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Dai R, Yang S, Pang T, Tian M, Wang H, Zhang D, Wu Y, Kondo H, Andika IB, Kang Z, Sun L. Identification of a negative-strand RNA virus with natural plant and fungal hosts. Proc Natl Acad Sci U S A 2024; 121:e2319582121. [PMID: 38483998 PMCID: PMC10962957 DOI: 10.1073/pnas.2319582121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024] Open
Abstract
The presence of viruses that spread to both plant and fungal populations in nature has posed intriguingly scientific question. We found a negative-strand RNA virus related to members of the family Phenuiviridae, named Valsa mali negative-strand RNA virus 1 (VmNSRV1), which induced strong hypovirulence and was prevalent in a population of the phytopathogenic fungus of apple Valsa canker (Valsa mali) infecting apple orchards in the Shaanxi Province of China. Intriguingly, VmNSRV1 encodes a protein with a viral cell-to-cell movement function in plant tissue. Mechanical leaf inoculation showed that VmNSRV1 could systemically infect plants. Moreover, VmNSRV1 was detected in 24 out of 139 apple trees tested in orchards in Shaanxi Province. Fungal inoculation experiments showed that VmNSRV1 could be bidirectionally transmitted between apple plants and V. mali, and VmNSRV1 infection in plants reduced the development of fungal lesions on leaves. Additionally, the nucleocapsid protein encoded by VmNSRV1 is associated with and rearranged lipid droplets in both fungal and plant cells. VmNSRV1 represents a virus that has adapted and spread to both plant and fungal hosts and shuttles between these two organisms in nature (phyto-mycovirus) and is potential to be utilized for the biocontrol method against plant fungal diseases. This finding presents further insights into the virus evolution and adaptation encompassing both plant and fungal hosts.
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Affiliation(s)
- Ruoyin Dai
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Shian Yang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Tianxing Pang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Mengyuan Tian
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Dong Zhang
- Yangling Sub-Center of National Center for Apple Improvement and College of Horticulture, Northwest A&F University, Yangling712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao266109, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
- Institute of Future Agriculture, Northwest A&F University, Yangling712100, China
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Andika IB, Cao X, Kondo H, Sun L. The intriguing phenomenon of cross-kingdom infections of plant and insect viruses to fungi: Can other animal viruses also cross-infect fungi? PLoS Pathog 2023; 19:e1011726. [PMID: 37883353 PMCID: PMC10602238 DOI: 10.1371/journal.ppat.1011726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Fungi are highly widespread and commonly colonize multicellular organisms that live in natural environments. Notably, studies on viruses infecting plant-associated fungi have revealed the interesting phenomenon of the cross-kingdom transmission of viruses and viroids from plants to fungi. This implies that fungi, in addition to absorbing water, nutrients, and other molecules from the host, can acquire intracellular parasites that reside in the host. These findings further suggest that fungi can serve as suitable alternative hosts for certain plant viruses and viroids. Given the frequent coinfection of fungi and viruses in humans/animals, the question of whether fungi can also acquire animal viruses and serve as their hosts is very intriguing. In fact, the transmission of viruses from insects to fungi has been observed. Furthermore, the common release of animal viruses into the extracellular space (viral shedding) could potentially facilitate their acquisition by fungi. Investigations of the cross-infection of animal viruses in fungi may provide new insights into the epidemiology of viral diseases in humans and animals.
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Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Agricultural University, Tai’an, China
- Shouguang International Vegetable Sci-tech Fair Management Service Center, Shouguang, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xianyang, China
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Dong K, Xu C, Kotta‐Loizou I, Jiang J, Lv R, Kong L, Li S, Hong N, Wang G, Coutts RHA, Xu W. Novel Viroid-Like RNAs Naturally Infect a Filamentous Fungus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204308. [PMID: 36515275 PMCID: PMC9875651 DOI: 10.1002/advs.202204308] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/19/2022] [Indexed: 06/17/2023]
Abstract
To date, viroids have been found to naturally infect only plants, resulting in substantial losses for some crops. Whether viroids or viroid-like RNAs naturally infect non-plant hosts remains unknown. Here the existence of a set of exogenous, single-stranded circular RNAs, ranging in size from 157 to 450 nucleotides, isolated from the fungus Botryosphaeria dothidea and nominated B. dothidea RNAs (BdcRNAs) is reported. BdcRNAs replicate autonomously in the nucleus via a rolling-circle mechanism following a symmetric pathway. BdcRNA infection induces symptoms, because BdcRNAs can apparently modulate, to different degrees, specific biological traits (e.g., alter morphology, decrease growth rate, attenuate virulence, and increase or decrease tolerance to osmotic and oxidative stress) of the host fungus. Overall, BdcRNAs have genome characteristics similar to those of viroids and exhibit pathogenic effects on fungal hosts. It is proposed that these novel fungus infecting RNAs should be termed mycoviroids. BdcRNA(s) may be considered additional inhabitants at the frontier of life in terms of genomic complexity, and represent a new class of acellular entities endowed with regulatory functions, and novel epigenomic carriers of biological information.
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Affiliation(s)
- Kaili Dong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Chuan Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ioly Kotta‐Loizou
- Department of Life SciencesFaculty of Natural SciencesImperial College LondonLondonSW7 2AZUK
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Jingjing Jiang
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ruiying Lv
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Linghong Kong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Shifang Li
- Environment and Plant Protection InstituteChinese Academy of Tropical Agricultural SciencesXueyuan Road, Longhua DistrictHaikouHainan571101P. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193P. R. China
| | - Ni Hong
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Guoping Wang
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Robert H. A. Coutts
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Wenxing Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
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Tian M, Wei S, Bian R, Luo J, Khan HA, Tai H, Kondo H, Hadidi A, Andika IB, Sun L. Natural Cross-Kingdom Spread of Apple Scar Skin Viroid from Apple Trees to Fungi. Cells 2022; 11:cells11223686. [PMID: 36429116 PMCID: PMC9688150 DOI: 10.3390/cells11223686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Viroids are the smallest known infectious agents that are thought to only infect plants. Here, we reveal that several species of plant pathogenic fungi that were isolated from apple trees infected with apple scar skin viroid (ASSVd) carried ASSVd naturally. This finding indicates the spread of viroids to fungi under natural conditions and further suggests the possible existence of mycoviroids in nature. A total of 117 fungal isolates were isolated from ASSVd-infected apple trees, with the majority (85.5%) being an ascomycete Alternaria alternata and the remaining isolates being other plant-pathogenic or -endophytic fungi. Out of the examined samples, viroids were detected in 81 isolates (69.2%) including A. alternata as well as other fungal species. The phenotypic comparison of ASSVd-free specimens developed by single-spore isolation and ASSVd-infected fungal isogenic lines showed that ASSVd affected the growth and pathogenicity of certain fungal species. ASSVd confers hypovirulence on ascomycete Epicoccum nigrum. The mycobiome analysis of apple tree-associated fungi showed that ASSVd infection did not generally affect the diversity and structure of fungal communities but specifically increased the abundance of Alternaria species. Taken together, these data reveal the occurrence of the natural spread of viroids to plants; additionally, as an integral component of the ecosystem, viroids may affect the abundance of certain fungal species in plants. Moreover, this study provides further evidence that viroid infection could induce symptoms in certain filamentous fungi.
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Affiliation(s)
- Mengyuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Shuang Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Ruiling Bian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Jingxian Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Haris Ahmed Khan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Tai
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Ahmed Hadidi
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
- Correspondence:
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Similar Characteristics of siRNAs of Plant Viruses Which Replicate in Plant and Fungal Hosts. BIOLOGY 2022; 11:biology11111672. [PMID: 36421386 PMCID: PMC9687825 DOI: 10.3390/biology11111672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary RNA silencing in fungi was shown to confer antiviral defense against plant viruses. In this study, using high-throughput sequencing and bioinformatic analyses, we showed that small interfering RNAs (siRNAs) of cucumber mosaic virus and tobacco mosaic virus (TMV) which replicated in phytopathogenic fungi Rhizoctonia solani and Fusarium graminearum had similarities with viral siRNAs produced in plant hosts in regard to the size distributions, proportion of plus and minus senses, and nucleotide preference for the 5′ termini. Additionally, our results also determined that both F. graminearum DCL1 and DCL2 were involved in the production of TMV siRNAs. Thus, the fungal RNA silencing machineries have adaptive capabilities to recognize and process the genome of invading plant viruses. Abstract RNA silencing is a host innate antiviral mechanism which acts via the synthesis of viral-derived small interfering RNAs (vsiRNAs). We have previously reported the infection of phytopathogenic fungi by plant viruses such as cucumber mosaic virus (CMV) and tobacco mosaic virus (TMV). Furthermore, fungal RNA silencing was shown to suppress plant virus accumulation, but the characteristics of plant vsiRNAs associated with the antiviral response in this nonconventional host remain unknown. Using high-throughput sequencing, we characterized vsiRNA profiles in two plant RNA virus–fungal host pathosystems: CMV infection in phytopathogenic fungus Rhizoctonia solani and TMV infection in phytopathogenic fungus Fusarium graminearum. The relative abundances of CMV and TMV siRNAs in the respective fungal hosts were much lower than those in the respective experimental plant hosts, Nicotiana benthamiana and Nicotiana tabacum. However, CMV and TMV siRNAs in fungi had similar characteristics to those in plants, particularly in their size distributions, proportion of plus and minus senses, and nucleotide preference for the 5′ termini of vsiRNAs. The abundance of TMV siRNAs largely decreased in F. graminearum mutants with a deletion in either dicer-like 1 (dcl1) or dcl2 genes which encode key proteins for the production of siRNAs and antiviral responses. However, deletion of both dcl1 and dcl2 restored TMV siRNA accumulation in F. graminearum, indicating the production of dcl-independent siRNAs with no antiviral function in the absence of the dcl1 and dcl2 genes. Our results suggest that fungal RNA silencing recognizes and processes the invading plant RNA virus genome in a similar way as in plants.
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