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Wang D, Yin Y, Zhang X, Ye J. An Interspecies Recombinant Sida Yellow Mosaic China Virus Isolate and Betasatellite Cause a Leaf Curl Disease in Tobacco in Hainan, China. PLANT DISEASE 2024; 108:877-886. [PMID: 37743589 DOI: 10.1094/pdis-07-23-1346-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Tobacco (Nicotiana tabacum) is an herbaceous crop. Cigar tobacco, a group of tobacco cultivars, has recently been planted in a few provinces in China. Since its introduction, symptoms such as leaf curling and vein thickening have appeared. Here we report a begomovirus, Sida yellow mosaic China virus-Hainan isolate (designated SiYMCNV-HN), associated with the betasatellite (designated SiYMCNB-HN) as the causal agent of a leaf curl disease in cigar tobacco (N. tabacum cv. Haiyan101) in Hainan Province, China. Phylogenetic and recombination analyses indicate that SiYMCNV-HN is an interspecies recombinant with a SiYMCNV isolate as the major parent and a Sida yellow vein Vietnam virus isolate as the minor parent. Full-length infectious clones of SiYMCNV-HN and SiYMCNB-HN were generated, which were highly infectious and induced high pathogenicity through agroinfiltration in Nicotiana benthamiana and N. tabacum. This newly reported recombinant begomovirus poses potential threats to tobacco plantations in the region.
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Affiliation(s)
- Duan Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuteng Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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Rosemarie Q, Sugden B. Five families of diverse DNA viruses comprehensively restructure the nucleus. PLoS Biol 2023; 21:e3002347. [PMID: 37930945 PMCID: PMC10627436 DOI: 10.1371/journal.pbio.3002347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Many viruses have evolved ways to restructure their host cell's nucleus profoundly and unexpectedly upon infection. In particular, DNA viruses that need to commandeer their host's cellular synthetic functions to produce their progeny can induce the condensation and margination of host chromatin during productive infection, a phenomenon known as virus-induced reorganization of cellular chromatin (ROCC). These ROCC-inducing DNA viruses belong to 5 families (herpesviruses, baculoviruses, adenoviruses, parvoviruses, and geminiviruses) that infect a wide range of hosts and are important for human and ecosystem health, as well as for biotechnology. Although the study of virus-induced ROCC is in its infancy, investigations are already raising important questions, such as why only some DNA viruses that replicate their genomes in the nucleus elicit ROCC. Studying the shared and distinct properties of ROCC-inducing viruses will provide valuable insights into viral reorganization of host chromatin that could have implications for future therapies that target the viral life cycle.
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Affiliation(s)
- Quincy Rosemarie
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bill Sugden
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Galewski PJ, Majumdar R, Lebar MD, Strausbaugh CA, Eujayl IA. Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection. Int J Mol Sci 2023; 24:15013. [PMID: 37834460 PMCID: PMC10573692 DOI: 10.3390/ijms241915013] [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] [Received: 09/01/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the 'R' lines (vs. 'S') included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the 'R' lines (vs. 'S'). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development.
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Affiliation(s)
- Paul J. Galewski
- Northwest Irrigation and Soils Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Kimberly, ID 83341, USA; (P.J.G.); (C.A.S.); (I.A.E.)
- Plant Germplasm Introduction and Testing Research Unit, United States Department of Agriculture—Agricultural Research Service, Pullman, WA 99164, USA
| | - Rajtilak Majumdar
- Northwest Irrigation and Soils Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Kimberly, ID 83341, USA; (P.J.G.); (C.A.S.); (I.A.E.)
| | - Matthew D. Lebar
- Food and Feed Safety Research Unit, Southern Regional Research Center, United States Department of Agriculture—Agricultural Research Service, New Orleans, LA 70179, USA;
| | - Carl A. Strausbaugh
- Northwest Irrigation and Soils Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Kimberly, ID 83341, USA; (P.J.G.); (C.A.S.); (I.A.E.)
| | - Imad A. Eujayl
- Northwest Irrigation and Soils Research Laboratory, United States Department of Agriculture—Agricultural Research Service, Kimberly, ID 83341, USA; (P.J.G.); (C.A.S.); (I.A.E.)
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Ijaz M, Khan F, Zaki HEM, Khan MM, Radwan KSA, Jiang Y, Qian J, Ahmed T, Shahid MS, Luo J, Li B. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091911. [PMID: 37176969 PMCID: PMC10180734 DOI: 10.3390/plants12091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.
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Affiliation(s)
- Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250, Australia
| | - Haitham E M Zaki
- Horticulture Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
- Applied Biotechnology Department, University of Technology and Applied Sciences-Sur, Sur 411, Oman
| | - Muhammad Munem Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khlode S A Radwan
- Plant Pathology Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou 311400, China
| | - Jiahui Qian
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod 123, Oman
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Zhong X, Li J, Yang L, Wu X, Xu H, Hu T, Wang Y, Wang Y, Wang Z. Genome-wide identification and expression analysis of wall-associated kinase (WAK) and WAK-like kinase gene family in response to tomato yellow leaf curl virus infection in Nicotiana benthamiana. BMC PLANT BIOLOGY 2023; 23:146. [PMID: 36927306 PMCID: PMC10021985 DOI: 10.1186/s12870-023-04112-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Tomato yellow leaf curl virus (TYLCV) is a major monopartite virus in the family Geminiviridae and has caused severe yield losses in tomato and tobacco planting areas worldwide. Wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) are a subfamily of the receptor-like kinase family implicated in cell wall signaling and transmitting extracellular signals to the cytoplasm, thereby regulating plant growth and development and resistance to abiotic and biotic stresses. Recently, many studies on WAK/WAKL family genes have been performed in various plants under different stresses; however, identification and functional survey of the WAK/WAKL gene family of Nicotiana benthamiana have not yet been performed, even though its genome has been sequenced for several years. Therefore, in this study, we aimed to identify the WAK/WAKL gene family in N. benthamiana and explore their possible functions in response to TYLCV infection. RESULTS Thirty-eight putative WAK/WAKL genes were identified and named according to their locations in N. benthamiana. Phylogenetic analysis showed that NbWAK/WAKLs are clustered into five groups. The protein motifs and gene structure compositions of NbWAK/WAKLs appear to be highly conserved among the phylogenetic groups. Numerous cis-acting elements involved in phytohormone and/or stress responses were detected in the promoter regions of NbWAK/WAKLs. Moreover, gene expression analysis revealed that most of the NbWAK/WAKLs are expressed in at least one of the examined tissues, suggesting their possible roles in regulating the growth and development of plants. Virus-induced gene silencing and quantitative PCR analyses demonstrated that NbWAK/WAKLs are implicated in regulating the response of N. benthamiana to TYLCV, ten of which were dramatically upregulated in locally or systemically infected leaves of N. benthamiana following TYLCV infection. CONCLUSIONS Our study lays an essential base for the further exploration of the potential functions of NbWAK/WAKLs in plant growth and development and response to viral infections in N. benthamiana.
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Affiliation(s)
- Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Hong Xu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yajun Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
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Rumbaugh AC, Durbin-Johnson B, Padhi E, Lerno L, Cauduro Girardello R, Britton M, Slupsky C, Sudarshana MR, Oberholster A. Investigating Grapevine Red Blotch Virus Infection in Vitis vinifera L. cv. Cabernet Sauvignon Grapes: A Multi-Omics Approach. Int J Mol Sci 2022; 23:ijms232113248. [PMID: 36362035 PMCID: PMC9658657 DOI: 10.3390/ijms232113248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Grapevine red blotch virus (GRBV) is a recently identified virus. Previous research indicates primarily a substantial impact on berry ripening in all varieties studied. The current study analyzed grapes’ primary and secondary metabolism across grapevine genotypes and seasons to reveal both conserved and variable impacts to GRBV infection. Vitis vinifera cv. Cabernet Sauvignon (CS) grapevines grafted on two different rootstocks (110R and 420A) were analyzed in 2016 and 2017. Metabolite profiling revealed a considerable impact on amino acid and malate acid levels, volatile aroma compounds derived from the lipoxygenase pathway, and anthocyanins synthesized in the phenylpropanoid pathway. Conserved transcriptional responses to GRBV showed induction of auxin-mediated pathways and photosynthesis with inhibition of transcription and translation processes mainly at harvest. There was an induction of plant-pathogen interactions at pre-veraison, for all genotypes and seasons, except for CS 110R in 2017. Lastly, differential co-expression analysis revealed a transcriptional shift from metabolic synthesis and energy metabolism to transcription and translation processes associated with a virus-induced gene silencing transcript. This plant-derived defense response transcript was only significantly upregulated at veraison for all genotypes and seasons, suggesting a phenological association with disease expression and plant immune responses.
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Affiliation(s)
- Arran C. Rumbaugh
- United States Department of Agriculture, Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Blythe Durbin-Johnson
- Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Emily Padhi
- Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Larry Lerno
- Department of Viticulture & Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Raul Cauduro Girardello
- Department of Viticulture & Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica Britton
- Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Carolyn Slupsky
- Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mysore R. Sudarshana
- United States Department of Agriculture, Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Anita Oberholster
- Department of Viticulture & Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
- Correspondence:
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Leaf Bacteriome in Sugar Beet Shows Differential Response against Beet curly top virus during Resistant and Susceptible Interactions. Int J Mol Sci 2022; 23:ijms23158073. [PMID: 35897649 PMCID: PMC9331236 DOI: 10.3390/ijms23158073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023] Open
Abstract
Beet curly top virus (BCTV) significantly reduces sugar beet yield in semi-arid production areas. Genetic resistance to BCTV is limited; therefore, identification of additional resistance-associated factors is highly desired. Using 16S rRNA sequencing and BCTV resistant (R) genotypes (KDH13, KDH4-9) along with a susceptible (S) genotype (KDH19-17), we investigated leaf bacteriome changes during BCTV post inoculation (pi). At day 6 (~6-week-old plants), Cyanobacteria were predominant (~90%); whereas, at week 4 (~10-week-old plants) Firmicutes (11–66%), Bacteroidetes (17–26%), and Verrucomicrobia (12–29%) were predominant phyla and genotype dependent. Both Bacteroidetes and Verrucomicrobia, increased post infection only in the R lines. The bacterial genera Brevibacillus increased at 6 dpi, and Akkermansia and Bacteroides at 4 wkpi in the R lines. Linear discriminant analysis effect size (LEfSe) identified potential biomarkers in the R vs. S lines. Functional profiling revealed bacterial enrichment associated with the TCA cycle, polyisoprenoid, and L-methionine biosynthesis pathways only in KDH4-9 at 6 dpi. At 4 wkpi, bacteria associated with tryptophan and palmitate biosynthesis in the R lines, and uridine monophosphate, phosphatidyl glycerol, and phospholipid biosynthesis in the S line, were enriched. Future characterization of bacterial genera with antiviral properties will help establish their use as biocontrol agents/biomarkers against BCTV.
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Koeda S, Onouchi M, Mori N, Pohan NS, Nagano AJ, Kesumawati E. A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2947-2964. [PMID: 34081151 DOI: 10.1007/s00122-021-03870-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/24/2021] [Indexed: 05/25/2023]
Abstract
A begomovirus resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, was identified in pepper (C. annuum) through map-based cloning and functional characterization. Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identification of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identified as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identified on chromosome 5 in an F2 population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identified. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Mika Onouchi
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Nadya Syafira Pohan
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, Banda Aceh, Aceh , 23111, Indonesia
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Positive selection and intrinsic disorder are associated with multifunctional C4(AC4) proteins and geminivirus diversification. Sci Rep 2021; 11:11150. [PMID: 34045539 PMCID: PMC8160170 DOI: 10.1038/s41598-021-90557-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses within the Geminiviridae family cause extensive agricultural losses. Members of four genera of geminiviruses contain a C4 gene (AC4 in geminiviruses with bipartite genomes). C4(AC4) genes are entirely overprinted on the C1(AC1) genes, which encode the replication-associated proteins. The C4(AC4) proteins exhibit diverse functions that may be important for geminivirus diversification. In this study, the influence of natural selection on the evolutionary diversity of 211 C4(AC4) genes relative to the C1(AC1) sequences they overlap was determined from isolates of the Begomovirus and Curtovirus genera. The ratio of nonsynonymous (dN) to synonymous (dS) nucleotide substitutions indicated that C4(AC4) genes are under positive selection, while the overlapped C1(AC1) sequences are under purifying selection. Ninety-one of 200 Begomovirus C4(AC4) genes encode elongated proteins with the extended regions being under neutral selection. C4(AC4) genes from begomoviruses isolated from tomato from native versus exotic regions were under similar levels of positive selection. Analysis of protein structure suggests that C4(AC4) proteins are entirely intrinsically disordered. Our data suggest that non-synonymous mutations and mutations that increase the length of C4(AC4) drive protein diversity that is intrinsically disordered, which could explain C4/AC4 functional variation and contribute to both geminivirus diversification and host jumping.
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Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limón-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR. Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Res 2021; 49:1046-1064. [PMID: 33410911 PMCID: PMC7826260 DOI: 10.1093/nar/gkaa1248] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.
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Affiliation(s)
- Kassidy J Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Lauren A Litzau
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Eric J Aird
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Blake A Everett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Andrew T Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Leland Pornschloegl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Lidia K Limón-Swanson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Robert L Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Karen Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
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