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Arad M, Ku K, Frey C, Hare R, McAfee A, Ghafourifar G, Foster LJ. What proteomics has taught us about honey bee (Apis mellifera) health and disease. Proteomics 2024:e2400075. [PMID: 38896501 DOI: 10.1002/pmic.202400075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/28/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
The Western honey bee, Apis mellifera, is currently navigating a gauntlet of environmental pressures, including the persistent threat of parasites, pathogens, and climate change - all of which compromise the vitality of honey bee colonies. The repercussions of their declining health extend beyond the immediate concerns of apiarists, potentially imposing economic burdens on society through diminished agricultural productivity. Hence, there is an imperative to devise innovative monitoring techniques for assessing the health of honey bee populations. Proteomics, recognized for its proficiency in biomarker identification and protein-protein interactions, is poised to play a pivotal role in this regard. It offers a promising avenue for monitoring and enhancing the resilience of honey bee colonies, thereby contributing to the stability of global food supplies. This review delves into the recent proteomic studies of A. mellifera, highlighting specific proteins of interest and envisioning the potential of proteomics to improve sustainable beekeeping practices amidst the challenges of a changing planet.
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Affiliation(s)
- Maor Arad
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC, Canada
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Kenneth Ku
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC, Canada
| | - Connor Frey
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rhien Hare
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Alison McAfee
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Golfam Ghafourifar
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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2
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Lin Z, Shen S, Wang K, Ji T. Biotic and abiotic stresses on honeybee health. Integr Zool 2024; 19:442-457. [PMID: 37427560 DOI: 10.1111/1749-4877.12752] [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] [Indexed: 07/11/2023]
Abstract
Honeybees are the most critical pollinators providing key ecosystem services that underpin crop production and sustainable agriculture. Amidst a backdrop of rapid global change, this eusocial insect encounters a succession of stressors during nesting, foraging, and pollination. Ectoparasitic mites, together with vectored viruses, have been recognized as central biotic threats to honeybee health, while the spread of invasive giant hornets and small hive beetles also increasingly threatens colonies worldwide. Cocktails of agrochemicals, including acaricides used for mite treatment, and other pollutants of the environment have been widely documented to affect bee health in various ways. Additionally, expanding urbanization, climate change, and agricultural intensification often result in the destruction or fragmentation of flower-rich bee habitats. The anthropogenic pressures exerted by beekeeping management practices affect the natural selection and evolution of honeybees, and colony translocations facilitate alien species invasion and disease transmission. In this review, the multiple biotic and abiotic threats and their interactions that potentially undermine bee colony health are discussed, while taking into consideration the sensitivity, large foraging area, dense network among related nestmates, and social behaviors of honeybees.
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Affiliation(s)
- Zheguang Lin
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Siyi Shen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kang Wang
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ting Ji
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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3
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Stuehler DS, Hunter WB, Carrillo-Tarazona Y, Espitia H, Cicero JM, Bell T, Mann HR, Clarke SKV, Paris TM, Metz JL, D'Elia T, Qureshi JA, Cano LM. Wild lime psyllid Leuronota fagarae Burckhardt (Hemiptera: Psylloidea) picorna-like virus full genome annotation and classification. J Invertebr Pathol 2023; 201:107995. [PMID: 37748676 DOI: 10.1016/j.jip.2023.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
Picorna-like viruses of the order Picornavirales are a poorly defined group of positive-sense, single-stranded RNA viruses that include numerous pathogens known to infect plants, animals, and insects. A new picorna-like viral species was isolated from the wild lime psyllid (WLP), Leuronota fagarae, in the state of Florida, USA, and labelled: Leuronota fagarae picorna-like virus isolate FL (LfPLV-FL). The virus was found to have homology to a picorna-like virus identified in the Asian Citrus Psyllid (ACP), Diaphorina citri, collected in the state of Florida. Computational analysis of RNA extracts from WLP adult heads identified a 10,006-nucleotide sequence encoding a 2,942 amino acid polyprotein with similar functional domain structure to polyproteins of both Dicistroviridae and Iflaviridae. Sequence comparisons of nucleic acid and amino acid translations of the conserved RNA-dependent RNA polymerase, along with the entire N-terminal nonstructural coding region, provided insight into an evolutionary relationship of LfPLV-FL to insect-infecting iflaviruses. Viruses belonging to the family Iflaviridae encode a polyprotein of around 3000 amino acids in length that is processed post-translationally to produce components necessary for replication. The classification of a novel picorna-like virus in L. fagarae, with evolutionary characteristics similar to picorna-like viruses infecting Bactericera cockerelli and D. citri, provides an opportunity to examine virus host specificity, as well as identify critical components of the virus' genome required for successful transmission, infection, and replication. This bioinformatic classification allows for further insight into a novel virus species, and aids in the research of a closely related virus of the invasive psyllid, D. citri, a major pest of Floridian citriculture. The potential use of viral pathogens as expression vectors to manage the spread D. citri is an area that requires additional research; however, it may bring forth an effective control strategy to reduce the transmission of Candidatus Liberibacter asiaticus (CLas), the causative agent of Huanglongbing (HLB).
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Affiliation(s)
- Douglas S Stuehler
- ORISE Participant, DOE/USDA, ARS, Fort Pierce, FL 34945, USA; USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Wayne B Hunter
- USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Yisel Carrillo-Tarazona
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Hector Espitia
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Joseph M Cicero
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA
| | - Tracey Bell
- Indian River State College, Fort Pierce, FL 34949, USA.
| | - Hannah R Mann
- Indian River State College, Fort Pierce, FL 34949, USA
| | | | - Thomson M Paris
- ORISE Participant, DOE/USDA, ARS, Fort Pierce, FL 34945, USA; USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Jackie L Metz
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Tom D'Elia
- Department of Biology, Indian River State College, Fort Pierce, FL 34949, USA.
| | - Jawwad A Qureshi
- University of Florida, Southwest Florida Research and Education Center (SWFREC), 2685 SR 29 North Immokalee, FL 34142, USA.
| | - Liliana M Cano
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
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Yue D, Li R, Zhang J, Chen Y, Palmer-Young EC, Huang S, Huang WF. A DNA Plasmid-Based Approach for Efficient Synthesis of Sacbrood Virus Infectious Clones within Host Cells. Viruses 2023; 15:1866. [PMID: 37766273 PMCID: PMC10537335 DOI: 10.3390/v15091866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
RNA viruses are often cited as a significant factor affecting the populations of both domestic honey bees and wild pollinators. To expedite the development of effective countermeasures against these viruses, a more comprehensive understanding of virus biology necessitates extensive collaboration among scientists from diverse research fields. While the infectious virus clone is a robust tool for studying virus diseases, the current methods for synthesizing infectious clones of bee-infecting RNA viruses entail the in vitro transcription of the viral genome RNA in 8-10 kb, presenting challenges in reproducibility and distribution. This article reports on the synthesis of an infectious clone of the Chinese variant sacbrood virus (SBV) using a DNA plasmid containing an Autographa californica multiple nucleopolyhedrovirus (AcMNPV) immediate-early protein (IE1) promoter to trigger transcription of the downstream viral genome within hosts. The results demonstrate that the IE1-SBV plasmid can synthesize SBV clones in a widely used lepidopteran immortal cell line (Sf9) and honey bee pupae. Furthermore, the negative strand of the clone was detected in both Sf9 cells and honey bee pupae, indicating active infection and replication. However, the transfection of Sf9 cells was observed in only a limited proportion (less than 10%) of the cells, and the infection did not appear to spread to adjacent cells or form infective virions. The injection of honey bee pupae with 2500 ng of the IE1-SBV plasmid resulted in high infection rates in Apis cerana pupae but low rates in A. mellifera pupae, although the dosage was comparatively high compared with other studies using in vitro transcribed viral RNA. Our findings suggest that the synthesis of bee-infecting RNA viruses using DNA plasmids is feasible, albeit requiring additional optimization. However, this method holds substantial potential for facilitating the production of clones with various sequence modifications, enabling the exploration of viral gene functions and biology. The ease of distributing infectious clones in DNA plasmid form may foster collaboration among scientists in applying the clone to bee biology, ecology, and behavior, ultimately offering a comprehensive approach to managing virus diseases in the future.
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Affiliation(s)
- Dandan Yue
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Runlin Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jikailang Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanping Chen
- Bee Research Laboratory, Agriculture Research Service, USDA, Beltsville, MD 20705, USA
| | - Evan C Palmer-Young
- Bee Research Laboratory, Agriculture Research Service, USDA, Beltsville, MD 20705, USA
| | - Shaokang Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Honeybee Biology Observation Station, Ministry of Agriculture and Rural Affairs, Fuzhou 350002, China
| | - Wei-Fone Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Bee Research Laboratory, Agriculture Research Service, USDA, Beltsville, MD 20705, USA
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Yoo MS, Truong AT, Jeong H, Hahn DH, Lee JS, Yoon SS, Youn SY, Cho YS. Large-Scale Application of Double-Stranded RNA Shows Potential for Reduction of Sacbrood Virus Disease in Apis cerana Apiaries. Viruses 2023; 15:v15040897. [PMID: 37112876 PMCID: PMC10145737 DOI: 10.3390/v15040897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Sacbrood virus (SBV) infection has emerged as a remarkable threat to Apis cerana colonies in South Korea, necessitating prompt control measures. In this study, RNA interference (RNAi) targeting the VP3 gene was developed to assess its safety and efficacy in protecting and treating SBV in vitro and in infected colonies in South Korean apiaries. The efficacy of VP3 double-stranded RNA (dsRNA) was demonstrated in laboratory-based experiments, wherein infected larvae treated with VP3 dsRNA exhibited a 32.7% increase in survival rate compared to untreated larvae. Data from a large-scale field trial indicate the efficacy of dsRNA treatment since none of the treated colonies had symptomatic SBV infections, whereas disease was observed in 43% (3/7) of the control colonies. In the 102 colonies exhibiting symptoms of SBV disease, RNAi treatment provided partial protection with weekly treatment, prolonging the survival period of colonies to 8 months compared to 2 months in colonies treated at 2- and 4-week intervals. Therefore, this study demonstrated that RNAi is a valuable tool for preventing SBV disease outbreaks in healthy and low-level SBV-infected colonies.
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Hassanyar AK, Nie H, Li Z, Lin Y, Huang J, Woldegiorgis ST, Hussain M, Feng W, Zhang Z, Yu K, Su S. Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing. Int J Mol Sci 2023; 24:ijms24076238. [PMID: 37047210 PMCID: PMC10094193 DOI: 10.3390/ijms24076238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infection in honeybees, but the genetic markers and molecular mechanisms underlying SBV resistance have not been identified. To explore single nucleotide polymorphisms (SNPs), insertions, deletions (Indels), and genes at the DNA level related to SBV resistance, we conducted whole-genome resequencing on 90 Apis cerana cerana larvae raised in vitro and challenged with SBV. After filtering, a total of 337.47 gigabytes of clean data and 31,000,613 high-quality SNP loci were detected in three populations. We used ten databases to annotate 9359 predicted genes. By combining population differentiation index (FST) and nucleotide polymorphisms (π), we examined genome variants between resistant (R) and susceptible (S) larvae, focusing on site integrity (INT < 0.5) and minor allele frequency (MAF < 0.05). A selective sweep analysis with the top 1% and top 5% was used to identify significant regions. Two SNPs on the 15th chromosome with GenBank KZ288474.1_322717 (Guanine > Cytosine) and KZ288479.1_95621 (Cytosine > Thiamine) were found to be significantly associated with SBV resistance based on their associated allele frequencies after SNP validation. Each SNP was authenticated in 926 and 1022 samples, respectively. The enrichment and functional annotation pathways from significantly predicted genes to SBV resistance revealed immune response processes, signal transduction mechanisms, endocytosis, peroxisomes, phagosomes, and regulation of autophagy, which may be significant in SBV resistance. This study presents novel and useful SNP molecular markers that can be utilized as assisted molecular markers to select honeybees resistant to SBV for breeding and that can be used as a biocontrol technique to protect honeybees from SBV.
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Fatehi S, Aikins M, Philips TW, Brown S, Zhu KY, Scully ED, Park Y. Characterization of Iflavirus in the Red Flour Beetle, Tribolium castaneum (Coleoptera; Tenebrionidae). INSECTS 2023; 14:220. [PMID: 36975905 PMCID: PMC10051554 DOI: 10.3390/insects14030220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Iflavirus is a group of viruses distributed mainly in arthropod species. We surveyed Tribolium castaneum iflavirus (TcIV) in different laboratory strains and in Sequence Read Archives (SRA) in GenBank. TcIV is highly specific to only T. castaneum and is not found in seven other Tenebrionid species, including the closely related species T. freemani. The same strains from different laboratories and different strains displayed largely different degrees of infections in the examination of 50 different lines by using Taqman-based quantitative PCR. We found that ~63% (27 out of 43 strains) of T. castaneum strains in different laboratories are positive for TcIV PCR with large degrees of variation, in the range of seven orders of magnitude, indicating that the TcIV is highly fluctuating depending on the rearing conditions. The TcIV was prevalent in the nervous system with low levels found in the gonad and gut. The transovarial transmission was supported in the experiment with surface-sterilized eggs. Interestingly, TcIV infection did not show observable pathogenicity. TcIV offers an opportunity to study the interaction between the virus and the immune system of this model beetle species.
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Affiliation(s)
- Soheila Fatehi
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael Aikins
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Thomas W. Philips
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS-CGAHR, Manhattan, KS 66502, USA
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
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Balkanska R, Shumkova R, Atsenova N, Salkova D, Dundarova H, Radoslavov G, Hristov P. Molecular Detection and Phylogenetic Analysis of Deformed Wing Virus and Sacbrood Virus Isolated from Pollen. Vet Sci 2023; 10:vetsci10020140. [PMID: 36851444 PMCID: PMC9965827 DOI: 10.3390/vetsci10020140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Among many pathogens and pests, honey bee viruses are known as one of the most common cause of diseases in honey bee colonies. In this study, we demonstrate that pollen grains and bee bread are potential sources of viral DNA. We extracted DNA from 3 types of pollen samples: directly provided by beekeepers (n = 12), purchased from trade markets (n = 5), and obtained from honeycombs (bee bread, n = 10). The extracted DNA was used for molecular detection (RT-PCR analysis) of six of the most widely distributed honey bee viruses: deformed wing virus, sacbrood virus, acute bee paralysis virus, black queen cell virus, Kashmir bee virus, Israeli acute paralysis virus, and chronic bee paralysis virus. We successfully managed to establish only the deformed wing virus (DWV) and the sacbrood virus (SBV), with different distribution frequencies depending on the territory of the country. The phylogenetic analyses of Bulgarian isolates were performed with the most similar sequences available in molecular databases from other countries. Phylogenies of Bulgarian viral strains demonstrated genetically heterogeneous populations of DWV and relatively homogenous populations of SBV. In conclusion, the results obtained from the current study have shown that pollen is a valuable source for molecular detection of honey bee pathogens. This allows epidemiological monitoring of honey bee diseases at a regional and a national level.
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Affiliation(s)
- Ralitsa Balkanska
- Department “Special Branches”, Institute of Animal Science, Agricultural Academy, 2230 Kostinbrod, Bulgaria
| | - Rositsa Shumkova
- Research Centre of Stockbreeding and Agriculture, Agricultural Academy, 4700 Smolyan, Bulgaria
| | - Nedyalka Atsenova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Delka Salkova
- Department of Experimental Parasitology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Heliana Dundarova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Department of Ecosystem Research, Environmental Risk Assessment and Conservation Biology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence:
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Sun L, Li M, Ma Y, Huang S, Ma M, Fei D. Interaction between the VP2 protein of deformed wing virus and host snapin protein and its effect on viral replication. Front Microbiol 2023; 14:1096306. [PMID: 36846748 PMCID: PMC9945523 DOI: 10.3389/fmicb.2023.1096306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/09/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Deformed wing virus (DWV) is one of the causative agents of colony collapse disorder. The structural protein of DWV plays a vital role in the process of viral invasion and host infection; however, there is limited research on DWV. Methods and Results In this study, we screened the host protein snapin, which can interact with the VP2 protein of DWV, using the yeast two-hybrid system. Through computer simulation and GST pull-down and CO-IP assays, an interaction between snapin and VP2 was confirmed. Furthermore, immunofluorescence and co-localization experiments revealed that VP2 and snapin primarily co-localized in the cytoplasm. Consequently, RNAi was used to interfere with the expression of snapin in worker bees to examine the replication of DWV after the interference. After silencing of snapin, the replication of DWV in worker bees was significantly downregulated. Hence, we speculated that snapin was associated with DWV infection and involved in at least one stage of the viral life cycle. Finally, we used an online server to predict the interaction domains between VP2 and snapin, and the results indicate that the interaction domain of VP2 was approximately located at 56-90, 136-145, 184-190, and 239-242 aa and the snapin interaction domain was approximately located at 31-54 and 115-136 aa. Conclusion This research confirmed that DWV VP2 protein could interacts with the snapin of host protein, which provides a theoretical basis for further investigation of its pathogenesis and development of targeted therapeutic drugs.
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Affiliation(s)
- Li Sun
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Ming Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Yueyu Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Sichao Huang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Mingxiao Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China,*Correspondence: Mingxiao Ma, ✉
| | - Dongliang Fei
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China,Dongliang Fei, ✉
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Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. MICROBIOME 2023; 11:6. [PMID: 36631833 PMCID: PMC9832778 DOI: 10.1186/s40168-022-01446-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/08/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. RESULTS We report the meta-transcriptomic sequencing of nearly 2000 samples of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016-2019. We document the natural diversity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within individual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. CONCLUSIONS Our data show that honeybee viruses are more widespread, prevalent, and genetically diverse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale. Video Abstract.
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Affiliation(s)
- Nannan Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Juan Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Hong Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jingkai Ji
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jiangli Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weipeng Kang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Edward C Holmes
- Sydeny Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Shufa Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Sacbrood Virus: A Growing Threat to Honeybees and Wild Pollinators. Viruses 2022; 14:v14091871. [PMID: 36146677 PMCID: PMC9505205 DOI: 10.3390/v14091871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Sacbrood virus (SBV) is one of the many viruses that infect both the Western honeybee (Apis mellifera) and the Eastern honeybee (Apis cerana). Recently, the interspecies transmission of SBV has been discovered, especially among wild pollinators. This newly discovered evolutionary occurrence regarding SBV indicates a much wider host range than previously believed, causing further concern about the future sustainability of agriculture and the resilience of ecosystems. Over the past few decades, vast numbers of studies have been undertaken concerning SBV infection in honeybees, and remarkable progress has been made in our understanding of the epidemiology, pathogenesis, transmission, and manifestations of SBV infection in honeybees and other pollinators. Meanwhile, some methods, including Chinese medicine, have been established to control and prevent sacbrood disease in A. cerana in Asian countries. In this review, we summarize the existing knowledge of SBV and address the gaps in the knowledge within the existing literature in the hope of providing future directions for the research and development of management strategies for controlling the spread of this deadly disease.
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Šimonová A, Romanská V, Benoni B, Škubník K, Šmerdová L, Prochazkova M, Spustová K, Moravčík O, Gahurova L, Pačes J, Plevka P, Cahova H. Honeybee iflaviruses pack specific tRNA fragments from host cells in their virions. Chembiochem 2022; 23:e202200281. [PMID: 35771148 PMCID: PMC9544947 DOI: 10.1002/cbic.202200281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/30/2022] [Indexed: 11/15/2022]
Abstract
The Picornavirales include viruses that infect vertebrates, insects, and plants. It was believed that they pack only their genomic mRNA in the particles; thus, we envisaged these viruses as excellent model systems for studies of mRNA modifications. We used LC–MS to analyze digested RNA isolated from particles of the sacbrood and deformed wing iflaviruses as well as of the echovirus 18 and rhinovirus 2 picornaviruses. Whereas in the picornavirus RNAs we detected only N6‐methyladenosine and 2’‐O‐methylated nucleosides, the iflavirus RNAs contained a wide range of methylated nucleosides, such as 1‐methyladenosine (m1A) and 5‐methylcytidine (m5C). Mapping of m1A and m5C through RNA sequencing of the SBV and DWV RNAs revealed the presence of tRNA molecules. Both modifications were detected only in tRNA. Further analysis revealed that tRNAs are present in form of 3’ and 5’ fragments and they are packed selectively. Moreover, these tRNAs are typically packed by other viruses.
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Affiliation(s)
- Anna Šimonová
- Charles University: Univerzita Karlova, First Faculty of Medicine, CZECH REPUBLIC
| | - Veronika Romanská
- Charles University: Univerzita Karlova, First Faculty of Medicine, CZECH REPUBLIC
| | - Barbora Benoni
- Charles University: Univerzita Karlova, First Faculty of Medicine, CZECH REPUBLIC
| | - Karel Škubník
- Masaryk University: Masarykova Univerzita, CEITEC, CZECH REPUBLIC
| | - Lenka Šmerdová
- Masaryk University: Masarykova Univerzita, CEITEC, CZECH REPUBLIC
| | | | - Kristina Spustová
- IOCB CAS: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Chemical Biology of Nucleic Acids, CZECH REPUBLIC
| | - Ondřej Moravčík
- Institute of Molecular Genetics Czech Academy of Sciences: Ustav molekularni genetiky Akademie Ved Ceske Republiky, Bioinformatic, CZECH REPUBLIC
| | - Lenka Gahurova
- University of South Bohemia Faculty of Science: Jihoceska Univerzita v Ceskych Budejovicich Prirodovedecka Fakulta, Departement of Molecular Biology, CZECH REPUBLIC
| | - Jan Pačes
- Institute of Molecular Genetics Czech Academy of Sciences: Ustav molekularni genetiky Akademie Ved Ceske Republiky, Bioinformatic, CZECH REPUBLIC
| | - Pavel Plevka
- Masaryk University: Masarykova Univerzita, CEITEC, CZECH REPUBLIC
| | - Hana Cahova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic, CZECH REPUBLIC
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Sukeník L, Mukhamedova L, Procházková M, Škubník K, Plevka P, Vácha R. Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation. ACS NANO 2021; 15:19233-19243. [PMID: 34881874 DOI: 10.1021/acsnano.1c04814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery.
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Affiliation(s)
- Lukáš Sukeník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Liya Mukhamedova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Michaela Procházková
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Karel Škubník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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14
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Lee SH, Oh TK, Oh S, Kim S, Noh HB, Vinod N, Lee JY, Moon ES, Choi CW. Development of a Kit for Rapid Immunochromatographic Detection of Sacbrood Virus Infecting Apis cerana (AcSBV) Based on Polyclonal and Monoclonal Antibodies Raised against Recombinant VP1 and VP2 Expressed in Escherichia coli. Viruses 2021; 13:v13122439. [PMID: 34960707 PMCID: PMC8707083 DOI: 10.3390/v13122439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
A Korean isolate of the sacbrood virus infecting Apis cerana (AcSBV-Kor) is the most destructive honeybee virus, causing serious economic damage losses in Korean apiculture. To address this, here, we attempted to develop an assay for the rapid detection of AcSBV-Kor based on immunochromatographic detection of constituent viral proteins. Genes encoding VP1 and VP2 proteins of AcSBV-Kor were cloned into an expression vector (pET-28a) and expressed in Escherichia coli BL21(DE3). During purification, recombinant VP1 (rVP1) and VP2 (rVP2) proteins were found in the insoluble fraction, with a molecular size of 26.7 and 24.9 kDa, respectively. BALB/c mice immunized with the purified rVP1 and rVP2 produced polyclonal antibodies (pAbs) such as pAb-rVP1 and pAb-rVP2. Western blot analysis showed that pAb-rVP1 strongly reacted with the homologous rVP1 but weakly reacted with heterologous rVP2. However, pAb-rVP2 strongly reacted not only with the homologous rVP2 but also with the heterologous rVP1. Spleen cells of the immunized mice fused with SP2/0-Ag14 myeloma cells produced monoclonal antibodies (mAbs) such as mAb-rVP1-1 and mAb-rVP2-13. Western blot analysis indicated that pAb-rVP1, pAb-rVP2, mAb-rVP1-1, and mAb-rVP2-13 reacted with AcSBV-infected honeybees and larvae as well as the corresponding recombinant proteins. These antibodies were then used in the development of a rapid immunochromatography (IC) strip assay kit with colloidal gold coupled to pAb-rVP1 and pAb-rVP2 at the conjugate pad and mAb-rVP1-1 and mAb-rVP2-13 at the test line. One antibody pair, pAb-rVP1/mAb-VP1-1, showed positive reactivity as low as 1.38 × 103 copies, while the other pair, pAb-rVP2/mAb-VP2-13, showed positive reactivity as low as 1.38 × 104 copies. Therefore, the antibody pair pAb-rVP1/mAb-VP1-1 was selected as a final candidate for validation. To validate the detection of AcSBV, the IC strip tests were conducted with 50 positive and 50 negative samples and compared with real-time PCR tests. The results confirm that the developed IC assay is a sufficiently sensitive and specific detection method for user-friendly and rapid detection of AcSBV.
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Affiliation(s)
- Song Hee Lee
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | | | - Sung Oh
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Seongdae Kim
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Han Byul Noh
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Nagarajan Vinod
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Ji Yoon Lee
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Eun Sun Moon
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
| | - Chang Won Choi
- Department of Biology & Medicinal Science, Pai Chai University, Daejeon 35345, Korea; (S.H.L.); (S.O.); (S.K.); (H.B.N.); (N.V.); (J.Y.L.); (E.S.M.)
- Correspondence: ; Tel.: +82-42-520-5617
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15
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Dang X, Li Y, Li X, Wang C, Ma Z, Wang L, Fan X, Li Z, Huang D, Xu J, Zhou Z. Lipidomic Profiling Reveals Distinct Differences in Sphingolipids Metabolic Pathway between Healthy Apis cerana cerana larvae and Chinese Sacbrood Disease. INSECTS 2021; 12:insects12080703. [PMID: 34442269 PMCID: PMC8396520 DOI: 10.3390/insects12080703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022]
Abstract
Chinese sacbrood disease (CSD), which is caused by Chinese sacbrood virus (CSBV), is a major viral disease in Apis cerana cerana larvae. Analysis of lipid composition is critical to the study of CSBV replication. The host lipidome profiling during CSBV infection has not been conducted. This paper identified the lipidome of the CSBV-larvae interaction through high-resolution mass spectrometry. A total of 2164 lipids were detected and divided into 20 categories. Comparison of lipidome between healthy and CSBV infected-larvae showed that 266 lipid species were altered by CSBV infection. Furthermore, qRT-PCR showed that various sphingolipid enzymes and the contents of sphingolipids in the larvae were increased, indicating that sphingolipids may be important for CSBV infection. Importantly, Cer (d14:1 + hO/21:0 + O), DG (41:0e), PE (18:0e/18:3), SM (d20:0/19:1), SM (d37:1), TG (16:0/18:1/18:3), TG (18:1/20:4/21:0) and TG (43:7) were significantly altered in both CSBV_24 h vs. CK_24 h and CSBV_48 h vs. CK_48 h. Moreover, TG (39:6), which was increased by more than 10-fold, could be used as a biomarker for the early detection of CSD. This study provides evidence that global lipidome homeostasis in A. c. cerana larvae is remodeled after CSBV infection. Detailed studies in the future may improve the understanding of the relationship between the sphingolipid pathway and CSBV replication.
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Affiliation(s)
- Xiaoqun Dang
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Yan Li
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Xiaoqing Li
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Chengcheng Wang
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Zhengang Ma
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Linling Wang
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Xiaodong Fan
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Zhi Li
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Dunyuan Huang
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
| | - Jinshan Xu
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
- Correspondence: (J.X.); (Z.Z.)
| | - Zeyang Zhou
- Chongqing Key Laboratory of Vector Insect, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.D.); (Y.L.); (X.L.); (C.W.); (Z.M.); (L.W.); (X.F.); (Z.L.); (D.H.)
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- Correspondence: (J.X.); (Z.Z.)
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Chavas LMG, Gourhant P, Guimaraes BG, Isabet T, Legrand P, Lener R, Montaville P, Sirigu S, Thompson A. PROXIMA-1 beamline for macromolecular crystallography measurements at Synchrotron SOLEIL. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:970-976. [PMID: 33950005 PMCID: PMC8127379 DOI: 10.1107/s1600577521002605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/09/2021] [Indexed: 05/07/2023]
Abstract
The undulator beamline PROXIMA-1 at Synchrotron SOLEIL scheduled its first users in March 2008. The endstation is dedicated to biomolecular crystallography experiments, with a layout designed to favour anomalous data recording and studies of crystals with large cell dimensions. In 12 years, the beamline has accommodated 4267 shifts of 8 h and more than 6300 visitors. By the end of 2020, it saw 1039 identified published scientific papers referring to 1415 coordinates deposited in the Protein Data Bank. The current paper describes the PROXIMA-1 beamline, including the recent specific implementations developed for the sample environment. The setup installed in the experimental station contains numerous beam-shaping equipment, a chi-geometry three-axis goniometer, a single-photon-counting pixel-array X-ray detector, combined with a medium-throughput sample exchange robot. As part of a standard experimental scheme, PROXIMA-1 can also be accessed via `mail-in' services or remotely.
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Affiliation(s)
- Leonard M. G. Chavas
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Nagoya University, Nagoya 464-8603, Japan
| | | | | | | | | | - Robin Lener
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
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Organization of the Structural Protein Region of La Jolla Virus Isolated from the Invasive Pest Insect Drosophila suzukii. Viruses 2021; 13:v13050740. [PMID: 33922699 PMCID: PMC8146151 DOI: 10.3390/v13050740] [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: 04/06/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/16/2023] Open
Abstract
Drosophila suzukii (Ds) is an invasive pest insect that infests ripening fruit, causing severe economic losses. Control measures based on chemical pesticides are inefficient and undesirable, so biological alternatives have been considered, including native Ds viruses. We previously isolated a strain of La Jolla virus (LJV-Ds-OS20) from Ds in Germany as a candidate biopesticide. Here we characterized the new strain in detail, focusing on the processing of its capsid proteins. We tested LJV growth during Ds development to optimize virus production, and established a laboratory production system using adult flies. This system was suitable for the preparation of virions for detailed analysis. The LJV-Ds-OS20 isolate was cloned by limiting dilution and the complete nucleotide sequence was determined as a basis for protein analysis. The terminal segments of the virus genome were completed by RACE-PCR. LJV virions were also purified by CsCl gradient centrifugation and analyzed by SDS-PAGE and electron microscopy. The capsid proteins of purified LJV virions were resolved by two-dimensional SDS-PAGE for N-terminal sequencing and peptide mass fingerprinting. The N-terminal sequences of VP1 and VP2, together with MS data representing several capsid proteins, allowed us to develop a model for the organization of the LJV structural protein region. This may facilitate the development of new viral strains as biopesticides.
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Jia W, Wang F, Li J, Chang X, Yang Y, Yao H, Bao Y, Song Q, Ye G. A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus. Front Microbiol 2021; 11:621141. [PMID: 33488564 PMCID: PMC7820178 DOI: 10.3389/fmicb.2020.621141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.
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Affiliation(s)
- Wenxi Jia
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingjing Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Xuefei Chang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yanyuan Bao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Škubník K, Sukeník L, Buchta D, Füzik T, Procházková M, Moravcová J, Šmerdová L, Přidal A, Vácha R, Plevka P. Capsid opening enables genome release of iflaviruses. SCIENCE ADVANCES 2021; 7:7/1/eabd7130. [PMID: 33523856 PMCID: PMC7775750 DOI: 10.1126/sciadv.abd7130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/11/2020] [Indexed: 05/29/2023]
Abstract
The family Iflaviridae includes economically important viruses of the western honeybee such as deformed wing virus, slow bee paralysis virus, and sacbrood virus. Iflaviruses have nonenveloped virions and capsids organized with icosahedral symmetry. The genome release of iflaviruses can be induced in vitro by exposure to acidic pH, implying that they enter cells by endocytosis. Genome release intermediates of iflaviruses have not been structurally characterized. Here, we show that conformational changes and expansion of iflavirus RNA genomes, which are induced by acidic pH, trigger the opening of iflavirus particles. Capsids of slow bee paralysis virus and sacbrood virus crack into pieces. In contrast, capsids of deformed wing virus are more flexible and open like flowers to release their genomes. The large openings in iflavirus particles enable the fast exit of genomes from capsids, which decreases the probability of genome degradation by the RNases present in endosomes.
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Affiliation(s)
- Karel Škubník
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Lukáš Sukeník
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - David Buchta
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Michaela Procházková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jana Moravcová
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Lenka Šmerdová
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Antonín Přidal
- Department of Zoology, Fishery, Hydrobiology, and Apidology, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1/1665, 613 00 Brno, Czech Republic
| | - Robert Vácha
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.
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Fernandez de la Mora J, Perez-Lorenzo LJ, Wick D. Singularly Narrow Viral Size and Mobility Standards from the 38.3 nm Chronic Bee Paralysis Virus and Its 17.5 nm Satellite. Anal Chem 2020; 92:13896-13903. [PMID: 32969651 DOI: 10.1021/acs.analchem.0c02687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The chronic bee paralysis virus (CBPV), extracted from sick or dead bees, was studied by mobility measurements via electrospray charge reduction with a differential mobility analyzer (DMA) of unusually high resolution. Three different particles are observed. The most abundant one contributes a mobility peak at 38.3 nm, approximately as expected for CBPV. The peak is very sharp in spite of the nonisometric nature of CBPV. We also observe a previously unreported weaker well-resolved shoulder 4.8% more mobile, perhaps due to empty (genome-free) particles. Another sharp peak appearing at approximately 17.51 nm is likely associated with the known icosahedral CBPV satellite (CBPVS). The 17.51 and 38.3 nm peaks offer size and mobility standards much narrower than previously reported at any size above 5 nm, with relative full peak width at half-maximum (FWHM) in mobility approaching 2% (∼1% in diameter). Slight but clear imperfections in the DMA response and the electrospraying process suggest that the real width of the viral mobility distribution is less than 2%.
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Affiliation(s)
- Juan Fernandez de la Mora
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, United States
| | - Luis Javier Perez-Lorenzo
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, United States
| | - David Wick
- BVS, Inc., Stevensville, Montana 59870, United States
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21
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Virion structures and genome delivery of honeybee viruses. Curr Opin Virol 2020; 45:17-24. [PMID: 32679289 DOI: 10.1016/j.coviro.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 10/23/2022]
Abstract
The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. However, the worldwide population of honeybees is under pressure from environmental stress and pathogens. Viruses from the families Iflaviridae and Dicistroviridae, together with their vector, the parasitic mite Varroa destructor, are the major threat to the world's honeybees. Dicistroviruses and iflaviruses have capsids with icosahedral symmetries. Acidic pH triggers the genome release of both dicistroviruses and iflaviruses. The capsids of iflaviruses expand, whereas those of dicistroviruses remain compact until the genome release. Furthermore, dicistroviruses use inner capsid proteins, whereas iflaviruses employ protruding domains or minor capsid proteins from the virion surface to penetrate membranes and deliver their genomes into the cell cytoplasm. The structural characterization of the infection process opens up possibilities for the development of antiviral compounds.
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22
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Huang S, Fei D, Ma Y, Wang C, Shi D, Liu K, Li M, Ma M. Identification of a novel host protein interacting with the structural protein VP2 of deformed wing virus by yeast two-hybrid screening. Virus Res 2020; 286:198072. [PMID: 32659307 DOI: 10.1016/j.virusres.2020.198072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022]
Abstract
Deformed wing virus (DWV) interacting with Varroa destructor is a possible cause of honeybee colony mortality. VP2 is the structural protein of DWV but its function remains unknown. To clarify the function of VP2 and screen for novel binding proteins that interact with VP2, we carried out a membrane protein yeast two-hybrid screening using VP2 as bait. Subsequently, the interaction between VP2 and the host interacting protein [heat shock protein 10 (Hsp10)] was further verified using glutathione S-transferase pull-down assay in vitro and co-immunoprecipitation assay in cells. Furthermore, fluorescence confocal microscopy revealed that VP2 and Hsp10 were mainly co-localized in the cytoplasm. Using real-time polymerase chain reaction, we found that Hsp10 expression in DWV-infected worker honey bees were downregulated compared with that in healthy honey bees. Additionally, we showed that overexpression of VP2 protein could reduce the expression of Hsp10. These results suggest that Hsp10 plays a vital role in host immunity and antiviral effects.
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Affiliation(s)
- Sichao Huang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Dongliang Fei
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Yueyu Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Chen Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Donghui Shi
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Kunyang Liu
- Liaoning Provincial Agricultural Development Service Center, China
| | - Ming Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China.
| | - Mingxiao Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China.
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23
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Capsid Structure of a Marine Algal Virus of the Order Picornavirales. J Virol 2020; 94:JVI.01855-19. [PMID: 32024776 DOI: 10.1128/jvi.01855-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first alga virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, revealed that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. The above-mentioned and other critical structural features provide new insights on three long-standing theories about Picornavirales: (i) the canyon hypothesis, (ii) the primordial VP2 domain swap, and (iii) the hypothesis that alga Picornavirales viruses could share characteristics with the Picornavirales ancestor.IMPORTANCE Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes and thus still share some characteristics with the Picornavirales ancestor. This article describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.
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Visualizing Sacbrood Virus of Honey Bees via Transformation and Coupling with Enhanced Green Fluorescent Protein. Viruses 2020; 12:v12020224. [PMID: 32085386 PMCID: PMC7077286 DOI: 10.3390/v12020224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 01/24/2023] Open
Abstract
Sacbrood virus (SBV) of honey bees is a picornavirus in the genus Iflavirus. Given its relatively small and simple genome structure, single positive-strand RNA with only one ORF, cloning the full genomic sequence is not difficult. However, adding nonsynonymous mutations to the bee iflavirus clone is difficult because of the lack of information about the viral protein processes. Furthermore, the addition of a reporter gene to the clones has never been accomplished. In preliminary trials, we found that the site between 3′ untranslated region (UTR) and poly(A) can retain added sequences. We added enhanced green fluorescent protein (EGFP) expression at this site, creating a SBV clone with an expression tag that does not affect virus genes. An intergenic region internal ribosome entry site (IRES) from Black queen cell virus (BQCV) was inserted to initiate EGFP expression. The SBV-IRES-EGFP clone successfully infected Apis cerana and Apis mellifera, and in A. cerana larvae, it was isolated and passaged using oral inoculation. The inoculated larvae had higher mortality and the dead larvae showed sacbrood symptoms. The added IRES-EGFP remained in the clone through multiple passages and expressed the expected EGFP in all infected bees. We demonstrated the ability to add gene sequences in the site between 3′-UTR and poly(A) in SBV and the potential to do so in other bee iflaviruses; however, further investigations of the mechanisms are needed. A clone with a desired protein expression reporter will be a valuable tool in bee virus studies.
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Natural Product Medicines for Honey Bees: Perspective and Protocols. INSECTS 2019; 10:insects10100356. [PMID: 31635365 PMCID: PMC6835950 DOI: 10.3390/insects10100356] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022]
Abstract
The western honey bee remains the most important pollinator for agricultural crops. Disease and stressors threaten honey bee populations and productivity during winter- and summertime, creating costs for beekeepers and negative impacts on agriculture. To combat diseases and improve overall bee health, researchers are constantly developing honey bee medicines using the tools of microbiology, molecular biology and chemistry. Below, we present a manifesto alongside standardized protocols that outline the development and a systematic approach to test natural products as ‘bee medicines’. These will be accomplished in both artificial rearing conditions and in colonies situated in the field. Output will be scored by gene expression data of host immunity, bee survivorship, reduction in pathogen titers, and more subjective merits of the compound in question. Natural products, some of which are already encountered by bees in the form of plant resins and nectar compounds, provide promising low-cost candidates for safe prophylaxis or treatment of bee diseases.
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Ramesh R, Lim XX, Raghuvamsi PV, Wu C, Wong SM, Anand GS. Uncovering metastability and disassembly hotspots in whole viral particles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:5-12. [PMID: 30553754 DOI: 10.1016/j.pbiomolbio.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/26/2018] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
Viruses are metastable macromolecular assemblies that toggle between multiple conformational states through molecular rearrangements that are critical for mediating viral host entry. Viruses respond to different host specific environmental cues to form disassembly intermediates for the eventual release of genomic material required for replication. Although static snapshots of these intermediates have been captured through structural techniques such as X-ray crystallography and cryo-EM, the mechanistic details of these conformational rearrangements underpinning viral metastability have been poorly understood. Amide hydrogen deuterium exchange mass spectrometry (HDXMS) is a powerful tool that measures hydrogen bonding propensities to probe changes in the dynamics of different macromolecular interactions. Chaotropic agents such as urea can be used to disrupt hydrogen bonds between different subunits, thereby ranking regions of the virus that are critical in maintaining viral stability. By controlled urea denaturation with HDXMS, we have identified specific loci in a Turnip Crinkle Virus (TCV) model showing increased deuterium exchange with even minimally disruptive concentrations of urea. These loci represent dynamic disassembly hotspots. These hotspots are predominantly present at the quaternary contacts at the 3-fold and 5-fold axes. This approach can be applied to detect vulnerabilities in virus icosahedral structures to uncover the molecular mechanism of viral disassembly.
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Affiliation(s)
- Ranita Ramesh
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Xin Xiang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | | | - Chao Wu
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Sek Man Wong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore; Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
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