1
|
Toth R, Ilic AM, Huettel B, Duduk B, Kube M. Divergence within the Taxon ' Candidatus Phytoplasma asteris' Confirmed by Comparative Genome Analysis of Carrot Strains. Microorganisms 2024; 12:1016. [PMID: 38792845 PMCID: PMC11123874 DOI: 10.3390/microorganisms12051016] [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: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon 'Candidatus Phytoplasma asteris' were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of 'Ca. P. asteris' and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.
Collapse
Affiliation(s)
- Rafael Toth
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | - Anna-Marie Ilic
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | | | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, 11080 Belgrade, Serbia;
| | - Michael Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| |
Collapse
|
2
|
Liu CY, Cheng HP, Lin CP, Liao YT, Ko TP, Lin SJ, Lin SS, Wang HC. Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein. IUCRJ 2024; 11:384-394. [PMID: 38656311 PMCID: PMC11067747 DOI: 10.1107/s2052252524003075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP-F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches' broom phytoplasma-infected Catharanthus roseus. The association between IMP and PHYL1 is substantiated through in vivo immunoprecipitation, an in vitro cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.
Collapse
Affiliation(s)
- Chang-Yi Liu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Han-Pin Cheng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chan-Pin Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shin-Jen Lin
- International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Center of Biotechnology, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
3
|
Xue C, Zhang Y, Li H, Liu Z, Gao W, Liu M, Wang H, Liu P, Zhao J. The genome of Candidatus phytoplasma ziziphi provides insights into their biological characteristics. BMC PLANT BIOLOGY 2023; 23:251. [PMID: 37173622 PMCID: PMC10176825 DOI: 10.1186/s12870-023-04243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Phytoplasmas are obligate cell wall-less prokaryotic bacteria that primarily multiply in plant phloem tissue. Jujube witches' broom (JWB) associated with phytoplasma is a destructive disease of jujube (Ziziphus jujuba Mill.). Here we report the complete 'Candidatus Phytoplasma ziziphi' chromosome of strain Hebei-2018, which is a circular genome of 764,108-base pairs with 735 predicted CDS. Notably, extra 19,825 bp (from 621,995 to 641,819 bp) compared to the previously reported one complements the genes involved in glycolysis, such as pdhA, pdhB, pdhC, pdhD, ackA, pduL and LDH. The synonymous codon usage bias (CUB) patterns by using comparative genomics analysis among the 9 phytoplasmas were similar for most codons. The ENc-GC3s analysis among the 9 phytoplasmas showed a greater effect under the selection on the CUBs of phytoplasmas genes than mutation and other factors. The genome exhibited a strongly reduced ability in metabolic synthesis, while the genes encoding transporter systems were well developed. The genes involved in sec-dependent protein translocation system were also identified.The expressions of nine FtsHs encoding membrane associated ATP-dependent Zn proteases and Mn-SodA with redox capacity in the Ca. P. ziziphi was positively correlated with the phytoplasma concentration. Taken together, the genome will not only expand the number of phytoplasma species and provide some new information about Ca. P. ziziphi, but also contribute to exploring its pathogenic mechanism.
Collapse
Affiliation(s)
- Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Hongtai Li
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Ping Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China.
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China.
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China.
| |
Collapse
|
4
|
Pang LJ, Adeel M, Shakoor N, Guo KR, Ma DF, Ahmad MA, Lu GQ, Zhao MH, Li SE, Rui YK. Engineered Nanomaterials Suppress the Soft Rot Disease ( Rhizopus stolonifer) and Slow Down the Loss of Nutrient in Sweet Potato. NANOMATERIALS 2021; 11:nano11102572. [PMID: 34685013 PMCID: PMC8537040 DOI: 10.3390/nano11102572] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022]
Abstract
About 45% of the world’s fruit and vegetables are wasted, resulting in postharvest losses and contributing to economic losses ranging from $10 billion to $100 billion worldwide. Soft rot disease caused by Rhizopus stolonifer leads to postharvest storage losses of sweet potatoes. Nanoscience stands as a new tool in our arsenal against these mounting challenges that will restrict efforts to achieve and maintain global food security. In this study, three nanomaterials (NMs) namely C60, CuO, and TiO2 were evaluated for their potential application in the restriction of Rhizopus soft rot disease in two cultivars of sweet potato (Y25, J26). CuO NM exhibited a better antifungal effect than C60 and TiO2 NMs. The contents of three important hormones, indolepropionic acid (IPA), gibberellic acid 3 (GA-3), and indole-3-acetic acid (IAA) in the infected J26 sweet potato treated with 50 mg/L CuO NM were significantly higher than those of the control by 14.5%, 10.8%, and 24.1%. CuO and C60 NMs promoted antioxidants in both cultivars of sweet potato. Overall, CuO NM at 50 mg/L exhibited the best antifungal properties, followed by TiO2 NM and C60 NM, and these results were further confirmed through scanning electron microscope (SEM) analysis. The use of CuO NMs as an antifungal agent in the prevention of Rhizopus stolonifer infections in sweet potatoes could greatly reduce postharvest storage and delivery losses.
Collapse
Affiliation(s)
- Lin-Jiang Pang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China; (L.-J.P.); (M.-H.Z.); (S.-E.L.)
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Muhammed Adeel
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; (M.A.); (N.S.); (K.-R.G.); (Y.-K.R.)
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University Zhuhai Subcampus, 18 Jinfeng Road, Tangjiawan, Zhuhai 519085, China
| | - Noman Shakoor
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; (M.A.); (N.S.); (K.-R.G.); (Y.-K.R.)
| | - Ke-Rui Guo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; (M.A.); (N.S.); (K.-R.G.); (Y.-K.R.)
- Laboratory of Soil Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Dai-Fu Ma
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
- Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture and Rural Affairs, Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou 221121, China
- Correspondence: or (D.-F.M.); (G.-Q.L.)
| | - Muhammad Arslan Ahmad
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Guo-Quan Lu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China; (L.-J.P.); (M.-H.Z.); (S.-E.L.)
- Correspondence: or (D.-F.M.); (G.-Q.L.)
| | - Mei-Hui Zhao
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China; (L.-J.P.); (M.-H.Z.); (S.-E.L.)
| | - Sheng-E Li
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China; (L.-J.P.); (M.-H.Z.); (S.-E.L.)
| | - Yu-Kui Rui
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; (M.A.); (N.S.); (K.-R.G.); (Y.-K.R.)
| |
Collapse
|
5
|
Rubio-Melgarejo A, Balois-Morales R, Ochoa-Jiménez VA, Casas-Junco PP, Jiménez-Zurita JO, Bautista-Rosales PU, Berumen-Varela G. Differential Responses of Antioxidative System during the Interaction of Soursop Fruits ( Annona muricata L.) and Nectria haematococca at Postharvest Storage. PLANTS (BASEL, SWITZERLAND) 2021; 10:1432. [PMID: 34371635 PMCID: PMC8309373 DOI: 10.3390/plants10071432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Soursop fruit (Annona muricata L.) production is diminished by the attack of pathogens such as Nectria haematococca. However, the fruit-pathogen interaction at the biochemical and molecular levels is still unknown. The objective of this study was to analyze the response of the soursop fruit to the presence of N. haematococca during postharvest storage. Soursop fruits were inoculated with the pathogen and total phenolic compounds, antioxidant capacity by Ferric reducing/antioxidant power (FRAP), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS•+), and 2,2'-diphenyl-1-picrylhydrazyl radical (DPPH•), as well as enzymatic activity and transcript levels of polyphenol oxidase (PPO) and superoxide dismutase (SOD), were evaluated at 1, 3, and 5 days of storage. The noninoculated fruits were the controls of the experiment. The highest total phenol content was recorded on day one in the inoculated fruits. FRAP, ABTS, and DPPH activity presented the highest values on day three in the control fruits. Inoculated fruits recorded the highest PPO activity on day five and a five-fold induction in the PPO transcript on day three. SOD activity showed a decrease during the days of storage and 10-fold induction of SOD transcript on day three in the inoculated fruits. Principal component analysis showed that total phenols were the variable that contributed the most to the observed variations. Furthermore, a positive correlation between total phenols and SOD activity, PPO expression, and SOD expression, as well as between DPPH and FRAP, was recorded. The results showed a differential response in antioxidant capacity, enzymatic activity, and gene expression during the interaction of soursop fruits-N. haematococca at postharvest storage.
Collapse
Affiliation(s)
- Alejandro Rubio-Melgarejo
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Carretera Tepic-Compostela km. 9, Xalisco C.P. 63780, Nayarit, Mexico; (A.R.-M.); (R.B.-M.)
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - Rosendo Balois-Morales
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Carretera Tepic-Compostela km. 9, Xalisco C.P. 63780, Nayarit, Mexico; (A.R.-M.); (R.B.-M.)
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - Verónica Alhelí Ochoa-Jiménez
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - Paloma Patricia Casas-Junco
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - José Orlando Jiménez-Zurita
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - Pedro Ulises Bautista-Rosales
- Programa de Doctorado en Ciencias Biológico Agropecuarias, Universidad Autónoma de Nayarit, Carretera Tepic-Compostela km. 9, Xalisco C.P. 63780, Nayarit, Mexico; (A.R.-M.); (R.B.-M.)
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| | - Guillermo Berumen-Varela
- Unidad de Tecnología de Alimentos-Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura S/N, Colonia Centro, Tepic C.P. 63000, Nayarit, Mexico; (V.A.O.-J.); (P.P.C.-J.); (J.O.J.-Z.)
| |
Collapse
|
6
|
Xue C, Liu Z, Wang L, Li H, Gao W, Liu M, Zhao Z, Zhao J. The antioxidant defense system in Chinese jujube is triggered to cope with phytoplasma invasion. TREE PHYSIOLOGY 2020; 40:1437-1449. [PMID: 32483619 DOI: 10.1093/treephys/tpaa067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 04/18/2020] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
Reactive oxygen species (ROS) in plants increase dramatically under pathogen attack, and the antioxidant defense system is then triggered to protect the plant against the ROS. Jujube witches' broom disease (JWB), caused by phytoplasma, is a destructive disease of Chinese jujube. The results of fluorescence-based measurement revealed that ROS were overproduced within jujube leaves after phytoplasma invasion. Furthermore, analysis based on mRNA and metabolite levels revealed that ascorbic acid (AsA) metabolism was strengthened under phytoplasma stress. The high expression of genes involved in the AsA/glutathione (GSH) cycle and thioredoxin (Trx) synthesis in diseased leaves indicated that GSH and Trx actively respond to phytoplasma infection. Moreover, higher activities of enzymatic antioxidants and the upregulated expression of related genes were confirmed in diseased tissues. Both nonenzymatic and enzymatic antioxidants in the host jujube were strongly stimulated to cope with ROS caused by phytoplasma stress. Compared with that in the susceptible variety, the activities of glutathione S-transferase and peroxidase in the resistant variety at the earlier infection stage were higher, indicating that enzymes might be involved in the resistance to phytoplasma. These results highlight the roles of the antioxidant defense system of the host plant in the tolerance to phytoplasma invasion.
Collapse
Affiliation(s)
- Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071000, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China
| | - Hongtai Li
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071000, China
| | - Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Zhihui Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071000, China
| |
Collapse
|
7
|
NAMBA S. Molecular and biological properties of phytoplasmas. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:401-418. [PMID: 31406061 PMCID: PMC6766451 DOI: 10.2183/pjab.95.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Phytoplasmas, a large group of plant-pathogenic, phloem-inhabiting bacteria were discovered by Japanese scientists in 1967. They are transmitted from plant to plant by phloem-feeding insect hosts and cause a variety of symptoms and considerable damage in more than 1,000 plant species. In the first quarter century following the discovery of phytoplasmas, their tiny cell size and the difficulty in culturing them hampered their biological classification and restricted research to ecological studies such as detection by electron microscopy and identification of insect vectors. In the 1990s, however, tremendous advances in molecular biology and related technologies encouraged investigation of phytoplasmas at the molecular level. In the last quarter century, molecular biology has revealed important properties of phytoplasmas. This review summarizes the history and current status of phytoplasma research, focusing on their discovery, molecular classification, diagnosis of phytoplasma diseases, reductive evolution of their genomes, characteristic features of their plasmids, molecular mechanisms of insect transmission, virulence factors, and chemotherapy.
Collapse
Affiliation(s)
- Shigetou NAMBA
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Correspondence should be addressed: S. Namba, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan (e-mail: )
| |
Collapse
|
8
|
Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease. BMC Genomics 2018; 19:689. [PMID: 30231900 PMCID: PMC6148798 DOI: 10.1186/s12864-018-5075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement. RESULTS The complete genome sequence of JWB phytoplasma (jwb-nky) was determined, which consisting of one circular chromosome of 750,803 bp with a GC content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31 tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA repeats were identified. Based on PHIbaes analysis, a large number of genes were genome-specific and approximately 13% of JWB phytoplasma genes were predicted to be associated with virulence. Although transporters for maltose, dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine were identified, KEGG pathway analysis revealed the reduced metabolic capabilities of JWB phytoplasma. Comparative genome analyses between JWB phytoplasma and other phytoplasmas shows the occurrence of large-scale gene rearrangements. The low synteny with other phytoplasmas indicated that the expansion of multiple gene families/duplication probably occurred separately after differentiation. CONCLUSIONS In this study, the complete genome sequence of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for the first time and a number of species-specific genes were identified in the genome. The study enhanced our understandings about genomic basis and the pathogenicity mechanism of this pathogen, which will aid in the development of improved strategies for efficient management of JWB diseases.
Collapse
|
9
|
Abbà S, Galetto L, Carle P, Carrère S, Delledonne M, Foissac X, Palmano S, Veratti F, Marzachì C. RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics 2014; 15:1088. [PMID: 25495145 PMCID: PMC4299374 DOI: 10.1186/1471-2164-15-1088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insecticides. Further studies of the pathogen, the vector and the mechanisms of phytoplasma-host interactions could improve our understanding of the disease. In this work, RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting field-grown Vitis vinifera leaves. RESULTS With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 215 annotated genes, and identified 10 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 draft genome. Furthermore, we improved the annotation of 44 genes with the addition of 5'/3' untranslated regions. Functional classification revealed that the most expressed genes were either related to translation and protein biosynthesis or hypothetical proteins with unknown function. Some of these hypothetical proteins were predicted to be secreted, so they could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies. CONCLUSIONS The RNA-Seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine infection. Our results provided new insights into the transcriptional organization and gene structure of FD. This may represent the starting point for the application of high-throughput sequencing technologies to study differential expression in FD and in other phytoplasmas with an unprecedented resolution.
Collapse
Affiliation(s)
- Simona Abbà
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Luciana Galetto
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Patricia Carle
- />INRA, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
- />Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
| | - Sébastien Carrère
- />INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326 France
- />CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326 France
| | - Massimo Delledonne
- />Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, I-37134 Verona, Italy
| | - Xavier Foissac
- />INRA, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
- />Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
| | - Sabrina Palmano
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Flavio Veratti
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Cristina Marzachì
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| |
Collapse
|
10
|
Genomic insights into processes driving the infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp. EUKARYOTIC CELL 2014; 13:1439-49. [PMID: 25239978 DOI: 10.1128/ec.00139-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The regulatory circuits during infection of dinoflagellates by their parasites are largely unknown on the molecular level. Here we provide molecular insights into these infection dynamics. Alexandrium tamarense is one of the most prominent harmful algal bloom dinoflagellates. Its pathogen, the dinoflagellate parasitoid Amoebophrya sp., has been observed to infect and control the blooms of this species. We generated a data set of transcripts from three time points (0, 6, and 96 h) during the infection of this parasite-host system. Assembly of all transcript data from the parasitoid (>900,000 reads/313 Mbp with 454/Roche next-generation sequencing [NGS]) yielded 14,455 contigs, to which we mapped the raw transcript reads of each time point of the infection cycle. We show that particular surface lectins are expressed at the beginning of the infection cycle which likely mediate the attachment to the host cell. In a later phase, signal transduction-related genes together with transmembrane transport and cytoskeleton proteins point to a high integration of processes involved in host recognition, adhesion, and invasion. At the final maturation stage, cell division- and proliferation-related genes were highly expressed, reflecting the fast cell growth and nuclear division of the parasitoid. Our molecular insights into dinoflagellate parasitoid interactions point to general mechanisms also known from other eukaryotic parasites, especially from the Alveolata. These similarities indicate the presence of fundamental processes of parasitoid infection that have remained stable throughout evolution within different phyla.
Collapse
|
11
|
Gu Y, Shen X, Zhou D, Wang Z, Zhang N, Shan Z, Jin L, Lei L. Selection and expression profiles of reference genes in mouse preimplantation embryos of different ploidies at various developmental stages. PLoS One 2014; 9:e98956. [PMID: 24927500 PMCID: PMC4057156 DOI: 10.1371/journal.pone.0098956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022] Open
Abstract
Real-time reverse transcription quantitative polymerase chain reaction (qPCR) has become the most frequently used system for studies of gene expression. Manystudies have provided reliable evidence that the transcription levels of reference genes are not constant at different developmental stages and in different experimental conditions. However, suitable reference genes which are stably expressed in polyploid preimplantation embryos of different developmental stages have not yet been identified. Therefore, it is critical to verify candidate reference genes to analyze gene expression accurately in both diploid and polyploid embryos. We examined the expression levels of 12 candidate reference genes in preimplantation embryos of four different ploidies at six developmental stages. Stability analysis of the reference genes was performed by four independent software programs, and the stability of three genes was evaluated by comparison with the Oct4 expression level during preimplantation development in diploid embryos. The expression levels of most genes in the polyploid embryos were higher than that in the diploid embryos, but the increasing degree were disproportionate with the ploidies. There were no significant difference in reference gene expressions among embryos of different ploidies when they reached the morula stage, and the expression level remained flat until the blastocyst stage. Ubc, Ppia, and Pgk1 were the three most stable reference genes in diploid and polyploid embryos.
Collapse
Affiliation(s)
- Yanli Gu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xinghui Shen
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Dongjie Zhou
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhendong Wang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Na Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhiyan Shan
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lianhong Jin
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LL); (LJ)
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LL); (LJ)
| |
Collapse
|
12
|
Chen W, Li Y, Wang Q, Wang N, Wu Y. Comparative genome analysis of wheat blue dwarf phytoplasma, an obligate pathogen that causes wheat blue dwarf disease in China. PLoS One 2014; 9:e96436. [PMID: 24798075 PMCID: PMC4010473 DOI: 10.1371/journal.pone.0096436] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, de novo assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on the pathogenic mechanisms of WBD phytoplasma and will also provide a perspective about the genome sequencing of other phytoplasmas and obligate organisms.
Collapse
Affiliation(s)
- Wang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
13
|
Oshima K, Maejima K, Namba S. Genomic and evolutionary aspects of phytoplasmas. Front Microbiol 2013; 4:230. [PMID: 23966988 PMCID: PMC3743221 DOI: 10.3389/fmicb.2013.00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/29/2013] [Indexed: 11/20/2022] Open
Abstract
Parasitic bacteria that infect eukaryotes, such as animals and plants, often have reduced genomes, having lost important metabolic genes as a result of their host-dependent life cycles. Genomic sequencing of these bacteria has revealed their survival strategies and adaptations to parasitism. Phytoplasmas (class Mollicutes, genus ‘Candidatus Phytoplasma’) are intracellular bacterial pathogens of plants and insects and cause devastating yield losses in diverse low- and high-value crops worldwide. The complete genomic sequences of four Candidatus Phytoplasma species have been reported. The genomes encode even fewer metabolic functions than other bacterial genomes do, which may be the result of reductive evolution as a consequence of their life as an intracellular parasite. This review summarizes current knowledge of the diversity and common features of phytoplasma genomes, including the factors responsible for pathogenicity.
Collapse
Affiliation(s)
- Kenro Oshima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Yayoi, Bunkyo-ku, Tokyo, Japan
| | | | | |
Collapse
|
14
|
Park SJ, Kim YH, Lee Y, Kim KM, Kim HS, Lee SR, Kim SU, Kim SH, Kim JS, Jeong KJ, Lee KM, Huh JW, Chang KT. Selection of appropriate reference genes for RT-qPCR analysis in a streptozotocin-induced Alzheimer's disease model of cynomolgus monkeys (Macaca fascicularis). PLoS One 2013; 8:e56034. [PMID: 23457495 PMCID: PMC3573079 DOI: 10.1371/journal.pone.0056034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/04/2013] [Indexed: 12/13/2022] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) has been widely used to quantify relative gene expression because of the specificity, sensitivity, and accuracy of this technique. In order to obtain reliable gene expression data from RT-qPCR experiments, it is important to utilize optimal reference genes for the normalization of target gene expression under varied experimental conditions. Previously, we developed and validated a novel icv-STZ cynomolgus monkey model for Alzheimer's disease (AD) research. However, in order to enhance the reliability of this disease model, appropriate reference genes must be selected to allow meaningful analysis of the gene expression levels in the icv-STZ cynomolgus monkey brain. In this study, we assessed the expression stability of 9 candidate reference genes in 2 matched-pair brain samples (5 regions) of control cynomolgus monkeys and those who had received intracerebroventricular injection of streptozotocin (icv-STZ). Three well-known analytical programs geNorm, NormFinder, and BestKeeper were used to choose the suitable reference genes from the total sample group, control group, and icv-STZ group. Combination analysis of the 3 different programs clearly indicated that the ideal reference genes are RPS19 and YWHAZ in the total sample group, GAPDH and RPS19 in the control group, and ACTB and GAPDH in the icv-STZ group. Additionally, we validated the normalization accuracy of the most appropriate reference genes (RPS19 and YWHAZ) by comparison with the least stable gene (TBP) using quantification of the APP and MAPT genes in the total sample group. To the best of our knowledge, this research is the first study to identify and validate the appropriate reference genes in cynomolgus monkey brains. These findings provide useful information for future studies involving the expression of target genes in the cynomolgus monkey.
Collapse
Affiliation(s)
- Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- Department of Rehabilitation Science in Interdisciplinary PhD Program, Graduate School of Inje University, Gimhae, Gyeongnam, Republic of Korea
| | - Kyoung-Min Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
| | - Sang-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
| | - Kyoung-Min Lee
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- * E-mail: (JWH); (KTC)
| | - Kyu-Tae Chang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk, Republic of Korea
- University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
- * E-mail: (JWH); (KTC)
| |
Collapse
|