenetically related to RnMBV1, SsMBV1 is markedly distinct from other reported megabirnaviruses with two features of VLPs and conserved domains. Our results convincingly showed that SsMBV1 is viable in the absence of L2-dsRNA/SsMBV1 (a potential large satellite-like RNA or genuine genomic virus component). More interestingly, we detected a conserved papain-like protease domain that commonly exists in ssRNA viruses, including members of the families Potyviridae and Hypoviridae. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer might have occurred from an ssRNA virus to a dsRNA virus, which may provide new insights into the evolutionary history of dsRNA and ssRNA viruses.
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37
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The complete nucleotide sequence and genomic organization of a novel victorivirus with two non-overlapping ORFs, identified in the plant-pathogenic fungus Phomopsis vexans. Arch Virol 2015; 160:1805-9. [DOI: 10.1007/s00705-015-2420-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
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Ghabrial SA, Castón JR, Jiang D, Nibert ML, Suzuki N. 50-plus years of fungal viruses. Virology 2015; 479-480:356-68. [PMID: 25771805 DOI: 10.1016/j.virol.2015.02.034] [Citation(s) in RCA: 454] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 01/31/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally lack an extracellular phase. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups, although recent advances have established expanded experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked effects on their hosts, those that reduce the virulence of their phytopathogenic fungal hosts are of considerable interest for development of novel biocontrol strategies. Mycoviruses that infect endophytic fungi and those that encode killer toxins are also of special interest. Structural analyses of mycoviruses have promoted better understanding of virus assembly, function, and evolution.
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Affiliation(s)
- Said A Ghabrial
- Plant Pathology Department, University of Kentucky, Lexington, KY, USA.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional Biotecnologıa/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Daohong Jiang
- State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Max L Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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Prevalence and diversity of mycoviruses infecting the plant pathogen Ustilaginoidea virens. Virus Res 2015; 195:47-56. [DOI: 10.1016/j.virusres.2014.08.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/15/2022]
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40
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Li H, Havens WM, Nibert ML, Ghabrial SA. An RNA cassette from Helminthosporium victoriae virus 190S necessary and sufficient for stop/restart translation. Virology 2015; 474:131-43. [DOI: 10.1016/j.virol.2014.10.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/10/2014] [Accepted: 10/17/2014] [Indexed: 12/16/2022]
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Haß M, Luttermann C, Meyers G. Feline calicivirus can tolerate gross changes of its minor capsid protein expression levels induced by changing translation reinitiation frequency or use of a separate VP2-coding mRNA. PLoS One 2014; 9:e102254. [PMID: 25007260 PMCID: PMC4090194 DOI: 10.1371/journal.pone.0102254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/16/2014] [Indexed: 12/31/2022] Open
Abstract
Caliciviruses use reinitiation of translation governed by a ‘termination upstream ribosomal binding site’ (TURBS) for expression of their minor capsid protein VP2. Mutation analysis allowed to identify sequences surrounding the translational start/stop site of the feline calicivirus (FCV) that fine tune reinitiation frequency. A selection of these changes was introduced into the infectious FCV cDNA clone to check the influence of altered VP2 levels on virus replication. In addition, full length constructs were established that displayed a conformation, in which VP2 expression occurred under control of a duplicated subgenomic promoter. Viable viruses recovered from such constructs revealed a rather broad range of VP2 expression levels but comparable growth kinetics showing that caliciviruses can tolerate gross changes of the VP2 expression level.
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Affiliation(s)
- Maria Haß
- Institut für Immunologie, Friedrich-Loeffler-Institut, Tübingen, Germany
| | | | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Tübingen, Germany
- * E-mail:
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Leishmania aethiopica Field Isolates Bearing an Endosymbiontic dsRNA Virus Induce Pro-inflammatory Cytokine Response. PLoS Negl Trop Dis 2014. [DOI: 10.1371/journal.pntd.0002836#s5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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43
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Leishmania aethiopica field isolates bearing an endosymbiontic dsRNA virus induce pro-inflammatory cytokine response. PLoS Negl Trop Dis 2014; 8:e2836. [PMID: 24762979 PMCID: PMC3998932 DOI: 10.1371/journal.pntd.0002836] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/19/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Infection with Leishmania parasites causes mainly cutaneous lesions at the site of the sand fly bite. Inflammatory metastatic forms have been reported with Leishmania species such as L. braziliensis, guyanensis and aethiopica. Little is known about the factors underlying such exacerbated clinical presentations. Leishmania RNA virus (LRV) is mainly found within South American Leishmania braziliensis and guyanensis. In a mouse model of L. guyanensis infection, its presence is responsible for an hyper-inflammatory response driven by the recognition of the viral dsRNA genome by the host Toll-like Receptor 3 leading to an exacerbation of the disease. In one instance, LRV was reported outside of South America, namely in the L. major ASKH strain from Turkmenistan, suggesting that LRV appeared before the divergence of Leishmania subgenera. LRV presence inside Leishmania parasites could be one of the factors implicated in disease severity, providing rationale for LRV screening in L. aethiopica. METHODOLOGY/PRINCIPAL FINDINGS A new LRV member was identified in four L. aethiopica strains (LRV-Lae). Three LRV-Lae genomes were sequenced and compared to L. guyanensis LRV1 and L. major LRV2. LRV-Lae more closely resembled LRV2. Despite their similar genomic organization, a notable difference was observed in the region where the capsid protein and viral polymerase open reading frames overlap, with a unique -1 situation in LRV-Lae. In vitro infection of murine macrophages showed that LRV-Lae induced a TLR3-dependent inflammatory response as previously observed for LRV1. CONCLUSIONS/SIGNIFICANCE In this study, we report the presence of an immunogenic dsRNA virus in L. aethiopica human isolates. This is the first observation of LRV in Africa, and together with the unique description of LRV2 in Turkmenistan, it confirmed that LRV was present before the divergence of the L. (Leishmania) and (Viannia) subgenera. The potential implication of LRV-Lae on disease severity due to L. aethiopica infections is discussed.
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Zhong J, Zhou Q, Lei XH, Chen D, Shang HH, Zhu HJ. The nucleotide sequence and genome organization of two victoriviruses from the rice false smut fungus Ustilaginoidea virens. Virus Genes 2014; 48:570-3. [DOI: 10.1007/s11262-014-1050-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/08/2014] [Indexed: 01/11/2023]
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Rao SS, El-Habbak MH, Havens WM, Singh A, Zheng D, Vaughn L, Haudenshield JS, Hartman GL, Korban SS, Ghabrial SA. Overexpression of GmCaM4 in soybean enhances resistance to pathogens and tolerance to salt stress. MOLECULAR PLANT PATHOLOGY 2014; 15:145-60. [PMID: 24118726 PMCID: PMC6638926 DOI: 10.1111/mpp.12075] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant diseases inflict heavy losses on soybean yield, necessitating an understanding of the molecular mechanisms underlying biotic/abiotic stress responses. Ca(2) (+) is an important universal messenger, and protein sensors, prominently calmodulins (CaMs), recognize cellular changes in Ca(2) (+) in response to diverse signals. Because the development of stable transgenic soybeans is laborious and time consuming, we used the Bean pod mottle virus (BPMV)-based vector for rapid and efficient protein expression and gene silencing. The present study focuses on the functional roles of the gene encoding the soybean CaM isoform GmCaM4. Overexpression of GmCaM4 in soybean resulted in enhanced resistance to three plant pathogens and increased tolerance to high salt conditions. To gain an understanding of the underlying mechanisms, we examined the potential defence pathways involved. Our studies revealed activation/increased expression levels of pathogenesis-related (PR) genes in GmCaM4-overexpressing plants and the accumulation of jasmonic acid (JA). Silencing of GmCaM4, however, markedly repressed the expression of PR genes. We confirmed the in vivo interaction between GmCaM4 and the CaM binding transcription factor Myb2, which regulates the expression of salt-responsive genes, using the yeast two-hybrid (Y2H) system and bimolecular fluorescence complementation assays. GmCaM4 and Glycine max CaM binding receptor-like kinase (GmCBRLK) did not interact in the Y2H assays, but the interaction between GmCaM2 and GmCBRLK was confirmed. Thus, a GmCaM2-GmCBRLK-mediated salt tolerance mechanism, similar to that reported in Glycine soja, may also be functional in soybean. Confocal microscopy showed subcellular localization of the green fluorescent protein (GFP)-GmCaM4 fusion protein in the nucleus and cytoplasm.
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Affiliation(s)
- Suryadevara S Rao
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546-0091, USA
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Abstract
Most of reported fungal viruses (mycoviruses) have double-stranded RNA (dsRNA) genomes. This may reflect the simple, easy method for mycovirus hunting that entails detection of dsRNAs as a sign of viral infections. There are an increasing number of screens of various fungi, particularly phytopathogenic fungi for viruses pathogenic to host fungi or able to confer hypovirulence to them. This bases on an attractive research field of biological control of fungal plant diseases using viruses (virocontrol), mainly targeting important phytopathogenic fungi. While isolated viruses usually induce asymptomatic symptoms, they show a considerably high level of diversity. As of 2014, fungal dsRNA viruses are classified into six families: Reoviridae, Totiviridae, Chrysoviridae, Partitiviridae, Megabirnaviridae and Quadriviridae. These exclude unassigned mycoviruses which will definitely be placed into distinct families and/or genera. In this review article, dsRNA viruses isolated from the kingdom Fungi including as-yet-unclassified taxa are overviewed. Some recent achievements in the related field are briefly introduced as well.
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47
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Xie J, Jiang D. New insights into mycoviruses and exploration for the biological control of crop fungal diseases. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:45-68. [PMID: 25001452 DOI: 10.1146/annurev-phyto-102313-050222] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mycoviruses are viruses that infect fungi. A growing number of novel mycoviruses have expanded our knowledge of virology, particularly in taxonomy, ecology, and evolution. Recent progress in the study of mycoviruses has comprehensively improved our understanding of the properties of mycoviruses and has strengthened our confidence to explore hypovirulence-associated mycoviruses that control crop diseases. In this review, the advantages of using hypovirulence-associated mycoviruses to control crop diseases are discussed, and, as an example, the potential for Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) to control the stem rot of rapeseed (Brassica napus) is also introduced. Fungal vegetative incompatibility is likely to be the key factor that limits the wide utilization of mycoviruses to control crop diseases; however, there are suggested strategies for resolving this problem.
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Affiliation(s)
- Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China;
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Molecular characterization of a novel victorivirus from the entomopathogenic fungus Beauveria bassiana. Arch Virol 2013; 159:1321-7. [PMID: 24327093 DOI: 10.1007/s00705-013-1938-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/29/2013] [Indexed: 10/25/2022]
Abstract
New Zealand isolates of the entomopathogenic fungus Beauveria were examined for the presence of dsRNAs and virus-like particles. Seven out of nine isolates contained one or more high-molecular-weight dsRNAs and all seven contained isometric virus particles ranging in size from 30 to 50 nm. B. bassiana isolate ICMP#6887 contained a single dsRNA band of ~6 kb and isometric virus-like particles of ~50 nm in diameter. Sequencing revealed that the virus from ICMP#6887 had a genome of 5,327 nt with two overlapping ORFs coding for a putative coat protein (CP) and an RNA-dependent RNA-polymerase (RdRp). The sequence showed a highest CP identity of 58.3 % to Tolypocladium cylindrosporum virus 1 (TcV1) and a highest RdRp identity of 48.8 % to Sphaeropsis sapinea RNA virus 1 (SsRV1). Since both TcV1 and SsRV1 belong to the genus Victorivirus, the new virus from B. bassiana ICMP#6887 was tentatively assigned the name Beauveria bassiana victorivirus 1 (BbVV1-6887).
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Bancells C, Deitsch KW. A molecular switch in the efficiency of translation reinitiation controls expression of var2csa, a gene implicated in pregnancy-associated malaria. Mol Microbiol 2013; 90:472-88. [PMID: 23980802 DOI: 10.1111/mmi.12379] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2013] [Indexed: 12/16/2022]
Abstract
Plasmodium falciparum malaria parasites export the protein PfEMP1 to the surface of infected erythrocytes, enabling them to adhere to receptors in the microvasculature and thereby avoid clearance by the spleen. The gene var2csa encodes the form of PfEMP1 that binds specifically within the placenta, causing pregnancy-associated malaria, and appears to not be expressed in the absence of a placenta. We previously described an upstream open reading frame (uORF) that is responsible for repression of translation of the downstream ORF (dORF) that encodes VAR2CSA, thus keeping the gene silent when parasites infect non-pregnant individuals. To elucidate the molecular mechanism by which this repression is overcome during pregnancy, we stably transformed parasites with reporter gene constructs designed to detect switches in the efficiency of dORF translation. We found that proper regulation of switching relies on two separate components, (i) active translation of the uORF and (ii) sequence-specific characteristics of the surrounding transcript, which together control the ability of the ribosome complex to reinitiate a second round of translation and thus express VAR2CSA. These results provide the first details of a molecular switch that allows parasites take advantage of the unique niche provided by the placenta.
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Affiliation(s)
- Cristina Bancells
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
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50
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Gene from a novel plant virus satellite from grapevine identifies a viral satellite lineage. Virus Genes 2013; 47:114-8. [DOI: 10.1007/s11262-013-0921-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/11/2013] [Indexed: 11/30/2022]
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