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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024; 114:1433-1446. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Roman-Reyna V, Heiden N, Butchacas J, Toth H, Cooperstone JL, Jacobs JM. The timing of bacterial mesophyll infection shapes the leaf chemical landscape. Microbiol Spectr 2024; 12:e0413823. [PMID: 38426767 PMCID: PMC10986523 DOI: 10.1128/spectrum.04138-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Chemistry in eukaryotic intercellular spaces is shaped by both hosts and symbiotic microorganisms such as bacteria. Pathogenic microorganisms like barley-associated Xanthomonas translucens (Xt) swiftly overtake the inner leaf tissue becoming the dominant microbial community member during disease development. The dynamic metabolic changes due to Xt pathogenesis in the mesophyll spaces remain unknown. Genomic group I of Xt consists of two barley-infecting lineages: pathovar translucens (Xtt) and pathovar undulosa (Xtu). Xtu and Xtt, although genomically distinct, cause similar water-soaked lesions. To define the metabolic signals associated with inner leaf colonization, we used untargeted metabolomics to characterize Xtu and Xtt metabolism signatures associated with mesophyll growth. We found that mesophyll apoplast fluid from infected tissue yielded a distinct metabolic profile and shift from catabolic to anabolic processes over time compared to water-infiltrated control. The pathways with the most differentially expressed metabolites by time were glycolysis, tricarboxylic acid cycle, sucrose metabolism, pentose interconversion, amino acids, galactose, and purine metabolism. Hierarchical clustering and principal component analysis showed that metabolic changes were more affected by the time point rather than the individual colonization of the inner leaves by Xtt compared to Xtu. Overall, in this study, we identified metabolic pathways that explain carbon and nitrogen usage during host-bacterial interactions over time for mesophyll tissue colonization. This foundational research provides initial insights into shared metabolic strategies of inner leaf colonization niche occupation by related but phylogenetically distinct phyllosphere bacteria. IMPORTANCE The phyllosphere is a habitat for microorganisms including pathogenic bacteria. Metabolic shifts in the inner leaf spaces for most plant-microbe interactions are unknown, especially for Xanthomonas species in understudied plants like barley (Hordeum vulgare). Xanthomonas translucens pv. translucens (Xtt) and Xanthomonas translucens pv. undulosa (Xtu) are phylogenomically distinct, but both colonize barley leaves for pathogenesis. In this study, we used untargeted metabolomics to shed light on Xtu and Xtt metabolic signatures. Our findings revealed a dynamic metabolic landscape that changes over time, rather than exhibiting a pattern associated with individual pathovars. These results provide initial insights into the metabolic mechanisms of X. translucens inner leaf pathogenesis.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jules Butchacas
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jessica L. Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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Gutierrez-Castillo DE, Barrett E, Roberts R. A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates. Microb Genom 2024; 10:001177. [PMID: 38189214 PMCID: PMC10868612 DOI: 10.1099/mgen.0.001177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens (Xtt) and CO237 belongs to pathovar undulosa (Xtu). We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently emerged isolates.
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Affiliation(s)
| | - Emma Barrett
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Robyn Roberts
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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Bonfim IM, Paixão DA, Andrade MDO, Junior JM, Persinoti GF, de Giuseppe PO, Murakami MT. Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens. Microbiol Spectr 2023; 11:e0228023. [PMID: 37855631 PMCID: PMC10714752 DOI: 10.1128/spectrum.02280-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/05/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Pathogenic Xanthomonas bacteria can affect a variety of economically relevant crops causing losses in productivity, limiting commercialization and requiring phytosanitary measures. These plant pathogens exhibit high level of host and tissue specificity through multiple molecular strategies including several secretion systems, effector proteins, and a broad repertoire of carbohydrate-active enzymes (CAZymes). Many of these CAZymes act on the plant cell wall and storage carbohydrates, such as cellulose and starch, releasing products used as nutrients and modulators of transcriptional responses to support host colonization by mechanisms yet poorly understood. Here, we reveal that structural and storage β-glucans from the plant cell function as spatial markers, providing distinct chemical stimuli that modulate the transition between higher and lower motility states in Xanthomonas citri, a key virulence trait for many bacterial pathogens.
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Affiliation(s)
- Isabela Mendes Bonfim
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Molecular and Morphofunctional Biology, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Douglas Alvarez Paixão
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Joaquim Martins Junior
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Ledman KE, Roman-Reyna V, Curland RD, Heiden N, Jacobs JM, Dill-Macky R. Comparative Genomics of Xanthomonas translucens pv. undulosa Strains Isolated from Weedy Grasses and Cultivated Wild Rice. PHYTOPATHOLOGY 2023; 113:2083-2090. [PMID: 37260072 DOI: 10.1094/phyto-09-22-0352-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial leaf streak (BLS) of wheat (Triticum aestivum), caused by Xanthomonas translucens pv. undulosa, is a disease of major concern in the Northern Great Plains. The host range for X. translucens pv. undulosa is relatively broad, including several small grains and perennial grasses. In Minnesota, X. translucens pv. undulosa was isolated from weedy grasses in and around wheat fields that exhibited BLS symptoms and from cultivated wild rice (Zizania palustris) with symptomatic leaf tissue. Currently, no genomic resources are available for X. translucens pv. undulosa strains isolated from non-wheat hosts. In this study, we sequenced and assembled the complete genomes of five strains isolated from weedy grass hosts, foxtail barley (Hordeum jubatum), green foxtail (Setaria viridis), and wild oat (Avena fatua), and from cultivated wild rice and wheat. These five genomes were compared with the publicly available genomes of seven X. translucens pv. undulosa strains originating from wheat and one genome of an X. translucens pv. secalis strain originating from rye (Secale cereale). Global alignments of the genomes revealed little variation in genomic structures. Average nucleotide identity-based phylogeny and life identification numbers revealed that the strains share ≥99.25% identity. We noted differences in the presence of Type III secreted effectors, including transcription activator-like effectors. Despite differences between strains, we did not identify unique features distinguishing strains isolated from wheat and non-wheat hosts. This study contributes to the availability of genomic data for X. translucens pv. undulosa from non-wheat hosts, thus increasing our understanding of the diversity within the pathogen population.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Veronica Roman-Reyna
- Plant Pathology Department, The Ohio State University, Columbus, OH
- Infectious Diseases Institute, The Ohio State University, Columbus, OH
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Nathaniel Heiden
- Plant Pathology Department, The Ohio State University, Columbus, OH
- Infectious Diseases Institute, The Ohio State University, Columbus, OH
| | - Jonathan M Jacobs
- Plant Pathology Department, The Ohio State University, Columbus, OH
- Infectious Diseases Institute, The Ohio State University, Columbus, OH
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN
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Ledman KE, Osdaghi E, Curland RD, Liu Z, Dill-Macky R. Epidemiology, Host Resistance, and Genomics of the Small Grain Cereals Pathogen Xanthomonas translucens: New Advances and Future Prospects. PHYTOPATHOLOGY 2023; 113:2037-2047. [PMID: 36996338 DOI: 10.1094/phyto-11-22-0403-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial leaf streak (BLS) primarily affects barley and wheat and is mainly caused by the pathogens Xanthomonas translucens pv. translucens and X. translucens pv. undulosa, respectively. BLS is distributed globally and poses a risk to food security and the supply of malting barley. X. translucens pv. cerealis can infect both wheat and barley but is rarely isolated from these hosts in natural infections. These pathogens have undergone a confusing taxonomic history, and the biology has been poorly understood, making it difficult to develop effective control measures. Recent advancements in the ability and accessibility to sequence bacterial genomes have shed light on phylogenetic relationships between strains and identified genes that may play a role in virulence, such as those that encode Type III effectors. In addition, sources of resistance to BLS have been identified in barley and wheat lines, and ongoing efforts are being made to map these genes and evaluate germplasm. Although there are still gaps in BLS research, progress has been made in recent years to further understand epidemiology, diagnostics, pathogen virulence, and host resistance.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
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Heiden N, Roman-Reyna V, Curland RD, Dill-Macky R, Jacobs JM. Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity. PHYTOPATHOLOGY 2023; 113:2056-2061. [PMID: 35727947 DOI: 10.1094/phyto-04-22-0113-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a diverse panel of Xtt.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
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Román-Reyna V, Curland RD, Velez-Negron Y, Ledman KE, Gutierrez-Castillo DE, Beutler J, Butchacas J, Brar GS, Roberts R, Dill-Macky R, Jacobs JM. Development of Genome-Driven, Lifestyle-Informed Markers for Identification of the Cereal-Infecting Pathogens Xanthomonas translucens Pathovars undulosa and translucens. PHYTOPATHOLOGY 2023; 113:2110-2118. [PMID: 36224751 DOI: 10.1094/phyto-07-22-0262-sa] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial leaf streak, bacterial blight, and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains; however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. We validated the primers across different Xanthomonas and non-Xanthomonas strains. To our knowledge, this is the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Verónica Román-Reyna
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Yesenia Velez-Negron
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | | | - Jonathan Beutler
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jules Butchacas
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Gurcharn Singh Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Robyn Roberts
- Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Jonathan M Jacobs
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
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Hong E, Bankole IA, Zhao B, Shi G, Buck JW, Feng J, Curland RD, Baldwin T, Chapara V, Liu Z. DNA Markers, Pathogenicity Test, and Multilocus Sequence Analysis to Differentiate and Characterize Cereal-Specific Xanthomonas translucens Strains. PHYTOPATHOLOGY 2023; 113:2062-2072. [PMID: 37551962 DOI: 10.1094/phyto-10-22-0381-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Xanthomonas translucens contains a group of bacterial pathogens that are closely related and have been divided into several pathovars based on their host range. X. translucens pv. undulosa (Xtu) and X. translucens pv. translucens (Xtt) are two important pathovars that cause bacterial leaf streak disease on wheat and barley, respectively. In this study, DNA markers were developed to differentiate Xtu and Xtt and were then used to characterize a collection of X. translucens strains with diverse origins, followed by confirmation and characterization with pathogenicity tests and multilocus sequence analysis/typing (MLSA/MLST). We first developed cleaved amplified polymorphic sequence markers based on the single-nucleotide polymorphisms within a cereal pathovar-specific DNA sequence. In addition, two Xtt-specific markers, designated Xtt-XopM and Xtt-SP1, were developed from comparative genomics among the sequenced Xtt/Xtu genomes. Using the developed markers, a collection of X. translucens strains were successfully identified as Xtu or Xtt. Pathogenicity tests on wheat and barley plants and MLSA of four housekeeping genes validated the pathovar assignation of those strains. Furthermore, MLSA revealed distinct subclades within both Xtu and Xtt groups. Seven and three sequence types were identified from MLST for Xtu and Xtt strains, respectively. The establishment of efficient Xtt/Xtu differentiation methods and characterization of those strains will be useful in studying disease epidemiology and host-pathogen interactions and breeding programs when screening for sources of resistance for these two important bacterial pathogens.
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Affiliation(s)
- Eunhye Hong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Ibukunoluwa A Bankole
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Bin Zhao
- Department of Statistics, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, AAFRED, Edmonton, AB, T5Y 6H3, Canada
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Thomas Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Venkata Chapara
- Langdon Research Extension Center, ND Agricultural Experimental Station, Langdon, ND 58249, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
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Heiden N, Broders KA, Hutin M, Castro MO, Roman-Reyna V, Toth H, Jacobs JM. Bacterial Leaf Streak Diseases of Plants: Symptom Convergence in Monocot Plants by Distant Pathogenic Xanthomonas Species. PHYTOPATHOLOGY 2023; 113:2048-2055. [PMID: 37996392 DOI: 10.1094/phyto-05-23-0155-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Bacterial leaf streak (BLS) is a disease of monocot plants caused by Xanthomonas translucens on small grains, X. vasicola on maize and sorghum, and X. oryzae on rice. These three pathogens cause remarkably similar symptomology in their host plants. Despite causing similar symptoms, BLS pathogens are dispersed throughout the larger Xanthomonas phylogeny. Each aforementioned species includes strain groups that do not cause BLS and instead cause vascular disease. In this commentary, we hypothesize that strains of X. translucens, X. vasicola, and X. oryzae convergently evolved to cause BLS due to shared evolutionary pressures. We examined the diversity of secreted effectors, which may be important virulence factors for BLS pathogens and their evolution. We discuss evidence that differences in gene regulation and abilities to manipulate plant hormones may also separate BLS pathogens from other Xanthomonas species or pathovars. BLS is becoming an increasing issue across the three pathosystems. Overall, we hope that a better understanding of conserved mechanisms used by BLS pathogens will enable researchers to translate findings across production systems and guide approaches to control this (re)emerging threat.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kirk A Broders
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, U.S.A
| | - Mathilde Hutin
- Plant Health Institute of Montpellier, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mary Ortiz Castro
- Horticulture and Extension Programs, Colorado State University, Castle Rock, CO 80106, U.S.A
| | - Verónica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
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12
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Tang B, Feng L, Hulin MT, Ding P, Ma W. Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics. Cell Host Microbe 2023; 31:1732-1747.e5. [PMID: 37741284 DOI: 10.1016/j.chom.2023.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/14/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023]
Abstract
Pathogen infection is a dynamic process. Here, we employ single-cell transcriptomics to investigate plant response heterogeneity. By generating an Arabidopsis thaliana leaf atlas encompassing 95,040 cells during infection by a fungal pathogen, Colletotrichum higginsianum, we unveil cell-type-specific gene expression, notably an enrichment of intracellular immune receptors in vasculature cells. Trajectory inference identifies cells that had different interactions with the invading fungus. This analysis divulges transcriptional reprogramming of abscisic acid signaling specifically occurring in guard cells, which is consistent with a stomatal closure dependent on direct contact with the fungus. Furthermore, we investigate the transcriptional plasticity of genes involved in glucosinolate biosynthesis in cells at the fungal infection sites, emphasizing the contribution of the epidermis-expressed MYB122 to disease resistance. This work underscores spatially dynamic, cell-type-specific plant responses to a fungal pathogen and provides a valuable resource that supports in-depth investigations of plant-pathogen interactions.
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Affiliation(s)
- Bozeng Tang
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, NR4 7UH Norwich, UK
| | - Li Feng
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, NR4 7UH Norwich, UK
| | - Michelle T Hulin
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, NR4 7UH Norwich, UK
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, NR4 7UH Norwich, UK.
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13
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Agarwal V, Stubits R, Nassrullah Z, Dillon MM. Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks. Front Microbiol 2023; 14:1213261. [PMID: 37476668 PMCID: PMC10356107 DOI: 10.3389/fmicb.2023.1213261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.
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Affiliation(s)
- Viplav Agarwal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Rachel Stubits
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Zain Nassrullah
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Marcus M. Dillon
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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14
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Donegan MA, Coletta-Filho HD, Almeida RPP. Parallel host shifts in a bacterial plant pathogen suggest independent genetic solutions. MOLECULAR PLANT PATHOLOGY 2023; 24:527-535. [PMID: 36992605 DOI: 10.1111/mpp.13316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
While there are documented host shifts in many bacterial plant pathogens, the genetic foundation of host shifts is largely unknown. Xylella fastidiosa is a bacterial pathogen found in over 600 host plant species. Two parallel host shifts occurred-in Brazil and Italy-in which X. fastidiosa adapted to infect olive trees, whereas related strains infected coffee. Using 10 novel whole-genome sequences from an olive-infecting population in Brazil, we investigated whether these olive-infecting strains diverged from closely related coffee-infecting strains. Several single-nucleotide polymorphisms, many derived from recombination events, and gene gain and loss events separated olive-infecting strains from coffee-infecting strains in this clade. The olive-specific variation suggests that this event was a host jump with genetic isolation between coffee- and olive-infecting X. fastidiosa populations. Next, we investigated the hypothesis of genetic convergence in the host shift from coffee to olive in both populations (Brazil and Italy). Each clade had multiple mutations and gene gain and loss events unique to olive, yet no overlap between clades. Using a genome-wide association study technique, we did not find any plausible candidates for convergence. Overall, this work suggests that the two populations adapted to infect olive trees through independent genetic solutions.
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Affiliation(s)
- Monica A Donegan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | | | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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15
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Castillo AI, Almeida RPP. The Multifaceted Role of Homologous Recombination in a Fastidious Bacterial Plant Pathogen. Appl Environ Microbiol 2023; 89:e0043923. [PMID: 37154680 PMCID: PMC10231230 DOI: 10.1128/aem.00439-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Homologous recombination plays a key function in the evolution of bacterial genomes. Within Xylella fastidiosa, an emerging plant pathogen with increasing host and geographic ranges, it has been suggested that homologous recombination facilitates host switching, speciation, and the development of virulence. We used 340 whole-genome sequences to study the relationship between inter- and intrasubspecific homologous recombination, random mutation, and natural selection across individual X. fastidiosa genes. Individual gene orthologs were identified and aligned, and a maximum likelihood (ML) gene tree was generated. Each gene alignment and tree pair were then used to calculate gene-wide and branch-specific r/m values (relative effect of recombination to mutation), gene-wide and branch-site nonsynonymous over synonymous substitution rates (dN/dS values; episodic selection), and branch length (as a proxy for mutation rate). The relationships between these variables were evaluated at the global level (i.e., for all genes among and within a subspecies), among specific functional classes (i.e., COGs), and between pangenome components (i.e., accessory versus core genes). Our analysis showed that r/m varied widely among genes as well as across X. fastidiosa subspecies. While r/m and dN/dS values were positively correlated in some instances (e.g., core genes in X. fastidiosa subsp. fastidiosa and both core and accessory genes in X. fastidiosa subsp. multiplex), low correlation coefficients suggested no clear biological significance. Overall, our results indicate that, in addition to its adaptive role in certain genes, homologous recombination acts as a homogenizing and a neutral force across phylogenetic clades, gene functional groups, and pangenome components. IMPORTANCE There is ample evidence that homologous recombination occurs frequently in the economically important plant pathogen Xylella fastidiosa. Homologous recombination has been known to occur among sympatric subspecies and is associated with host-switching events and virulence-linked genes. As a consequence, is it generally assumed that recombinant events in X. fastidiosa are adaptive. This mindset influences expectations of how homologous recombination acts as an evolutionary force as well as how management strategies for X. fastidiosa diseases are determined. Yet, homologous recombination plays roles beyond that of a source for diversification and adaptation. Homologous recombination can act as a DNA repair mechanism, as a means to facilitate nucleotide compositional change, as a homogenization mechanism within populations, or even as a neutral force. Here, we provide a first assessment of long-held beliefs regarding the general role of recombination in adaptation for X. fastidiosa. We evaluate gene-specific variations in homologous recombination rate across three X. fastidiosa subspecies and its relationship to other evolutionary forces (e.g., natural selection, mutation, etc.). These data were used to assess the role of homologous recombination in X. fastidiosa evolution.
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Affiliation(s)
- Andreina I. Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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16
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Tokuda R, Iwabuchi N, Kitazawa Y, Nijo T, Suzuki M, Maejima K, Oshima K, Namba S, Yamaji Y. Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes. Front Genet 2023; 14:1132432. [PMID: 37252660 PMCID: PMC10210161 DOI: 10.3389/fgene.2023.1132432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.
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Affiliation(s)
- Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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17
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Paauw M, van Hulten M, Chatterjee S, Berg JA, Taks NW, Giesbers M, Richard MMS, van den Burg HA. Hydathode immunity protects the Arabidopsis leaf vasculature against colonization by bacterial pathogens. Curr Biol 2023; 33:697-710.e6. [PMID: 36731466 DOI: 10.1016/j.cub.2023.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/27/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023]
Abstract
Plants prevent disease by passively and actively protecting potential entry routes against invading microbes. For example, the plant immune system actively guards roots, wounds, and stomata. How plants prevent vascular disease upon bacterial entry via guttation fluids excreted from specialized glands at the leaf margin remains largely unknown. These so-called hydathodes release xylem sap when root pressure is too high. By studying hydathode colonization by both hydathode-adapted (Xanthomonas campestris pv. campestris) and non-adapted pathogenic bacteria (Pseudomonas syringae pv. tomato) in immunocompromised Arabidopsis mutants, we show that the immune hubs BAK1 and EDS1-PAD4-ADR1 restrict bacterial multiplication in hydathodes. Both immune hubs effectively confine bacterial pathogens to hydathodes and lower the number of successful escape events of an hydathode-adapted pathogen toward the xylem. A second layer of defense, which is dependent on the plant hormones' pipecolic acid and to a lesser extent on salicylic acid, reduces the vascular spread of the pathogen. Thus, besides glands, hydathodes represent a potent first line of defense against leaf-invading microbes.
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Affiliation(s)
- Misha Paauw
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Marieke van Hulten
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sayantani Chatterjee
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jeroen A Berg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Nanne W Taks
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Marcel Giesbers
- Wageningen Electron Microscopy Centre, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands
| | - Manon M S Richard
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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18
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Merfa MV, Zhu X, Shantharaj D, Gomez LM, Naranjo E, Potnis N, Cobine PA, De La Fuente L. Complete functional analysis of type IV pilus components of a reemergent plant pathogen reveals neofunctionalization of paralog genes. PLoS Pathog 2023; 19:e1011154. [PMID: 36780566 PMCID: PMC9956873 DOI: 10.1371/journal.ppat.1011154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Type IV pilus (TFP) is a multifunctional bacterial structure involved in twitching motility, adhesion, biofilm formation, as well as natural competence. Here, by site-directed mutagenesis and functional analysis, we determined the phenotype conferred by each of the 38 genes known to be required for TFP biosynthesis and regulation in the reemergent plant pathogenic fastidious prokaryote Xylella fastidiosa. This pathogen infects > 650 plant species and causes devastating diseases worldwide in olives, grapes, blueberries, and almonds, among others. This xylem-limited, insect-transmitted pathogen lives constantly under flow conditions and therefore is highly dependent on TFP for host colonization. In addition, TFP-mediated natural transformation is a process that impacts genomic diversity and environmental fitness. Phenotypic characterization of the mutants showed that ten genes were essential for both movement and natural competence. Interestingly, seven sets of paralogs exist, and mutations showed opposing phenotypes, indicating evolutionary neofunctionalization of subunits within TFP. The minor pilin FimT3 was the only protein exclusively required for natural competence. By combining approaches of molecular microbiology, structural biology, and biochemistry, we determined that the minor pilin FimT3 (but not the other two FimT paralogs) is the DNA receptor in TFP of X. fastidiosa and constitutes an example of neofunctionalization. FimT3 is conserved among X. fastidiosa strains and binds DNA non-specifically via an electropositive surface identified by homolog modeling. This protein surface includes two arginine residues that were exchanged with alanine and shown to be involved in DNA binding. Among plant pathogens, fimT3 was found in ~ 10% of the available genomes of the plant associated Xanthomonadaceae family, which are yet to be assessed for natural competence (besides X. fastidiosa). Overall, we highlight here the complex regulation of TFP in X. fastidiosa, providing a blueprint to understand TFP in other bacteria living under flow conditions.
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Affiliation(s)
- Marcus V. Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Xinyu Zhu
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Deepak Shantharaj
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Laura M. Gomez
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Eber Naranjo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Paul A. Cobine
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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19
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Jiang L, Ji Q, Liu Y. Change of wind: MKP1 positively regulates vascular immunity. TRENDS IN PLANT SCIENCE 2022; 27:1193-1195. [PMID: 36057532 DOI: 10.1016/j.tplants.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Plants lack immunocytes but possess tissue-specific immune responses. Recent studies by Lin et al. demonstrate that mitogen-activated protein kinase (MPK) phosphatase 1 (MKP1), a repressor of plant mesophyll immunity, positively regulates vascular immunity in both Arabidopsis thaliana and Oryza sativa, providing insights into how plants mount immune responses against vascular pathogens.
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Affiliation(s)
- Lingyan Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China.
| | - Qing Ji
- College of Agriculture and Forestry, Puer University, Puer 665000, Yunnan, China.
| | - Yukun Liu
- College of Forestry, Southwest Forestry University, Kunming 650224, Yunnan, China
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20
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Koshimizu S, Minamino N, Nishiyama T, Yoro E, Sato M, Wakazaki M, Toyooka K, Ebine K, Sakakibara K, Ueda T, Yano K. Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis. THE NEW PHYTOLOGIST 2022; 236:1182-1196. [PMID: 35842793 DOI: 10.1111/nph.18385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Land plant spermatozoids commonly possess characteristic structures such as the spline, which consists of a microtubule array, the multilayered structure (MLS) in which the uppermost layer is a continuum of the spline, and multiple flagella. However, the molecular mechanisms underpinning spermatogenesis remain to be elucidated. We successfully identified candidate genes involved in spermatogenesis, deeply divergent BLD10s, by computational analyses combining multiple methods and omics data. We then examined the functions of BLD10s in the liverwort Marchantia polymorpha and the moss Physcomitrium patens. MpBLD10 and PpBLD10 are required for normal basal body (BB) and flagella formation. Mpbld10 mutants exhibited defects in remodeling of the cytoplasm and nucleus during spermatozoid formation, and thus MpBLD10 should be involved in chromatin reorganization and elimination of the cytoplasm during spermiogenesis. We identified orthologs of MpBLD10 and PpBLD10 in diverse Streptophyta and found that MpBLD10 and PpBLD10 are orthologous to BLD10/CEP135 family proteins, which function in BB assembly. However, BLD10s evolved especially quickly in land plants and MpBLD10 might have acquired additional functions in spermatozoid formation through rapid molecular evolution.
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Affiliation(s)
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan
| | - Emiko Yoro
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kazuo Ebine
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
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21
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Dubrow ZE, Carpenter SCD, Carter ME, Grinage A, Gris C, Lauber E, Butchachas J, Jacobs JM, Smart CD, Tancos MA, Noël LD, Bogdanove AJ. Cruciferous Weed Isolates of Xanthomonas campestris Yield Insight into Pathovar Genomic Relationships and Genetic Determinants of Host and Tissue Specificity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:791-802. [PMID: 35536128 DOI: 10.1094/mpmi-01-22-0024-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pathovars of Xanthomonas campestris cause distinct diseases on different brassicaceous hosts. The genomic relationships among pathovars as well as the genetic determinants of host range and tissue specificity remain poorly understood despite decades of research. Here, leveraging advances in multiplexed long-read technology, we fully sequenced the genomes of a collection of X. campestris strains isolated from cruciferous crops and weeds in New York and California as well as strains from global collections, to investigate pathovar relationships and candidate genes for host- and tissue-specificity. Pathogenicity assays and genomic comparisons across this collection and publicly available X. campestris genomes revealed a correlation between pathovar and genomic relatedness and provide support for X. campestris pv. barbareae, the validity of which had been questioned. Linking strain host range with type III effector repertoires identified AvrAC (also 'XopAC') as a candidate host-range determinant, preventing infection of Matthiola incana, and this was confirmed experimentally. Furthermore, the presence of a copy of the cellobiosidase gene cbsA with coding sequence for a signal peptide was found to correlate with the ability to infect vascular tissues, in agreement with a previous study of diverse Xanthomonas species; however, heterologous expression in strains lacking the gene gave mixed results, indicating that factors in addition to cbsA influence tissue specificity of X. campestris pathovars. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Zoë E Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Morgan E Carter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
- School of Plant Sciences, University of Arizona, Tucson, AZ, U.S.A
| | - Ayress Grinage
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Jules Butchachas
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, U.S.A
| | - Laurent D Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
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22
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Clavijo F, Barrera C, Benčič A, Croce V, Jacobs JM, Bernal AJ, Koebnik R, Roman-Reyna V. Complete Genome Sequence Resource for Xanthomonas translucens pv. undulosa MAI5034, a Wheat Pathogen from Uruguay. PHYTOPATHOLOGY 2022; 112:2036-2039. [PMID: 35559654 DOI: 10.1094/phyto-01-22-0025-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: 06/15/2023]
Affiliation(s)
- Felipe Clavijo
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Claudia Barrera
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Aleksander Benčič
- National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Valentina Croce
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
| | - Adriana J Bernal
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
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23
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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24
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De La Fuente L, Merfa MV, Cobine PA, Coleman JJ. Pathogen Adaptation to the Xylem Environment. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:163-186. [PMID: 35472277 DOI: 10.1146/annurev-phyto-021021-041716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A group of aggressive pathogens have evolved to colonize the plant xylem. In this vascular tissue, where water and nutrients are transported from the roots to the rest of the plant, pathogens must be able to thrive under acropetal xylem sap flow and scarcity of nutrients while having direct contact only with predominantly dead cells. Nevertheless, a few bacteria have adapted to exclusively live in the xylem, and various pathogens may colonize other plant niches without causing symptoms unless they reach the xylem. Once established, the pathogens modulate its physicochemical conditions to enhance their growth and virulence. Adaptation to the restrictive lifestyle of the xylem leads to genome reduction in xylem-restricted bacteria, as they have a higher proportion of pseudogenes in their genome. The basis of xylem adaptation is not completely understood; therefore, a need still exists for model systems to advance the knowledge on this topic.
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Affiliation(s)
- Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA;
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA;
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA;
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25
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Michalopoulou VA, Mermigka G, Kotsaridis K, Mentzelopoulou A, Celie PHN, Moschou PN, Jones JDG, Sarris PF. The host exocyst complex is targeted by a conserved bacterial type-III effector that promotes virulence. THE PLANT CELL 2022; 34:3400-3424. [PMID: 35640532 PMCID: PMC9421483 DOI: 10.1093/plcell/koac162] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/23/2022] [Indexed: 05/30/2023]
Abstract
For most Gram-negative bacteria, pathogenicity largely depends on the type-III secretion system that delivers virulence effectors into eukaryotic host cells. The subcellular targets for the majority of these effectors remain unknown. Xanthomonas campestris, the causal agent of black rot disease of crucifers such as Brassica spp., radish, and turnip, delivers XopP, a highly conserved core-effector protein produced by X. campestris, which is essential for virulence. Here, we show that XopP inhibits the function of the host-plant exocyst complex by direct targeting of Exo70B, a subunit of the exocyst complex, which plays a significant role in plant immunity. XopP interferes with exocyst-dependent exocytosis and can do this without activating a plant NOD-like receptor that guards Exo70B in Arabidopsis. In this way, Xanthomonas efficiently inhibits the host's pathogen-associated molecular pattern (PAMP)-triggered immunity by blocking exocytosis of pathogenesis-related protein-1A, callose deposition, and localization of the FLAGELLIN SENSITIVE2 (FLS2) immune receptor to the plasma membrane, thus promoting successful infection. Inhibition of exocyst function without activating the related defenses represents an effective virulence strategy, indicating the ability of pathogens to adapt to host defenses by avoiding host immunity responses.
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Affiliation(s)
- Vassiliki A Michalopoulou
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Konstantinos Kotsaridis
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | | | - Patrick H N Celie
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Uppsala S-75007, Sweden
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Biosciences, University of Exeter, Exeter, UK
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26
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Yin X, Qian W. Sword in the woods: How plant hosts defend against vascular pathogens. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1465-1468. [PMID: 35766351 DOI: 10.1111/jipb.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
This Commentary discusses two recent papers exploring how plants combat infection by vascular pathogens via modulating lignin production and via MAP kinase signaling cascades.
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Affiliation(s)
- Xin Yin
- State Key Laboratory of Plant Genomics, Institution of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institution of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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27
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Nathawat R, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. Role of the FnIII domain associated with a cell wall-degrading enzyme cellobiosidase of Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2022; 23:1011-1021. [PMID: 35278018 PMCID: PMC9190976 DOI: 10.1111/mpp.13205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Cellobiosidase (CbsA) is an important secreted virulence factor of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight of rice. CbsA is one of several cell wall-degrading enzymes secreted by Xoo via the type II secretion system (T2SS). CbsA is considered a fundamental virulence factor for vascular pathogenesis. CbsA has an N-terminal glycosyl hydrolase domain and a C-terminal fibronectin type III (FnIII) domain. Interestingly, the secreted form of CbsA lacks the FnIII domain during in planta growth. Here we show that the presence of the FnIII domain inhibits the enzyme activity of CbsA on polysaccharide substrates like carboxymethylcellulose. The FnIII domain is required for the interaction of CbsA with SecB chaperone, and this interaction is crucial for the stability and efficient transport of CbsA across the inner membrane. Deletion of the FnIII domain reduced virulence similar to ΔcbsA Xoo, which corroborates the importance of the FnIII domain in CbsA. Our work elucidates a hitherto unknown function of the FnIII domain in enabling the virulence-promoting activity of CbsA.
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Affiliation(s)
| | - Roshan V. Maku
- CSIR – Centre for Cellular and Molecular BiologyHyderabadIndia
- Present address:
DBT – National Institute of Animal BiotechnologyHyderabadIndia
| | | | | | - Ramesh V. Sonti
- CSIR – Centre for Cellular and Molecular BiologyHyderabadIndia
- Present address:
Indian Institute of Science Education and Research TirupatiTirupatiIndia
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28
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Novel indole-mediated potassium ion import system confers a survival advantage to the Xanthomonadaceae family. THE ISME JOURNAL 2022; 16:1717-1729. [PMID: 35319020 DOI: 10.1038/s41396-022-01219-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 12/30/2022]
Abstract
Interspecific and intraspecific communication systems of microorganisms are involved in the regulation of various stress responses in microbial communities. Although the significance of signaling molecules in the ubiquitous family Xanthomonadaceae has been reported, the role bacterial communications play and their internal mechanisms are largely unknown. Here, we use Lysobacter enzymogenes, a member of Xanthomonadaceae, to identify a novel potassium ion import system, LeKdpXFABC. This import system participates in the indole-mediated interspecies signaling pathway and matters in environmental adaptation. Compared with the previously reported kdpFABC of Escherichia coli, LekdpXFABC contains a novel indispensable gene LekdpX and is directly regulated by the indole-related two-component system QseC/B. QseC autophosphorylation is involved in this process. The operon LekdpXFABC widely exists in Xanthomonadaceae. Moreover, indole promotes antimicrobial product production at the early exponential phase. Further analyses show that indole enhances potassium ion adsorption on the cell surface by upregulating the production of O-antigenic polysaccharides. Finally, we confirm that LeKdpXFABC mediation by indole is subject to the intraspecific signaling molecules DSFs, of which the biosynthesis genes always exist together with LekdpXFABC. Therefore, as a new idea, the signal collaborative strategy of indole and DSFs might ensure the persistent fitness advantage of Xanthomonadaceae in variable environments.
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29
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Zhang D, Lv B, Qiu JL. Being tough: The secret weapon of plants against vascular pathogens. MOLECULAR PLANT 2022; 15:934-936. [PMID: 35477854 DOI: 10.1016/j.molp.2022.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Dandan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Bin Lv
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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30
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Redkar A, Sabale M, Zuccaro A, Di Pietro A. Determinants of endophytic and pathogenic lifestyle in root colonizing fungi. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102226. [PMID: 35526366 DOI: 10.1016/j.pbi.2022.102226] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some root-colonizing fungi shift between endophytic and pathogenic behaviour depending on the host species and that combinations of effector proteins collectively shape the fungal lifestyle on a given plant. In this review we discuss recent advances in our understanding of how fungal infection strategies on roots can lead to contrasting outcomes for the host. We highlight functional similarities and differences in compatibility determinants that control the colonization of specific-cell layers within plant roots, ultimately shaping the continuum between endophytic and pathogenic lifestyle.
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Affiliation(s)
- Amey Redkar
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain; Department of Botany, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
| | - Mugdha Sabale
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, D-50674, Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), D-50674, Cologne, Germany
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain.
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31
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Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems. Microorganisms 2022; 10:microorganisms10050914. [PMID: 35630358 PMCID: PMC9148166 DOI: 10.3390/microorganisms10050914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.
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32
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Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Front Microbiol 2022; 13:840308. [PMID: 35495725 PMCID: PMC9048695 DOI: 10.3389/fmicb.2022.840308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
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Affiliation(s)
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
- *Correspondence: Neha Potnis,
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33
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Lin H, Wang M, Chen Y, Nomura K, Hui S, Gui J, Zhang X, Wu Y, Liu J, Li Q, Deng Y, Li L, Yuan M, Wang S, He SY, He Z. An MKP-MAPK protein phosphorylation cascade controls vascular immunity in plants. SCIENCE ADVANCES 2022; 8:eabg8723. [PMID: 35263144 PMCID: PMC8906744 DOI: 10.1126/sciadv.abg8723] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Global crop production is greatly reduced by vascular diseases. These diseases include bacterial blight of rice and crucifer black rot caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas campestris pv. campestris (Xcc). The molecular mechanisms that activate vascular defense against such pathogens remains underexplored. Here, we show that an Arabidopsis MAPK phosphatase 1 (MKP1) mutant has increased host susceptibility to the adapted pathogen Xcc and is compromised in nonhost resistance to the rice pathogen Xoo. MKP1 regulates MAPK-mediated phosphorylation of the transcription factor MYB4 that negatively regulates vascular lignification through inhibiting lignin biosynthesis. Induction of lignin biosynthesis is, therefore, an important part of vascular-specific immunity. The role of MKP-MAPK-MYB signaling in lignin biosynthesis and vascular resistance to Xoo is conserved in rice, indicating that these factors form a tissue-specific defense regulatory network. Our study likely reveals a major vascular immune mechanism that underlies tissue-specific disease resistance against bacterial pathogens in plants.
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Affiliation(s)
- Hui Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Muyang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kinya Nomura
- Department of Biology, Duke University, Durham, NC, USA
| | - Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiawei Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yue Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Yang He
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Zuhua He
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author.
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34
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Sharma P, Johnson MA, Mazloom R, Allen C, Heath LS, Lowe-Power TM, Vinatzer BA. Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology. Microb Genom 2022; 8:000791. [PMID: 35297758 PMCID: PMC9176288 DOI: 10.1099/mgen.0.000791] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem tissue and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures and physiological traits. To increase our understanding of the evolution, diversity and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4940 genes on average, and a pangenome analysis found that there are 3262 genes in the core genome (~60 % of the mean RSSC genome) with 13 128 genes in the extensive flexible genome. A core genome phylogenetic tree and a whole-genome similarity matrix aligned with the previously named species (R. solanacearum, R. pseudosolanacearum, R. syzygii) and phylotypes (I–IV). These analyses also highlighted a third unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. We also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved, cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced RSSC strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.
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Affiliation(s)
- Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Graduate Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Graduate Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Tiffany M. Lowe-Power
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
- *Correspondence: Tiffany M. Lowe-Power,
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- *Correspondence: Boris A. Vinatzer,
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35
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Wang Y, Wu J, Yan J, Guo M, Xu L, Hou L, Zou Q. Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies. BMC Genomics 2022; 23:34. [PMID: 34996360 PMCID: PMC8740420 DOI: 10.1186/s12864-021-08165-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies. Results We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between plant biotrophic pathogens and other groups (including human, necrotrophic and hemibiotrophic pathogens). The results revealed the biotroph-specific and lifestyle-conserved candidate effector families. These data have been configured in web-based genome browser applications for public display (http://lab.malab.cn/soft/PFPG). This resource allows researchers to profile the genome, proteome, secretome and effectome of plant fungal pathogens. Conclusions Our findings demonstrated different genome evolution strategies of plant fungal pathogens with different lifestyles and explored their lifestyle-conserved and specific candidate effectors. It will provide a new basis for discovering the novel effectors and their pathogenic mechanisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08165-1.
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Affiliation(s)
- Yansu Wang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, 518000, Shenzhen, P. R. China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, P. R. China
| | - Jie Wu
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, P. R. China
| | - Jiacheng Yan
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, 221116, Xuzhou, P. R. China
| | - Ming Guo
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, USA
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, 518000, Shenzhen, P. R. China
| | - Liping Hou
- Beidahuang Industry Group General Hospital, Harbin, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, P. R. China. .,State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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Mijatović J, Severns PM, Kemerait RC, Walcott RR, Kvitko BH. Patterns of Seed-to-Seedling Transmission of Xanthomonas citri pv. malvacearum, the Causal Agent of Cotton Bacterial Blight. PHYTOPATHOLOGY 2021; 111:2176-2184. [PMID: 34032522 DOI: 10.1094/phyto-02-21-0057-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum, was a major disease of cotton in the United States in the early part of the twentieth century. The reemergence of CBB revealed many gaps in our understanding of this important disease. In this study, we employed a wild-type (WT) field isolate of X. citri pv. malvacearum from Georgia (U.S.A.) to generate a nonpathogenic hrcV mutant lacking a functional type-III secretion system (T3SS-). We tagged the WT and T3SS- strains with an auto-bioluminescent Tn7 reporter and compared colonization patterns of CBB-susceptible and CBB-resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. WT and T3SS- X. citri pv. malvacearum strains colonized cotton cotyledons of CBB-resistant and CBB-susceptible cotton cultivars. However, X. citri pv. malvacearum populations were significantly higher in CBB-susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS- X. citri pv. malvacearum strains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission of X. citri pv. malvacearum may involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potential X. citri pv. malvacearum reservoirs for CBB outbreaks.
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Affiliation(s)
- Jovana Mijatović
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Paul M Severns
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Robert C Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793
| | - Ron R Walcott
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
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Drew GC, Stevens EJ, King KC. Microbial evolution and transitions along the parasite-mutualist continuum. Nat Rev Microbiol 2021; 19:623-638. [PMID: 33875863 PMCID: PMC8054256 DOI: 10.1038/s41579-021-00550-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Virtually all plants and animals, including humans, are home to symbiotic microorganisms. Symbiotic interactions can be neutral, harmful or have beneficial effects on the host organism. However, growing evidence suggests that microbial symbionts can evolve rapidly, resulting in drastic transitions along the parasite-mutualist continuum. In this Review, we integrate theoretical and empirical findings to discuss the mechanisms underpinning these evolutionary shifts, as well as the ecological drivers and why some host-microorganism interactions may be stuck at the end of the continuum. In addition to having biomedical consequences, understanding the dynamic life of microorganisms reveals how symbioses can shape an organism's biology and the entire community, particularly in a changing world.
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Affiliation(s)
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, UK.
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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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Redkar A, Sabale M, Di Pietro A. A 'Hydrolase Switch' for Vascular Specialization in Plant Pathogenic Bacteria. TRENDS IN PLANT SCIENCE 2021; 26:427-429. [PMID: 33771467 DOI: 10.1016/j.tplants.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Plant vascular diseases are tissue-specific systemic infections provoked by bacterial and fungal pathogens adapted to thrive in the xylem vessels. A recent report by Gluck-Thaler et al. reveals that, in the phytopathogenic bacterium Xanthomonas, the switch from non-vascular to vascular pathogenesis is determined by a single gene encoding a plant cell wall-degrading hydrolase.
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Affiliation(s)
- Amey Redkar
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain.
| | - Mugdha Sabale
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain.
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40
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Castillo AI, Almeida RPP. Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen. G3-GENES GENOMES GENETICS 2021; 11:6170658. [PMID: 33715000 PMCID: PMC8495750 DOI: 10.1093/g3journal/jkab076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022]
Abstract
Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
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