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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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2
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Shakir S, Mubin M, Nahid N, Serfraz S, Qureshi MA, Lee TK, Liaqat I, Lee S, Nawaz-ul-Rehman MS. REPercussions: how geminiviruses recruit host factors for replication. Front Microbiol 2023; 14:1224221. [PMID: 37799604 PMCID: PMC10548238 DOI: 10.3389/fmicb.2023.1224221] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
Circular single-stranded DNA viruses of the family Geminiviridae encode replication-associated protein (Rep), which is a multifunctional protein involved in virus DNA replication, transcription of virus genes, and suppression of host defense responses. Geminivirus genomes are replicated through the interaction between virus Rep and several host proteins. The Rep also interacts with itself and the virus replication enhancer protein (REn), which is another essential component of the geminivirus replicase complex that interacts with host DNA polymerases α and δ. Recent studies revealed the structural and functional complexities of geminivirus Rep, which is believed to have evolved from plasmids containing a signature domain (HUH) for single-stranded DNA binding with nuclease activity. The Rep coding sequence encompasses the entire coding sequence for AC4, which is intricately embedded within it, and performs several overlapping functions like Rep, supporting virus infection. This review investigated the structural and functional diversity of the geminivirus Rep.
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Affiliation(s)
- Sara Shakir
- Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liѐge, Gembloux, Belgium
| | - Muhammad Mubin
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saad Serfraz
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Taek-Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Iram Liaqat
- Microbiology Lab, Department of Zoology, Government College University, Lahore, Pakistan
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Muhammad Shah Nawaz-ul-Rehman
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
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3
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Gnanasekaran P, Gupta N, Ponnusamy K, Devendran R, George B, Chakraborty S. Betasatellite-encoded βC1 protein regulates helper virus accumulation by interfering with the ATP hydrolysis activity of geminivirus-encoded replication initiator protein. J Gen Virol 2023; 104. [PMID: 37326617 DOI: 10.1099/jgv.0.001866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Geminivirus-betasatellite disease complexes are an epidemic threat to the majority of economically important crops across the world. Plant virus satellites including betasatellites are maintained by their associated helper virus. Geminivirus-betasatellites influence viral pathogenesis by substantially increasing or decreasing their helper virus accumulation. In the present study, we attempted to understand the mechanistic details of the geminivirus-betasatellite interaction. Here, we used tomato leaf curl Gujarat virus (ToLCGV) and tomato leaf curl Patna betasatellite (ToLCPaB) as a model system. This study reveals that ToLCGV can efficiently trans-replicate ToLCPaB in Nicotiana benthamiana plants, but ToLCPaB greatly reduced the accumulation of its helper virus DNA. For the first time, we have identified that the ToLCPaB-encoded βC1 protein is able to interact with ToLCGV-encoded replication initiator protein (Rep). In addition, we demonstrate that the C-terminal region of βC1 interacts with the C-terminus of Rep (RepC) protein. Our previous study had established that βC1 proteins encoded by diverse betasatellites possess a novel ATP hydrolysis activity and the conserved lysine/arginine residues at positions 49 and 91 are necessary for this function. Here, we show that mutating lysine at positions 49 to alanine of βC1 (βC1K49A) protein did not affect its ability to interact with RepC protein. Biochemical studies performed with ATP hydrolysis activity-deficient K49A mutated βC1 (βC1K49A) and RepC proteins revealed that Rep-βC1 interaction interferes with the ATP hydrolysis activity of Rep protein. Further, we demonstrate that βC1 protein is able to interact with D227A and D289A mutated RepC proteins but not with D262A, K272A or D286A mutated RepC proteins, suggesting that the βC1-interacting region of Rep protein encompasses its Walker-B and B' motifs. The results of docking studies supported that the βC1-interacting region of Rep protein encompasses its motifs associated with ATP binding and ATP hydrolysis activities. Docking studies also provided evidence that the Rep-βC1 interaction interferes with the ATP binding activity of Rep protein. Together, our findings suggest that βC1 protein regulates helper virus accumulation by interfering with the ATP hydrolysis activity of helper virus Rep protein.
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Affiliation(s)
- Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control, New Delhi-110 054, India
| | - Ragunathan Devendran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Biju George
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
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4
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Rizvi I, Hisamuddin M, Malik A, Khan RH. Identification of mungbean yellow mosaic India virus (MYMIV) Rep interacting partners using phage display and influence of Arabidopsis thaliana MCM3 on geminivirus DNA replication. J Biomol Struct Dyn 2022; 40:10507-10517. [PMID: 34121621 DOI: 10.1080/07391102.2021.1935319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Geminiviruses consist of a single-stranded DNA genome that replicates by a rolling circle (RCR) and recombination-dependent (RDR) modes of replication. The AC1 or Rep is the indispensable viral protein required for the RCR mode of replication. Since these viruses encode only a few proteins, they depend on several host factors for replication, transcription, and other physiological processes. To get insights into the repertoire of host factors influencing the replication of geminiviruses, we performed phage display experiments which led to the identification of putative mungbean yellow mosaic India virus (MYMIV) Rep interacting host proteins. These proteins might directly or indirectly participate in geminivirus biology. MCM3 was one of the Rep-interacting partners obtained in the phage display results. Using bimolecular fluorescence complementation (BiFC), the interaction of the MYMIV Rep with Arabidopsis thaliana MCM3 (AtMCM3) was confirmed. We report the involvement of AtMCM3 in the replication of MYMIV DNA through an ex vivo system. The physiological relevance of the interaction between AtMCM3 and MYMIV Rep is reflected by yeast replication assay.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Irum Rizvi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.,International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Ajamaluddin Malik
- Department of Biochemistry, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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5
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Tintor N, Nieuweboer GAM, Bakker IAW, Takken FLW. The Intracellularly Acting Effector Foa3 Suppresses Defense Responses When Infiltrated Into the Apoplast. FRONTIERS IN PLANT SCIENCE 2022; 13:813181. [PMID: 35677245 PMCID: PMC9169155 DOI: 10.3389/fpls.2022.813181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Plant pathogens employ secreted proteins, among which are effectors, to manipulate and colonize their hosts. A large fraction of effectors is translocated into host cells, where they can suppress defense signaling. Bacterial pathogens directly inject effectors into host cells via the type three secretion system, but it is little understood how eukaryotic pathogens, such as fungi, accomplish this critical process and how their secreted effectors enter host cells. The root-infecting fungus Fusarium oxysporum (Fo) secrets numerous effectors into the extracellular space. Some of these, such as Foa3, function inside the plant cell to suppress host defenses. Here, we show that Foa3 suppresses pattern-triggered defense responses to the same extent when it is produced in planta irrespective of whether the protein carries the PR1 secretory signal peptide or not. When a GFP-tagged Foa3 was targeted for secretion it localized, among other locations, to mobile subcellular structures of unknown identity. Furthermore, like the well-known cell penetrating peptide Arginine 9, Foa3 was found to deliver an orthotospovirus avirulence protein-derived peptide into the cytosol, resulting in the activation of the matching resistance protein. Finally, we show that infiltrating Foa3 into the apoplast results in strong suppression of the pattern-triggered immune responses, potentially indicating its uptake by the host cells in absence of a pathogen.
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6
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Sun S, Ren Y, Wang D, Farooq T, He Z, Zhang C, Li S, Yang X, Zhou X. A group I WRKY transcription factor regulates mulberry mosaic dwarf-associated virus-triggered cell death in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2022; 23:237-253. [PMID: 34738705 PMCID: PMC8743015 DOI: 10.1111/mpp.13156] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 05/27/2023]
Abstract
Geminiviruses constitute the largest group of known plant viruses and cause devastating losses to a wide range of crops and woody plants globally. Mulberry mosaic dwarf-associated virus (MMDaV), identified from Chinese mulberry trees via small RNA-based deep sequencing, is a divergent monopartite geminivirus belonging to the genus Mulcrilevirus of the family Geminiviridae. Previous studies have shown that plants employ multiple layers of defence to protect themselves from geminivirus infection. The interplay between plant and MMDaV is nevertheless less studied. This study presents evidence that MMDaV triggers hypersensitive response (HR)-mediated antiviral defence in Nicotiana benthamiana plants. We show that the RepA protein of MMDaV is engaged in HR-type cell death induction. We find that the RepA mutants with compromised nuclear localization ability impair their capabilities of cell death induction. Virus-induced gene silencing of the key components of the R protein-mediated signalling pathway reveals that down-regulation of the nucleus-targeting NbWRKY1 alleviates the cell death induction activity of RepA. We further demonstrate that RepA up-regulates the transcript level of NbWRKY1. Furthermore, expression of RepA in N. benthamiana confers plant resistance against two begomoviruses. We propose that plant resistance against RepA can be potentially used to improve plant defence against geminiviruses in crops.
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Affiliation(s)
- Shaoshuang Sun
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yanxiang Ren
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dongxue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Tahir Farooq
- Plant Protection Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Zifu He
- Plant Protection Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Chao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Rice Biology, Institute of BiotechnologyZhejiang UniversityHangzhouChina
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7
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Devendran R, Namgial T, Reddy KK, Kumar M, Zarreen F, Chakraborty S. Insights into the multifunctional roles of geminivirus-encoded proteins in pathogenesis. Arch Virol 2022; 167:307-326. [PMID: 35079902 DOI: 10.1007/s00705-021-05338-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/23/2021] [Indexed: 12/18/2022]
Abstract
Geminiviruses are a major threat to agriculture in tropical and subtropical regions of the world. Geminiviruses have small genome with limited coding capacity. Despite this limitation, these viruses have mastered hijacking the host cellular metabolism for their survival. To compensate for the small size of their genome, geminiviruses encode multifunctional proteins. In addition, geminiviruses associate themselves with satellite DNA molecules which also encode proteins that support the virus in establishing successful infection. Geminiviral proteins recruit multiple host factors, suppress the host defense, and manipulate host metabolism to establish infection. We have updated the knowledge accumulated about the proteins of geminiviruses and their satellites in the context of pathogenesis in a single review. We also discuss their interactions with host factors to provide a mechanistic understanding of the infection process.
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Affiliation(s)
- Ragunathan Devendran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tsewang Namgial
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kishore Kumar Reddy
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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8
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Sharma M, Fuertes D, Perez-Gil J, Lois LM. SUMOylation in Phytopathogen Interactions: Balancing Invasion and Resistance. Front Cell Dev Biol 2021; 9:703795. [PMID: 34485289 PMCID: PMC8415633 DOI: 10.3389/fcell.2021.703795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/20/2021] [Indexed: 12/03/2022] Open
Abstract
Plants are constantly confronted by a multitude of biotic stresses involving a myriad of pathogens. In crops, pathogen infections result in significant agronomical losses worldwide posing a threat to food security. In order to enter plant tissues and establish a successful infection, phytopathogens have to surpass several physical, and chemical defense barriers. In recent years, post-translational modification (PTM) mechanisms have emerged as key players in plant defense against pathogens. PTMs allow a highly dynamic and rapid response in front of external challenges, increasing the complexity and precision of cellular responses. In this review, we focus on the role of SUMO conjugation (SUMOylation) in plant immunity against fungi, bacteria, and viruses. In plants, SUMO regulates multiple biological processes, ranging from development to responses arising from environmental challenges. During pathogen attack, SUMO not only modulates the activity of plant defense components, but also serves as a target of pathogen effectors, highlighting its broad role in plant immunity. Here, we summarize known pathogenic strategies targeting plant SUMOylation and, the plant SUMO conjugates involved in host-pathogen interactions. We also provide a catalog of candidate SUMO conjugates according to their role in defense responses. Finally, we discuss the complex role of SUMO in plant defense, focusing on key biological and experimental aspects that contribute to some controversial conclusions, and the opportunities for improving agricultural productivity by engineering SUMOylation in crop species.
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Affiliation(s)
- Manisha Sharma
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain.,Biosciences, College of Life and Environment Sciences, University of Exeter, Exeter, United Kingdom
| | - Diana Fuertes
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Jordi Perez-Gil
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - L Maria Lois
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain.,Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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9
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Gupta N, Reddy K, Bhattacharyya D, Chakraborty✉ S. Plant responses to geminivirus infection: guardians of the plant immunity. Virol J 2021; 18:143. [PMID: 34243802 PMCID: PMC8268416 DOI: 10.1186/s12985-021-01612-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Geminiviruses are circular, single-stranded viruses responsible for enormous crop loss worldwide. Rapid expansion of geminivirus diversity outweighs the continuous effort to control its spread. Geminiviruses channelize the host cell machinery in their favour by manipulating the gene expression, cell signalling, protein turnover, and metabolic reprogramming of plants. As a response to viral infection, plants have evolved to deploy various strategies to subvert the virus invasion and reinstate cellular homeostasis. MAIN BODY Numerous reports exploring various aspects of plant-geminivirus interaction portray the subtlety and flexibility of the host-pathogen dynamics. To leverage this pool of knowledge towards raising antiviral resistance in host plants, a comprehensive account of plant's defence response against geminiviruses is required. This review discusses the current knowledge of plant's antiviral responses exerted to geminivirus in the light of resistance mechanisms and the innate genetic factors contributing to the defence. We have revisited the defence pathways involving transcriptional and post-transcriptional gene silencing, ubiquitin-proteasomal degradation pathway, protein kinase signalling cascades, autophagy, and hypersensitive responses. In addition, geminivirus-induced phytohormonal fluctuations, the subsequent alterations in primary and secondary metabolites, and their impact on pathogenesis along with the recent advancements of CRISPR-Cas9 technique in generating the geminivirus resistance in plants have been discussed. CONCLUSIONS Considering the rapid development in the field of plant-virus interaction, this review provides a timely and comprehensive account of molecular nuances that define the course of geminivirus infection and can be exploited in generating virus-resistant plants to control global agricultural damage.
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Affiliation(s)
- Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Kishorekumar Reddy
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Dhriti Bhattacharyya
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Supriya Chakraborty✉
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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10
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Ruhel R, Mazumder M, Gnanasekaran P, Kumar M, Gourinath S, Chakraborty S. Functional implications of residues of the B' motif of geminivirus replication initiator protein in its helicase activity. FEBS J 2021; 288:6492-6509. [PMID: 34092039 DOI: 10.1111/febs.16053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/15/2021] [Accepted: 06/04/2021] [Indexed: 01/03/2023]
Abstract
Geminivirus replication initiator protein (Rep) is a multifunctional viral protein required for replication. During the process of viral replication, Rep acts as a site- and strand-specific endonuclease, ligase, ATPase, and helicase. B' motif and β-hairpin loop of the geminivirus Rep are conserved and important for Rep-mediated helicase activity required for viral replication. To dissect the roles of various amino acid residues of the B' motif and β-hairpin loop of the geminivirus Rep helicase in its process of unwinding DNA, we investigated eight conserved residues near the ATP active site or the ssDNA contact channel. Our strategy was to mutate these residues to alanines and investigate the effects of these mutations on various biochemical activities associated with DNA unwinding. We looked into the ATP binding, ATP hydrolysis, DNA binding, and DNA unwinding activities of the wild-type and mutant Rep proteins. These investigations showed four residues (Arg279, Asp280, Tyr287, and Pro290) affecting the DNA unwinding activity. A structural model analysis confirmed the B' loop and ssDNA binding loop to be connected through a β-hairpin structure, suggesting that changes on one loop might affect the other and that these residues function by acting in concert. Viral genomes containing Rep proteins having these mutations in the B' motif did not replicate in planta. Taken together, these results indicated all four residues to be implicated in helicase activity mediated by Rep and demonstrated the significance, for viral replication, of the B' motif and β-hairpin loop of the C-terminal region of the Rep protein.
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Affiliation(s)
- Rajrani Ruhel
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohit Mazumder
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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11
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Wang D, Sun S, Ren Y, Li S, Yang X, Zhou X. RepA Promotes the Nucleolar Exclusion of the V2 Protein of Mulberry Mosaic Dwarf-Associated Virus. Front Microbiol 2020; 11:1828. [PMID: 32903838 PMCID: PMC7438950 DOI: 10.3389/fmicb.2020.01828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/13/2020] [Indexed: 01/23/2023] Open
Abstract
Plant viruses have limited coding capacities so that they rely heavily on the expression of multifunctional viral proteins to achieve a successful infection. The functional specification of viral proteins is often related to their differential interaction with plant and viral components and somewhat depends on their localization to various subcellular compartments. In this study, we analyzed the intracellular localization of the V2 protein of Mulberry mosaic dwarf-associated virus (MMDaV), an unsigned species of the family Geminiviridae. We show that the V2 protein colocalizes with the nucleolar protein fibrillarin (NbFib2) in the nucleolus upon transient expression in the epidermal cells of Nicotiana benthamiana. A yeast-two hybrid assay, followed by bimolecular fluorescence complementation assays, demonstrated the specific interaction between V2 and NbFib2. Intriguingly, we find that the presence of MMDaV excludes the V2 protein from the nucleolus to nucleoplasm. We present evidence that the replication-associated protein A (RepA) protein of MMDaV interacts with V2 and enables the nucleolar exclusion of V2. We also show that, while V2 interacts with itself primarily in the nucleolus, the presence of RepA redirects the site of V2-V2 interaction from the nucleolus to the nucleoplasm. We further reveal that RepA promotes V2 out of the nucleolus presumably by directing the NbFib2-V2 complex from the nucleolus to the nucleoplasm. Considering the critical role of the nucleolus in plant virus infection, this RepA-dependent modulation of V2 nucleolar localization would be crucial for understanding the involvement of this subcellular compartment in plant-virus interactions.
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Affiliation(s)
- Dongxue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoshuang Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanxiang Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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12
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Maio F, Helderman TA, Arroyo-Mateos M, van der Wolf M, Boeren S, Prins M, van den Burg HA. Identification of Tomato Proteins That Interact With Replication Initiator Protein (Rep) of the Geminivirus TYLCV. FRONTIERS IN PLANT SCIENCE 2020; 11:1069. [PMID: 32760417 PMCID: PMC7373745 DOI: 10.3389/fpls.2020.01069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/29/2020] [Indexed: 05/23/2023]
Abstract
Geminiviruses are plant-infecting DNA viruses that reshape the intracellular environment of their host in order to create favorable conditions for viral replication and propagation. Viral manipulation is largely mediated via interactions between viral and host proteins. Identification of this protein network helps us to understand how these viruses manipulate their host and therefore provides us potentially with novel leads for resistance against this class of pathogens, as genetic variation in the corresponding plant genes could subvert viral manipulation. Different studies have already yielded a list of host proteins that interact with one of the geminiviral proteins. Here, we use affinity purification followed by mass spectrometry (AP-MS) to further expand this list of interacting proteins, focusing on an important host (tomato) and the Replication initiator protein (Rep, AL1, C1) from Tomato yellow leaf curl virus (TYLCV). Rep is the only geminiviral protein proven to be essential for geminiviral replication and it forms an integral part of viral replisomes, a protein complex that consists of plant and viral proteins that allows for viral DNA replication. Using AP-MS, fifty-four 'high confidence' tomato proteins were identified that specifically co-purified with Rep. For two of them, an unknown EWS-like RNA-binding protein (called Geminivirus Rep interacting EWS-like protein 1 or GRIEP1) and an isoform of the THO complex subunit 4A (ALY1), we were able to confirm this interaction with Rep in planta using a second method, bimolecular fluorescence complementation (BiFC). The THO subunit 4 is part of the THO/TREX (TRanscription-EXport) complex, which controls RNA splicing and nuclear export of mRNA to the cytoplasm and is also connected to plant disease resistance. This work represents the first step towards characterization of novel host factors with a putative role in the life cycle of TYLCV and possibly other geminiviruses.
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Affiliation(s)
- Francesca Maio
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Tieme A. Helderman
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Manuel Arroyo-Mateos
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Miguel van der Wolf
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Wageningen, Netherlands
| | - Marcel Prins
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
- Keygene N.V., Wageningen, Netherlands
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
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Pérez-Padilla V, Fortes IM, Romero-Rodríguez B, Arroyo-Mateos M, Castillo AG, Moyano C, De León L, Moriones E. Revisiting Seed Transmission of the Type Strain of Tomato yellow leaf curl virus in Tomato Plants. PHYTOPATHOLOGY 2020; 110:121-129. [PMID: 31584339 DOI: 10.1094/phyto-07-19-0232-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Isolates of the Tomato yellow leaf curl virus (TYLCV) species (genus Begomovirus, family Geminiviridae) infect tomato crops worldwide, causing severe economic damage. Members of the whitefly Bemisia tabaci sibling species group are the vector of begomoviruses, including TYLCV. However, transmission of isolates of the type strain (Israel [IL]) of TYLCV (TYLCV-IL) by tomato seed has recently been reported based on infections occurring in Korea. Because of the consequences of this finding on the epidemiology and control of the disease caused by TYLCV and on the seed market, it was considered essential to revisit and expand those results to other tomato-growing areas. TYLCV DNA content was detected in tomato and Nicotiana benthamiana seed collected from plants naturally or experimentally infected with TYLCV-IL, supporting its seedborne nature. The TYLCV-IL replication detected in tomato and N. benthamiana flower reproductive organs demonstrated close association of this virus with the seed during maturation. However, the significant reduction of TYLCV DNA load after surface disinfections of tomato seed suggests that most of the virus is located externally, as contaminant of the seed coat. Transmission assays, carried out with seven tomato genotypes and more than 3,000 tomato plants, revealed no evidence of seed transmission from "surface-disinfected" or untreated seed for two Mediterranean isolates of TYLCV-IL. Similar results were also obtained for seed collected from TYLCV-IL-infected N. benthamiana plants. The results support the conclusion that TYLCV-IL is seedborne but is not seed transmitted in tomato or N. benthamiana, suggesting that transmission through seed is not a general property of TYLCV.
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Affiliation(s)
- Verónica Pérez-Padilla
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Isabel M Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Beatriz Romero-Rodríguez
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Manuel Arroyo-Mateos
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Araceli G Castillo
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Cristina Moyano
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Leandro De León
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
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