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Improving cassava bacterial blight resistance by editing the epigenome. Nat Commun 2023; 14:85. [PMID: 36604425 PMCID: PMC9816117 DOI: 10.1038/s41467-022-35675-7] [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: 07/06/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.
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2
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Lyons JB, Bredeson JV, Mansfeld BN, Bauchet GJ, Berry J, Boyher A, Mueller LA, Rokhsar DS, Bart RS. Current status and impending progress for cassava structural genomics. PLANT MOLECULAR BIOLOGY 2022; 109:177-191. [PMID: 33604743 PMCID: PMC9162999 DOI: 10.1007/s11103-020-01104-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/08/2020] [Indexed: 05/26/2023]
Abstract
We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.
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Affiliation(s)
- Jessica B. Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
| | - Jessen V. Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Ben N. Mansfeld
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Jeffrey Berry
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | - Adam Boyher
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Daniel S. Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Chan-Zuckerberg BioHub, 499 Illinois, San Francisco, CA 94158 USA
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
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3
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Zhu S, Pan Y, Li K, Fan R, Xiang L, Huang S, Jia S, Niu X, Li C, Chen Y. Complete Genome Sequence of Xanthomonas phaseoli pv. manihotis Strain CHN01, the Causal Agent of Cassava Bacterial Blight. PLANT DISEASE 2022; 106:1039-1041. [PMID: 35259300 DOI: 10.1094/pdis-09-21-2016-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Shousong Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Yueyun Pan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
- Jiaxing Academy of Agricultural Science, Jiaxing 314016, Zhejiang, China
| | - Ke Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Ruochen Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Li Xiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Siyuan Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Suhang Jia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Xiaolei Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Chunxia Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Yinhua Chen
- College of Life Science, Hainan University, Haikou 570228, Hainan, China
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4
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Zhang H, Ye Z, Liu Z, Sun Y, Li X, Wu J, Zhou G, Wan Y. The Cassava NBS-LRR Genes Confer Resistance to Cassava Bacterial Blight. FRONTIERS IN PLANT SCIENCE 2022; 13:790140. [PMID: 35178059 PMCID: PMC8844379 DOI: 10.3389/fpls.2022.790140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/07/2022] [Indexed: 05/25/2023]
Abstract
Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Genes encoding nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are among the most important disease resistance genes in plants that are specifically involved in the response to diverse pathogens. However, the in vivo roles of NBS-LRR remain unclear in cassava (Manihot esculenta). In this study, we isolated four MeLRR genes and assessed their expression under salicylic acid (SA) treatment and Xam inoculation. Four MeLRR genes positively regulate cassava disease general resistance against Xam via virus-induced gene silencing (VIGS) and transient overexpression. During cassava-Xam interaction, MeLRRs positively regulated endogenous SA and reactive oxygen species (ROS) accumulation and pathogenesis-related gene 1 (PR1) transcripts. Additionally, we revealed that MeLRRs positively regulated disease resistance in Arabidopsis. These pathogenic microorganisms include Pseudomonas syringae pv. tomato, Alternaria brassicicola, and Botrytis cinerea. Our findings shed light on the molecular mechanism underlying the regulation of cassava resistance against Xam inoculation.
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Affiliation(s)
- He Zhang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Zi Ye
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhixin Liu
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yu Sun
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xinyu Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Jiao Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Guangzhen Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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5
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Zárate‐Chaves CA, Gómez de la Cruz D, Verdier V, López CE, Bernal A, Szurek B. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae. MOLECULAR PLANT PATHOLOGY 2021; 22:1520-1537. [PMID: 34227737 PMCID: PMC8578842 DOI: 10.1111/mpp.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
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Affiliation(s)
| | | | - Valérie Verdier
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
| | - Camilo E. López
- Manihot Biotec, Departamento de BiologíaUniversidad Nacional de ColombiaBogotáColombia
| | - Adriana Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos AgrícolasDepartamento de Ciencias BásicasUniversidad de los AndesBogotáColombia
| | - Boris Szurek
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
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6
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Zlobin N, Lebedeva M, Monakhova Y, Ustinova V, Taranov V. An ERF121 transcription factor from Brassica oleracea is a target for the conserved TAL-effectors from different Xanthomonas campestris pv. campestris strains. MOLECULAR PLANT PATHOLOGY 2021; 22:618-624. [PMID: 33650275 PMCID: PMC8035633 DOI: 10.1111/mpp.13048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 02/04/2021] [Indexed: 05/19/2023]
Abstract
Transcription activator-like effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of various Xanthomonas bacteria. However, investigation of TALEs from Xanthomonas campestris pv. campestris, which causes black rot disease of crucifers, received little attention. In this study, we used PCR-based amplification followed by SMRT amplicon sequencing to identify TALE genes in several X. campestris pv. campestris strains. Computational prediction in conjunction with quantitative reverse transcription PCR analysis was used to find their targets in the Brassica oleracea genome. Transcription factor ERF121, from the AP2/ERF family, was identified as target gene for the conserved TALEs from multiple X. campestris pv. campestris strains. Several members of this family from diverse plants were previously identified as targets of TALEs from different Xanthomonas species. We propose that TALE-dependent activation of AP2/ERF transcription factors promotes susceptibility to Xanthomonas through the misregulation of plant defence pathways.
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Affiliation(s)
- Nikolay Zlobin
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Marina Lebedeva
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Yuliya Monakhova
- Laboratory of Synthesis and Analysis of Bioorganic CompoundsAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Vera Ustinova
- Pushchino Scientific Center for Biological Research of the Russian Academy of SciencesG.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of SciencesPushchinoRussia
- Syntol LLCMoscowRussia
| | - Vasiliy Taranov
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
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7
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Veley KM, Okwuonu I, Jensen G, Yoder M, Taylor NJ, Meyers BC, Bart RS. Gene tagging via CRISPR-mediated homology-directed repair in cassava. G3 (BETHESDA, MD.) 2021; 11:jkab028. [PMID: 33855431 PMCID: PMC8049417 DOI: 10.1093/g3journal/jkab028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
Research on a few model plant-pathogen systems has benefitted from years of tool and resource development. This is not the case for the vast majority of economically and nutritionally important plants, creating a crop improvement bottleneck. Cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in all regions where cassava (Manihot esculenta Crantz) is grown. Here, we describe the development of cassava that can be used to visualize one of the initial steps of CBB infection in vivo. Using CRISPR-mediated homology-directed repair (HDR), we generated plants containing scarless insertion of GFP at the 3' end of CBB susceptibility (S) gene MeSWEET10a. Activation of MeSWEET10a-GFP by the transcription activator-like (TAL) effector TAL20 was subsequently visualized at transcriptional and translational levels. To our knowledge, this is the first such demonstration of HDR via gene editing in cassava.
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Affiliation(s)
- Kira M Veley
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Ihuoma Okwuonu
- Biotechnology Research Division, National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | - Greg Jensen
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Marisa Yoder
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
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8
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Zhang L, Zhang J, Wei Y, Hu W, Liu G, Zeng H, Shi H. Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:689-701. [PMID: 33095967 PMCID: PMC8051613 DOI: 10.1111/pbi.13495] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/18/2020] [Indexed: 05/07/2023]
Abstract
Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.
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Affiliation(s)
- Lin Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Jiachao Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
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9
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TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale. Microorganisms 2021; 9:microorganisms9020315. [PMID: 33557009 PMCID: PMC7913752 DOI: 10.3390/microorganisms9020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Transcription activator-like effectors (TALEs) play a significant role for pathogenesis in several xanthomonad pathosystems. Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of Cassava Bacterial Blight (CBB), uses TALEs to manipulate host metabolism. Information about Xpm TALEs and their target genes in cassava is scarce, but has been growing in the last few years. We aimed to characterize the TALE diversity in Colombian strains of Xpm and to screen for TALE-targeted gene candidates. We selected eighteen Xpm strains based on neutral genetic diversity at a country scale to depict the TALE diversity among isolates from cassava productive regions. RFLP analysis showed that Xpm strains carry TALomes with a bimodal size distribution, and affinity-based clustering of the sequenced TALEs condensed this variability mainly into five clusters. We report on the identification of 13 novel variants of TALEs in Xpm, as well as a functional variant with 22 repeats that activates the susceptibility gene MeSWEET10a, a previously reported target of TAL20Xam668. Transcriptomics and EBE prediction analyses resulted in the selection of several TALE-targeted candidate genes and two potential cases of functional convergence. This study provides new bases for assessing novel potential TALE targets in the Xpm–cassava interaction, which could be important factors that define the fate of the infection.
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Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front Genet 2020; 11:837. [PMID: 32849823 PMCID: PMC7432306 DOI: 10.3389/fgene.2020.00837] [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: 09/20/2019] [Accepted: 07/10/2020] [Indexed: 01/05/2023] Open
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)+ balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
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Affiliation(s)
- David Botero
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Jonathan Monk
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - María Juliana Rodríguez Cubillos
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | | | - Mariana Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Vivian Bernal-Galeano
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, LIMMA, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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Abstract
Genome editing technologies, such as CRISPR/Cas, have recently become valuable tools for plant reverse genetics as well as crop improvement, including enhancement of disease resistance. Targeting susceptibility (S) genes by genome editing has proven to be a viable strategy for generating resistance to both bacterial and fungal pathogens in various crops. Examples include generating loss-of-function mutations in promoter elements of the SWEET S genes, which are targeted by transcription activator-like effectors secreted by many phytopathogenic Xanthomonas bacteria, as well as in the conserved MLO locus that confers susceptibility to powdery mildew fungal pathogens in many monocots and dicots. In addition to genome editing applications, CRISPR/Cas systems can be used as means of defending plants against viruses via targeting viral genomic DNA or RNA. Genome editing is therefore a highly promising approach that enables engineering disease resistance to various plant pathogens directly in elite cultivar background in a highly precise manner. Unlike conventional crop breeding, genome editing approaches are not relying on lengthy and laborious crosses/back-crosses involving parental and progeny lines and can significantly shorten the breeding timeline. Taking into account the high potential of genome editing technologies for both basic and applied plant science, the recent decision of the European Court of Justice to define transgene-free genetically edited crops as GMOs is, clearly, a backward step for the EU.
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Affiliation(s)
- Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.
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12
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Abstract
Manihot esculenta Crantz (cassava) is a food crop originating from South America grown primarily for its starchy storage roots. Today, cassava is grown in the tropics of South America, Africa, and Asia with an estimated 800 million people relying on it as a staple source of calories. In parts of sub-Saharan Africa, cassava is particularly crucial for food security. Cassava root starch also has use in the pharmaceutical, textile, paper, and biofuel industries. Cassava has seen strong demand since 2000 and production has increased consistently year-over-year, but potential yields are hampered by susceptibility to biotic and abiotic stresses. In particular, bacterial and viral diseases can cause severe yield losses. Of note are cassava bacterial blight (CBB), cassava mosaic disease (CMD), and cassava brown streak disease (CBSD), all of which can cause catastrophic losses for growers. In this article, we provide an overview of the major microbial diseases of cassava, discuss current and potential future efforts to engineer new sources of resistance, and conclude with a discussion of the regulatory hurdles that face biotechnology.
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Affiliation(s)
- Z J Daniel Lin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Rebecca Bart
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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13
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Pérez-Quintero AL, Lamy L, Zarate CA, Cunnac S, Doyle E, Bogdanove A, Szurek B, Dereeper A. daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:471-480. [PMID: 29143556 DOI: 10.1094/mpmi-06-17-0153-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements. By contrasting differential expression data and binding site predictions across different datasets, patterns of TALE diversification or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind, we present daTALbase, a curated relational database that integrates TALE-related data including bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover new candidate S genes as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp.-Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs.
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Affiliation(s)
- Alvaro L Pérez-Quintero
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
- 2 Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Léo Lamy
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Carlos A Zarate
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Sébastien Cunnac
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Erin Doyle
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
| | - Adam Bogdanove
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
- 4 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Boris Szurek
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Alexis Dereeper
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
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14
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Medina CA, Reyes PA, Trujillo CA, Gonzalez JL, Bejarano DA, Montenegro NA, Jacobs JM, Joe A, Restrepo S, Alfano JR, Bernal A. The role of type III effectors from Xanthomonas axonopodis pv. manihotis in virulence and suppression of plant immunity. MOLECULAR PLANT PATHOLOGY 2018; 19:593-606. [PMID: 28218447 PMCID: PMC6638086 DOI: 10.1111/mpp.12545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 05/29/2023]
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) using heterologous systems. AvrBs2, XopR and XopAO1 are capable of suppressing PTI. ETI suppression activity was only detected for XopE4 and XopAO1. These results demonstrate the overall importance and diversity in functions of major virulence effectors AvrBs2 and XopAO1 in Xam during cassava infection.
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Affiliation(s)
- Cesar Augusto Medina
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Paola Andrea Reyes
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Cesar Augusto Trujillo
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Juan Luis Gonzalez
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - David Alejandro Bejarano
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Nathaly Andrea Montenegro
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - Jonathan M. Jacobs
- Institut de Recherche pour le De´veloppement (IRD), CiradUniversite´ Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394MontpellierFrance
| | - Anna Joe
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588‐0660USA
- Department of Plant PathologyUniversity of NebraskaLincolnNE68588‐0722USA
- Present address:
Department of Plant Pathology and the Genome CenterUniversity of California, Davis, CA 95616, USA, and Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Silvia Restrepo
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
| | - James R. Alfano
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588‐0660USA
- Department of Plant PathologyUniversity of NebraskaLincolnNE68588‐0722USA
| | - Adriana Bernal
- Universidad de los Andes, Laboratorio de Micología y Fitopatología de la Universidad de los Andes111711 BogotáColombia
- Present address:
Novozymes, Inc., DavisCA95618USA
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15
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McCallum EJ, Anjanappa RB, Gruissem W. Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta). CURRENT OPINION IN PLANT BIOLOGY 2017; 38:50-58. [PMID: 28477536 DOI: 10.1016/j.pbi.2017.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
Cassava is an important staple food crop for millions of people in tropical regions across Africa, South America and Asia. Viral, bacterial and fungal diseases impact cassava yield in all three regions. The viruses causing cassava mosaic disease and cassava brown streak disease have been particularly devastating to cassava production in Africa. Improved farming practices and disease monitoring can reduce the impact of cassava diseases in the field. The availability of disease resistant cassava varieties developed through breeding or genetic engineering is key to tackling disease incidence and severity.
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Affiliation(s)
- Emily J McCallum
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Ravi B Anjanappa
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092 Zurich, Switzerland.
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16
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Schwartz AR, Morbitzer R, Lahaye T, Staskawicz BJ. TALE-induced bHLH transcription factors that activate a pectate lyase contribute to water soaking in bacterial spot of tomato. Proc Natl Acad Sci U S A 2017; 114:E897-E903. [PMID: 28100489 PMCID: PMC5293091 DOI: 10.1073/pnas.1620407114] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AvrHah1 [avirulence (avr) gene homologous to avrBs3 and hax2, no. 1] is a transcription activator-like (TAL) effector (TALE) in Xanthomonas gardneri that induces water-soaked disease lesions on fruits and leaves during bacterial spot of tomato. We observe that water from outside the leaf is drawn into the apoplast in X. gardneri-infected, but not X. gardneriΔavrHah1 (XgΔavrHah1)-infected, plants, conferring a dark, water-soaked appearance. The pull of water can facilitate entry of additional bacterial cells into the apoplast. Comparing the transcriptomes of tomato infected with X. gardneri vs. XgΔavrHah1 revealed the differential up-regulation of two basic helix-loop-helix (bHLH) transcription factors with predicted effector binding elements (EBEs) for AvrHah1. We mined our RNA-sequencing data for differentially up-regulated genes that could be direct targets of the bHLH transcription factors and therefore indirect targets of AvrHah1. We show that two pectin modification genes, a pectate lyase and pectinesterase, are targets of both bHLH transcription factors. Designer TALEs (dTALEs) for the bHLH transcription factors and the pectate lyase, but not for the pectinesterase, complement water soaking when delivered by XgΔavrHah1 By perturbing transcriptional networks and/or modifying the plant cell wall, AvrHah1 may promote water uptake to enhance tissue damage and eventual bacterial egression from the apoplast to the leaf surface. Understanding how disease symptoms develop may be a useful tool for improving the tolerance of crops from damaging disease lesions.
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Affiliation(s)
- Allison R Schwartz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Robert Morbitzer
- Department of General Genetics, Center of Plant Molecular Biology, University of Tübingen, D-72076 Tubingen, Germany
| | - Thomas Lahaye
- Department of General Genetics, Center of Plant Molecular Biology, University of Tübingen, D-72076 Tubingen, Germany
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120;
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Díaz Tatis P, Zárate CA, Bernal Giraldo A, López Carrascal C. Infección de callo embriogénico friable de yuca con Xanthomonas axonopodis pv. manihotis (Xam). REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2016. [DOI: 10.15446/rev.colomb.biote.v18n2.61523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Las nuevas tecnologías para la edición de genomas, como los TALEN y el sistema CRISPR/Cas9, representan una gran oportunidad para mejorar características deseables en diferentes organismos. Los TALEN son el resultado del acoplamiento de nucleasas a los TALE (Transcription Activator-Like Effectors), los cuales son efectores naturales de gran importancia en la patogénesis de las especies de Xanthomonas. Xanthomonas axonopodis pv. manihotis (Xam) es el agente causal del añublo bacteriano de la yuca, quien durante el proceso patogénico es capaz de translocar sus efectores a la célula vegetal mediante el sistema de secreción tipo tres (SSTT). Actualmente no hay protocolos estándar para la edición de genomas en yuca. En este estudio se exploró la posibilidad de translocar efectores sobre callo embriogénico friable (CEF) a través de la inoculación con Xam, con el fin de determinar el potencial de este patógeno como sistema de entrega de TALEN. El CEF de dos variedades de yuca susceptibles (COL2215 y cv. 60444) se cocultivaron con la cepa Xam668 a diferentes tiempos. Posteriormente, se evaluó la expresión de marcadores correspondientes a los genes blanco conocidos para los TALE presentes en esta cepa bacteriana. Aunque no se logró demostrar la translocación de los mismos en el tejido embriogénico, sí se lograron establecer condiciones adecuadas de cocultivo con Xam y el efecto que la infección bacteriana tiene sobre la regeneración de embriones a partir de este tejido. Palabras clave: cultivo de tejidos vegetales, edición de genomas, sistema de secreción tipo tres, efectores TALE, transformación.
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