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Möller H, Coetzee B, van Niekerk J, Rose LJ. Reference Genome Resource for the Citrus Pathogen Phytophthora citrophthora. J Genomics 2024; 12:14-18. [PMID: 38164508 PMCID: PMC10751748 DOI: 10.7150/jgen.89324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/12/2023] [Indexed: 01/03/2024] Open
Abstract
Phytophthora citrophthora is an oomycete pathogen that infects citrus. Its occurrence in citrus-growing regions worldwide is considered a major contributor to crop losses. This study presents a high-quality genome resource for P. citrophthora, which was generated using PacBio HiFi long-read high-throughput sequencing technology. We successfully assembled a 48.5 Mb genome containing 16,409 protein-coding genes from high-quality reads. This marks the first complete genome assembly of P. citrophthora, providing a valuable resource to enhance the understanding of pathogenic behaviour and fungicide sensitivity of this destructive citrus pathogen.
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Affiliation(s)
- Heike Möller
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Beatrix Coetzee
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Jan van Niekerk
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa
| | - Lindy Joy Rose
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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2
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Sun L, Yin X, Sossah FL, Han X, Li Y. Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes. Front Mol Biosci 2023; 10:1292556. [PMID: 38028535 PMCID: PMC10658006 DOI: 10.3389/fmolb.2023.1292556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Pleurotus placentodes (PPL) and Pleurotus cystidiosus (PCY) are economically valuable species. PPL grows on conifers, while PCY grows on broad-leaved trees. To reveal the genetic mechanism behind PPL's adaptability to conifers, we performed de novo genome sequencing and comparative analysis of PPL and PCY. We determined the size of the genomes for PPL and PCY to be 36.12 and 42.74 Mb, respectively, and found that they contain 10,851 and 15,673 protein-coding genes, accounting for 59.34% and 53.70% of their respective genome sizes. Evolution analysis showed PPL was closely related to P. ostreatus with the divergence time of 62.7 MYA, while PCY was distantly related to other Pleurotus species with the divergence time of 111.7 MYA. Comparative analysis of carbohydrate-active enzymes (CAZYmes) in PPL and PCY showed that the increase number of CAZYmes related to pectin and cellulose degradation (e.g., AA9, PL1) in PPL may be important for the degradation and colonization of conifers. In addition, geraniol degradation and peroxisome pathways identified by comparative genomes should be another factors for PPL's tolerance to conifer substrate. Our research provides valuable genomes for Pleurotus species and sheds light on the genetic mechanism of PPL's conifer adaptability, which could aid in breeding new Pleurotus varieties for coniferous utilization.
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Affiliation(s)
- Lei Sun
- Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, China
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiaolei Yin
- Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, China
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Frederick Leo Sossah
- Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, China
- Council for Scientific and Industrial Research (CSIR), Oil Palm Research Institute, Coconut Research Programme, Sekondi, Ghana
| | - Xuerong Han
- Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, China
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, China
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
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Piombo E, Kelbessa BG, Sundararajan P, Whisson SC, Vetukuri RR, Dubey M. RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents. Front Microbiol 2023; 14:1076522. [PMID: 37032886 PMCID: PMC10080066 DOI: 10.3389/fmicb.2023.1076522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Oomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors. Methods To gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species. Results and discussion Each of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bekele Gelena Kelbessa
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Poorva Sundararajan
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Stephen C. Whisson
- Department of Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- *Correspondence: Ramesh Raju Vetukuri, ; Mukesh Dubey,
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Ramesh Raju Vetukuri, ; Mukesh Dubey,
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The molecular dialog between oomycete effectors and their plant and animal hosts. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
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Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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Short Linear Motifs (SLiMs) in “Core” RxLR Effectors of
Phytophthora parasitica
var.
nicotianae
: a Case of PpRxLR1 Effector. Microbiol Spectr 2022; 10:e0177421. [PMID: 35404090 PMCID: PMC9045269 DOI: 10.1128/spectrum.01774-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Oomycetes of the genus Phytophthora encompass several of the most successful plant pathogens described to date. The success of infection by Phytophthora species is attributed to the pathogens’ ability to secrete effector proteins that alter the host’s physiological processes. Structural analyses of effector proteins mainly from bacterial and viral pathogens have revealed the presence of intrinsically disordered regions that host short linear motifs (SLiMs). These motifs play important biological roles by facilitating protein-protein interactions as well as protein translocation. Nonetheless, SLiMs in Phytophthora species RxLR effectors have not been investigated previously and their roles remain unknown. Using a bioinformatics pipeline, we identified 333 candidate RxLR effectors in the strain INRA 310 of Phytophthora parasitica. Of these, 71 (21%) were also found to be present in 10 other genomes of P. parasitica, and hence, these were designated core RxLR effectors (CREs). Within the CRE sequences, the N terminus exhibited enrichment in intrinsically disordered regions compared to the C terminus, suggesting a potential role of disorder in effector translocation. Although the disorder content was reduced in the C-terminal regions, it is important to mention that most SLiMs were in this terminus. PpRxLR1 is one of the 71 CREs identified in this study, and its genes encode a 6-amino acid (aa)-long SLiM at the C terminus. We showed that PpRxLR1 interacts with several host proteins that are implicated in defense. Structural analysis of this effector using homology modeling revealed the presence of potential ligand-binding sites. Among key residues that were predicted to be crucial for ligand binding, L102 and Y106 were of interest since they form part of the 6-aa-long PpRxLR1 SLiM. In silico substitution of these two residues to alanine was predicted to have a significant effect on both the function and the structure of PpRxLR1 effector. Molecular docking simulations revealed possible interactions between PpRxLR1 effector and ubiquitin-associated proteins. The ubiquitin-like SLiM carried in this effector was shown to be a potential mediator of these interactions. Further studies are required to validate and elucidate the underlying molecular mechanism of action. IMPORTANCE The continuous gain and loss of RxLR effectors makes the control of Phytophthora spp. difficult. Therefore, in this study, we endeavored to identify RxLR effectors that are highly conserved among species, also known as “core” RxLR effectors (CREs). We reason that these highly conserved effectors target conserved proteins or processes; thus, they can be harnessed in breeding for durable resistance in plants. To further understand the mechanisms of action of CREs, structural dissection of these proteins is crucial. Intrinsically disordered regions (IDRs) that do not adopt a fixed, three-dimensional fold carry short linear motifs (SLiMs) that mediate biological functions of proteins. The presence and potential role of these SLiMs in CREs of Phytophthora spp. have been overlooked. To our knowledge, we have effectively identified CREs as well as SLiMs with the potential of promoting effector virulence. Together, this work has advanced our comprehension of Phytophthora RxLR effector function and may facilitate the development of innovative and effective control strategies.
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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8
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Sabbadin F, Urresti S, Henrissat B, Avrova AO, Welsh LRJ, Lindley PJ, Csukai M, Squires JN, Walton PH, Davies GJ, Bruce NC, Whisson SC, McQueen-Mason SJ. Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes. Science 2021; 373:774-779. [PMID: 34385392 DOI: 10.1126/science.abj1342] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/06/2021] [Indexed: 01/19/2023]
Abstract
The oomycete Phytophthora infestans is a damaging crop pathogen and a model organism to study plant-pathogen interactions. We report the discovery of a family of copper-dependent lytic polysaccharide monooxygenases (LPMOs) in plant pathogenic oomycetes and its role in plant infection by P. infestans We show that LPMO-encoding genes are up-regulated early during infection and that the secreted enzymes oxidatively cleave the backbone of pectin, a charged polysaccharide in the plant cell wall. The crystal structure of the most abundant of these LPMOs sheds light on its ability to recognize and degrade pectin, and silencing the encoding gene in P. infestans inhibits infection of potato, indicating a role in host penetration. The identification of LPMOs as virulence factors in pathogenic oomycetes opens up opportunities in crop protection and food security.
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Affiliation(s)
- Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
| | - Saioa Urresti
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Anna O Avrova
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Lydia R J Welsh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J Lindley
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Michael Csukai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Julie N Squires
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Gideon J Davies
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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Wang S, Vetukuri RR, Kushwaha SK, Hedley PE, Morris J, Studholme DJ, Welsh LRJ, Boevink PC, Birch PRJ, Whisson SC. Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae. MOLECULAR PLANT PATHOLOGY 2021; 22:954-968. [PMID: 34018655 PMCID: PMC8295517 DOI: 10.1111/mpp.13072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 05/29/2023]
Abstract
Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.
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Affiliation(s)
- Shumei Wang
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
| | - Ramesh R. Vetukuri
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
| | - Sandeep K. Kushwaha
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
- National Institute of Animal BiotechnologyHyderabadIndia
| | - Pete E. Hedley
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Jenny Morris
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Lydia R. J. Welsh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Paul R. J. Birch
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
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10
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Solanský M, Mikulášek K, Zapletalová M, Petřivalský M, Chiltz A, Zdráhal Z, Leborgne-Castel N, Lochman J. The oligomeric states of elicitins affect the hypersensitive response and resistance in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3219-3234. [PMID: 33475728 DOI: 10.1093/jxb/erab011] [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: 06/25/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Successful plant defence against microbial pathogens is based on early recognition and fast activation of inducible responses. Key mechanisms include detection of microbe-associated molecular patterns by membrane-localized pattern recognition receptors that induce a basal resistance response. A well-described model of such responses to pathogens involves the interactions between Solanaceae plants and proteinaceous elicitors secreted by oomycetes, called elicitins. It has been hypothesized that the formation of oligomeric structures by elicitins could be involved in their recognition and activation of defensive transduction cascades. In this study, we tested this hypothesis using several approaches, and we observed differences in tobacco plant responses induced by the elicitin β-cryptogein (β-CRY) and its homodimer, β-CRYDIM. We also found that the C-terminal domain of elicitins of other ELI (true-elicitin) clades plays a significant role in stabilization of their oligomeric structure and restraint in the cell wall. In addition, covalently cross-linking β-CRYDIM impaired the formation of signalling complexes, thereby reducing its capacity to elicit the hypersensitive response and resistance in the host plant, with no significant changes in pathogenesis-related protein expression. By revealing the details of the effects of β-CRY dimerization on recognition and defence responses in tobacco, our results shed light on the poorly understood role of elicitins' oligomeric structures in the interactions between oomycetes and plants.
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Affiliation(s)
- Martin Solanský
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Martina Zapletalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Marek Petřivalský
- Department of Biochemistry, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Annick Chiltz
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Nathalie Leborgne-Castel
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
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Boevink PC, Birch PRJ, Turnbull D, Whisson SC. Devastating intimacy: the cell biology of plant-Phytophthora interactions. THE NEW PHYTOLOGIST 2020; 228:445-458. [PMID: 32394464 PMCID: PMC7540312 DOI: 10.1111/nph.16650] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/15/2020] [Indexed: 05/07/2023]
Abstract
An understanding of the cell biology underlying the burgeoning molecular genetic and genomic knowledge of oomycete pathogenicity is essential to gain the full context of how these pathogens cause disease on plants. An intense research focus on secreted Phytophthora effector proteins, especially those containing a conserved N-terminal RXLR motif, has meant that most cell biological studies into Phytophthora diseases have focussed on the effectors and their host target proteins. While these effector studies have provided novel insights into effector secretion and host defence mechanisms, there remain many unanswered questions about fundamental processes involved in spore biology, host penetration and haustorium formation and function.
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Affiliation(s)
- Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Dionne Turnbull
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Stephen C. Whisson
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
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Abstract
Lupinus mutabilis is an important source of protein in different Andean countries, and its use in diets, particularly those of less wealthy individuals, has been observed for thousands of years. There is an increasing demand for protein crops suitable for Europe and this species is a potential candidate. Assessment of Lupinus mutabilis genetic material in European conditions started more than 40 years ago, with the characterization of a vast number of accessions from the Andean region. In this review, abiotic and biotic constraints to L. mutabilis cultivation in European soil and climatic conditions are discussed, and cultivation management practices are suggested. The beneficial interaction of L. mutabilis with Bradyrhizobium strains in the soil and various pollinator species is also discussed, and the effect of abiotic stresses on these interactions is highlighted. Prospects of alternative uses of L. mutabilis biomass in Northern Europe and opportunities for breeding strategies are discussed. In conclusion, the different approach to crop modeling for Southern and Northern European climatic conditions is highlighted.
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Organize, Don't Agonize: Strategic Success of Phytophthora Species. Microorganisms 2020; 8:microorganisms8060917. [PMID: 32560346 PMCID: PMC7355776 DOI: 10.3390/microorganisms8060917] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Plants are constantly challenged by various environmental stressors ranging from abiotic-sunlight, elevated temperatures, drought, and nutrient deficits, to biotic factors-microbial pathogens and insect pests. These not only affect the quality of harvest but also the yield, leading to substantial annual crop losses, worldwide. Although plants have a multi-layered immune system, phytopathogens such as species of the oomycete genus Phytophthora, can employ elaborate mechanisms to breach this defense. For the last two decades, researchers have focused on the co-evolution between Phytophthora and interacting hosts to decouple the mechanisms governing their molecular associations. This has provided a comprehensive understanding of the pathobiology of plants affected by oomycetes. Ultimately, this is important for the development of strategies to sustainably improve agricultural production. Therefore, this paper discusses the present-day state of knowledge of the strategic mode of operation employed by species of Phytophthora for successful infection. Specifically, we consider motility, attachment, and host cell wall degradation used by these pathogenic species to obtain nutrients from their host. Also discussed is an array of effector types from apoplastic (hydrolytic proteins, protease inhibitors, elicitins) to cytoplastic (RxLRs, named after Arginine-any amino acid-Leucine-Arginine consensus sequence and CRNs, for CRinkling and Necrosis), which upon liberation can subvert the immune response and promote diseases in plants.
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Salem H, Kirsch R, Pauchet Y, Berasategui A, Fukumori K, Moriyama M, Cripps M, Windsor D, Fukatsu T, Gerardo NM. Symbiont Digestive Range Reflects Host Plant Breadth in Herbivorous Beetles. Curr Biol 2020; 30:2875-2886.e4. [PMID: 32502409 DOI: 10.1016/j.cub.2020.05.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Numerous adaptations are gained in light of a symbiotic lifestyle. Here, we investigated the obligate partnership between tortoise leaf beetles (Chrysomelidae: Cassidinae) and their pectinolytic Stammera symbionts to detail how changes to the bacterium's streamlined metabolic range can shape the digestive physiology and ecological opportunity of its herbivorous host. Comparative genomics of 13 Stammera strains revealed high functional conservation, highlighted by the universal presence of polygalacturonase, a primary pectinase targeting nature's most abundant pectic class, homogalacturonan (HG). Despite this conservation, we unexpectedly discovered a disparate distribution for rhamnogalacturonan lyase, a secondary pectinase hydrolyzing the pectic heteropolymer, rhamnogalacturonan I (RG-I). Consistent with the annotation of rhamnogalacturonan lyase in Stammera, cassidines are able to depolymerize RG-I relative to beetles whose symbionts lack the gene. Given the omnipresence of HG and RG-I in foliage, Stammera that encode pectinases targeting both substrates allow their hosts to overcome a greater diversity of plant cell wall polysaccharides and maximize access to the nutritionally rich cytosol. Possibly facilitated by their symbionts' expanded digestive range, cassidines additionally endowed with rhamnogalacturonan lyase appear to utilize a broader diversity of angiosperms than those beetles whose symbionts solely supplement polygalacturonase. Our findings highlight how symbiont metabolic diversity, in concert with host adaptations, may serve as a potential source of evolutionary innovations for herbivorous lineages.
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Affiliation(s)
- Hassan Salem
- Department of Biology, Emory University, Atlanta, GA 30322, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Mutualisms Research Group, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Minoru Moriyama
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
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Huang X, Zhang R, Qiu Y, Wu H, Xiang Q, Yu X, Zhao K, Zhang X, Chen Q, Penttinen P, Gu Y. RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns in Lentinula edodes at Brown Film Formation Stage Under Blue Light Induction. Front Microbiol 2020; 11:1044. [PMID: 32536907 PMCID: PMC7267012 DOI: 10.3389/fmicb.2020.01044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Lentinula edodes (shiitake mushroom) is one of the most important edible mushrooms worldwide. The L. edodes cultivation cycle includes a unique developing stage called brown film formation that directly affects the development of primordium and the quality of fruiting body. Brown film formation is induced by light, especially blue light. To promote our understanding of the role of blue light in brown film formation mechanisms of L. edodes, we used RNA-seq and compared the transcriptomes of L. edodes grown under blue light and in dark, and validated the expression profiles using qRT-PCR. Blue light stimulated the formation of brown film and increased the content of polysaccharides in L. edodes. Blue light also promoted L. edodes to absorb more polysaccharides by enhancing the activities of enzymes. Among the 730 differentially expressed genes (DEGs), 433 genes were up-regulated and 297 were down-regulated. Most of the DEGs were in the oxidoreductase activity group. Pentose and glucuronic acid conversion and starch and sucrose metabolism were the most important pathways in the formation of brown film. A total of 79 genes of DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes). Fifty-one of the CAZymes genes were up-regulated, suggesting that CAZymes play important roles in brown film formation to provide sufficient nutrition for L. edodes. The results will facilitate future functional investigations of the genes involved in the developmental control of L. edodes.
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Affiliation(s)
- Xiying Huang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Runji Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yijie Qiu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Haibing Wu
- Department of Livestock and Fisheries, Mianyang Academy of Agricultural University, Mianyang, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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16
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Thines M, Sharma R, Rodenburg SYA, Gogleva A, Judelson HS, Xia X, van den Hoogen J, Kitner M, Klein J, Neilen M, de Ridder D, Seidl MF, van den Ackerveken G, Govers F, Schornack S, Studholme DJ. The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:742-753. [PMID: 32237964 DOI: 10.1094/mpmi-07-19-0211-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N50 scaffold length of around 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of P. belbahrii. P. belbahrii has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
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Affiliation(s)
- Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Rahul Sharma
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna Gogleva
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521 U.S.A
| | - Xiaojuan Xia
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manon Neilen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guido van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
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17
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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18
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Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR. Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes. PLoS One 2019; 14:e0226106. [PMID: 31830116 PMCID: PMC6907798 DOI: 10.1371/journal.pone.0226106] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.
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Affiliation(s)
- Wenjie Wu
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
| | | | - Leila M. Blackman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, the Australian National University, Canberra, Australia
| | | | | | - David A. Jones
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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19
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Phytophthora ramorum and Phytophthora gonapodyides Differently Colonize and Contribute to the Decomposition of Green and Senesced Umbellularia californica Leaves in a Simulated Stream Environment. FORESTS 2019. [DOI: 10.3390/f10050434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Plant pathogenic as well as saprotrophic Phytophthora species are now known to inhabit forest streams and other surface waters. How they survive and function in aquatic ecosystems, however, remains largely uninvestigated. Phytophthora ramorum, an invasive pathogen in California forests, regularly occurs in forest streams, where it can colonize green leaves shed in the stream but is quickly and largely succeeded by saprotrophically competent clade 6 Phytophthora species, such as Phytophthora gonapodyides. We investigated, using controlled environment experiments, whether leaf litter quality, based on senescence, affects how P. ramorum and P. gonapodyides compete in leaf colonization and to what extent each species can contribute to leaf decomposition. We found that both Phytophthora species effectively colonized and persisted on green or yellow (senescing) bay leaves, but only P. gonapodyides could also colonize and persist on brown (fully senesced and dried) leaves. Both Phytophthora species similarly accelerated the decomposition of green leaves and yellow leaves compared with non-inoculated controls, but colonization of brown leaves by P. gonapodyides did not affect their decomposition rate.
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Toljamo A, Blande D, Munawar M, Kärenlampi SO, Kokko H. Expression of the GAF Sensor, Carbohydrate-Active Enzymes, Elicitins, and RXLRs Differs Markedly Between Two Phytophthora cactorum Isolates. PHYTOPATHOLOGY 2019; 109:726-735. [PMID: 30412010 DOI: 10.1094/phyto-04-18-0136-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant species. P. cactorum isolates differ in host specificity; for example, strawberry crown rot is often caused by a specialized pathotype. Here we compared the transcriptomes of two P. cactorum isolates that differ in their virulence to garden strawberry (Pc407: high virulence; Pc440: low virulence). De novo transcriptome assembly and clustering of contigs resulted in 19,372 gene clusters. Two days after inoculation of Fragaria vesca roots, 3,995 genes were differently expressed between the P. cactorum isolates. One of the genes that were highly expressed only in Pc407 encodes a GAF sensor protein potentially involved in membrane trafficking processes. Two days after inoculation, elicitins were highly expressed in Pc407 and lipid catabolism appeared to be more active than in Pc440. Of the carbohydrate-active enzymes, those that degrade pectin were often more highly expressed in Pc440, whereas members of glycosyl hydrolase family 1, potentially involved in the metabolism of glycosylated secondary metabolites, were more highly expressed in Pc407 at the time point studied. Differences were also observed among the RXLR effectors: Pc407 appears to rely on a smaller set of key RXLR effectors, whereas Pc440 expresses a greater number of RXLRs. This study is the first step toward improving understanding of the molecular basis of differences in the virulence of P. cactorum isolates. Identification of the key effectors is important, as it enables effector-assisted breeding strategies toward crown rot-resistant strawberry cultivars.
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Affiliation(s)
- Anna Toljamo
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Daniel Blande
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Mustafa Munawar
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Sirpa O Kärenlampi
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Harri Kokko
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
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21
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Judelson HS, Ah-Fong AMV. Exchanges at the Plant-Oomycete Interface That Influence Disease. PLANT PHYSIOLOGY 2019; 179:1198-1211. [PMID: 30538168 PMCID: PMC6446794 DOI: 10.1104/pp.18.00979] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
Molecular exchanges between plants and biotrophic, hemibiotrophic, and necrotrophic oomycetes affect disease progression.
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Affiliation(s)
- Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521
| | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521
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22
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Hee WY, Blackman LM, Hardham AR. Characterisation of Stramenopile-specific mastigoneme proteins in Phytophthora parasitica. PROTOPLASMA 2019; 256:521-535. [PMID: 30302550 DOI: 10.1007/s00709-018-1314-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
Mastigonemes, tripartite tubular hairs on the anterior flagellum of Phytophthora zoospores, are instrumental for disease dissemination to new host plants. A previous study showed that PnMas2 was part of the tubular shaft of Phytophthora parasitica mastigonemes. In the current study, genes encoding two related proteins, PnMas1 and PnMas3, were identified in the genome of P. parasitica. PnMas1 interacts with PnMas2 and also occurs along the mastigoneme shaft. RNA-Seq analyses indicate that PnMas1 and PnMas2 genes have similar expression profiles both in vitro and in planta but that PnMas3 is expressed temporally prior to PnMas1 and PnMas2 during asexual development and plant infection. Immunocytochemistry and GFP-tagging document the occurrence of all three PnMas proteins within the specialised compartments of the ER during mastigoneme formation, but only PnMas1 and PnMas2 occur in mature mastigonemes on the flagellar surface. Anti-PnMas1 and anti-PnMas2 antibodies co-labelled two high-molecular-weight (~400 kDa) protein complexes in native gels but anti-PnMas3 antibodies labelled a 65 kDa protein complex. Liquid chromatography-mass spectrometry analysis identified PnMas1 and PnMas2 but not PnMas3 in flagellar extracts. These results suggest that PnMas3 associates with mastigonemes during their assembly within the ER but is not part of mature mastigonemes on the anterior flagellum. Phylogenetic analyses using homologues of Mas genes from the genomes of 28 species of Stramenopiles give evidence of three Mas sub-families, namely Mas1, Mas2 and Mas3. BLAST analyses showed that Mas genes only occur in flagellate species within the Stramenopile taxon.
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Affiliation(s)
- Wei Yih Hee
- Plant Science Division, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia.
| | - Leila M Blackman
- Plant Science Division, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Adrienne R Hardham
- Plant Science Division, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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23
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Ajengui A, Bertolini E, Ligorio A, Chebil S, Ippolito A, Sanzani SM. Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms. PLANT CELL REPORTS 2018; 37:483-499. [PMID: 29290008 DOI: 10.1007/s00299-017-2244-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.
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Affiliation(s)
- Arwa Ajengui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisia
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Angela Ligorio
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Samir Chebil
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
| | - Antonio Ippolito
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Simona Marianna Sanzani
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
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What has happened to the “aquatic phycomycetes” (sensu Sparrow)? Part II: Shared properties of zoosporic true fungi and fungus-like microorganisms. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Lai MW, Liou RF. Two genes encoding GH10 xylanases are essential for the virulence of the oomycete plant pathogen Phytophthora parasitica. Curr Genet 2018; 64:931-943. [PMID: 29470644 DOI: 10.1007/s00294-018-0814-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/29/2022]
Abstract
Plant cell walls are pivotal battlegrounds between microbial pathogens and their hosts. To penetrate the cell wall and thereby to facilitate infection, microbial pathogens are equipped with a wide array of cell wall-degrading enzymes to depolymerize the polysaccharides in the cell wall. However, many of these enzymes and their role in the pathogenesis of microbial pathogens are not characterized, especially those from Oomycetes. In this study, we analyzed the function of four putative endo-beta-1,4-xylanase-encoding genes (ppxyn1-ppxyn4) from Phytophthora parasitica, an oomycete plant pathogen known to cause severe disease in a wide variety of plant species. All four genes belong to the glycoside hydrolase family 10 (GH10). Recombinant proteins of ppxyn1, ppxyn2, and ppxyn4 obtained from the yeast Pichia pastoris showed degrading activities toward birch wood xylan, but they behaved differently in terms of the conditions for optimal activity, thermostability, and durability. Quantitative RT-PCR revealed upregulated expression of all four genes, especially ppxyn1 and ppxyn2, during plant infection. In contrast, ppxyn3 was highly expressed in cysts and its close homolog, ppxyn4, in germinating cysts. To uncover the role of ppxyn1 and ppxyn2 in the pathogenesis of P. parasitica, we generated silencing transformants for these two genes by double-stranded RNA-mediated gene silencing. Silencing ppxyn1 and ppxyn2 reduced the virulence of P. parasitica toward tobacco (Nicotiana benthamiana) and tomato plants. These results demonstrate the crucial role of xylanase-encoding ppxyn1 and ppxyn2 in the infection process of P. parasitica.
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Affiliation(s)
- Ming-Wei Lai
- Department of Plant Pathology and Microbiology, National Taiwan University, #1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan
| | - Ruey-Fen Liou
- Department of Plant Pathology and Microbiology, National Taiwan University, #1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
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Hardham AR, Blackman LM. Phytophthora cinnamomi. MOLECULAR PLANT PATHOLOGY 2018; 19:260-285. [PMID: 28519717 PMCID: PMC6637996 DOI: 10.1111/mpp.12568] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/20/2017] [Accepted: 05/11/2017] [Indexed: 05/12/2023]
Abstract
Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5000 species of plants, including many of importance in agriculture, forestry and horticulture. The inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognized Global Biodiversity Hotspots, has had disastrous consequences for the environment and the biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores. Disease control is difficult in agricultural and forestry situations and even more challenging in natural ecosystems as a result of the scale of the problem and the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires a comprehensive understanding of the cellular and molecular basis of pathogen development and pathogenicity. The application of next-generation sequencing technologies to generate genomic and transcriptomic data promises to underpin a new era in P. cinnamomi research and discovery. The aim of this review is to integrate bioinformatic analyses of P. cinnamomi sequence data with current knowledge of the cellular and molecular basis of P. cinnamomi growth, development and plant infection. The goal is to provide a framework for future research by highlighting potential pathogenicity genes, shedding light on their possible functions and identifying suitable targets for future control measures. TAXONOMY Phytophthora cinnamomi Rands; Kingdom Chromista; Phylum Oomycota or Pseudofungi; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 5000 species of plants, including 4000 Australian native species. Host plants important for agriculture and forestry include avocado, chestnut, macadamia, oak, peach and pineapple. DISEASE SYMPTOMS A root pathogen which causes rotting of fine and fibrous roots, but which can also cause stem cankers. Root damage may inhibit water movement from roots to shoots, leading to dieback of young shoots. USEFUL WEBSITES: http://fungidb.org/fungidb/; http://genome.jgi.doe.gov/Phyci1/Phyci1.home.html; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314365.1; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314505.1.
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Affiliation(s)
- Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
| | - Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
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27
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Noronha MF, Lacerda Júnior GV, Gilbert JA, de Oliveira VM. Taxonomic and functional patterns across soil microbial communities of global biomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1064-1074. [PMID: 28787780 DOI: 10.1016/j.scitotenv.2017.07.159] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 05/24/2023]
Affiliation(s)
- Melline Fontes Noronha
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil; Institute of Biology, Campinas University, Brazil.
| | - Gileno Vieira Lacerda Júnior
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil; Institute of Biology, Campinas University, Brazil
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA; The Microbiome Center, Bioscience Division, Argonne National Laboratory, Lemont, IL, USA
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil
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28
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Huang J, Gu L, Zhang Y, Yan T, Kong G, Kong L, Guo B, Qiu M, Wang Y, Jing M, Xing W, Ye W, Wu Z, Zhang Z, Zheng X, Gijzen M, Wang Y, Dong S. An oomycete plant pathogen reprograms host pre-mRNA splicing to subvert immunity. Nat Commun 2017; 8:2051. [PMID: 29233978 PMCID: PMC5727057 DOI: 10.1038/s41467-017-02233-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
The process of RNA splicing influences many physiological processes, including plant immunity. However, how plant parasites manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, physically binds to and stabilizes soybean serine/lysine/arginine-rich proteins GmSKRPs. The SKRPs are novel proteins that associate with a complex that contains plant spliceosome components, and are negative regulators of plant immunity. Analysis by RNA-seq data indicates that alternative splicing of pre-mRNAs from 401 soybean genes, including defense-related genes, is altered in GmSKRP1 and PsAvr3c overexpressing lines compared to control plants. Representative splicing events mediated by GmSKRP1 and PsAvr3c are tested by infection assays or by transient expression in soybean plants. Our results show that plant pathogen effectors can reprogram host pre-mRNA splicing to promote disease, and we propose that pathogens evolved such strategies to defeat host immune systems.
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Affiliation(s)
- Jie Huang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingxiu Yan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanghui Kong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liang Kong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baodian Guo
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Min Qiu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiman Xing
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
| | - Zhe Wu
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Zhengguang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
| | - Mark Gijzen
- Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China.
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Salem H, Bauer E, Kirsch R, Berasategui A, Cripps M, Weiss B, Koga R, Fukumori K, Vogel H, Fukatsu T, Kaltenpoth M. Drastic Genome Reduction in an Herbivore's Pectinolytic Symbiont. Cell 2017; 171:1520-1531.e13. [PMID: 29153832 DOI: 10.1016/j.cell.2017.10.029] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023]
Abstract
Pectin, an integral component of the plant cell wall, is a recalcitrant substrate against enzymatic challenges by most animals. In characterizing the source of a leaf beetle's (Cassida rubiginosa) pectin-degrading phenotype, we demonstrate its dependency on an extracellular bacterium housed in specialized organs connected to the foregut. Despite possessing the smallest genome (0.27 Mb) of any organism not subsisting within a host cell, the symbiont nonetheless retained a functional pectinolytic metabolism targeting the polysaccharide's two most abundant classes: homogalacturonan and rhamnogalacturonan I. Comparative transcriptomics revealed pectinase expression to be enriched in the symbiotic organs, consistent with enzymatic buildup in these structures following immunostaining with pectinase-targeting antibodies. Symbiont elimination results in a drastically reduced host survivorship and a diminished capacity to degrade pectin. Collectively, our findings highlight symbiosis as a strategy for an herbivore to metabolize one of nature's most complex polysaccharides and a universal component of plant tissues.
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Affiliation(s)
- Hassan Salem
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biology, Emory University, Atlanta, GA 30320, USA.
| | - Eugen Bauer
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Aileen Berasategui
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biology, Emory University, Atlanta, GA 30320, USA; Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Benjamin Weiss
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Evolutionary Ecology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Ryuichi Koga
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Evolutionary Ecology, Johannes Gutenberg University, Mainz 55128, Germany
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30
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Ah-Fong AMV, Shrivastava J, Judelson HS. Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. BMC Genomics 2017; 18:764. [PMID: 29017458 PMCID: PMC5635513 DOI: 10.1186/s12864-017-4151-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/02/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND How pathogen genomes evolve to support distinct lifestyles is not well-understood. The oomycete Phytophthora infestans, the potato blight agent, is a largely biotrophic pathogen that feeds from living host cells, which become necrotic only late in infection. The related oomycete Pythium ultimum grows saprophytically in soil and as a necrotroph in plants, causing massive tissue destruction. To learn what distinguishes their lifestyles, we compared their gene contents and expression patterns in media and a shared host, potato tuber. RESULTS Genes related to pathogenesis varied in temporal expression pattern, mRNA level, and family size between the species. A family's aggregate expression during infection was not proportional to size due to transcriptional remodeling and pseudogenization. Ph. infestans had more stage-specific genes, while Py. ultimum tended towards more constitutive expression. Ph. infestans expressed more genes encoding secreted cell wall-degrading enzymes, but other categories such as secreted proteases and ABC transporters had higher transcript levels in Py. ultimum. Species-specific genes were identified including new Pythium genes, perforins, which may disrupt plant membranes. Genome-wide ortholog analyses identified substantial diversified expression, which correlated with sequence divergence. Pseudogenization was associated with gene family expansion, especially in gene clusters. CONCLUSION This first large-scale analysis of transcriptional divergence within oomycetes revealed major shifts in genome composition and expression, including subfunctionalization within gene families. Biotrophy and necrotrophy seem determined by species-specific genes and the varied expression of shared pathogenicity factors, which may be useful targets for crop protection.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Jolly Shrivastava
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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31
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Antony B, Johny J, Aldosari SA, Abdelazim MM. Identification and expression profiling of novel plant cell wall degrading enzymes from a destructive pest of palm trees, Rhynchophorus ferrugineus. INSECT MOLECULAR BIOLOGY 2017; 26:469-484. [PMID: 28556365 DOI: 10.1111/imb.12314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant cell wall degrading enzymes (PCWDEs) from insects were recently identified as a multigene family of proteins that consist primarily of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) and play essential roles in the degradation of the cellulose/hemicellulose/pectin network in the invaded host plant. Here we applied transcriptomic and degenerate PCR approaches to identify the PCWDEs from a destructive pest of palm trees, Rhynchophorus ferrugineus, followed by a gut-specific and stage-specific differential expression analysis. We identified a total of 27 transcripts encoding GH family members and three transcripts of the CE family with cellulase, hemicellulase and pectinase activities. We also identified two GH9 candidates, which have not previously been reported from Curculionidae. The gut-specific quantitative expression analysis identified key cellulases, hemicellulases and pectinases from R. ferrugineus. The expression analysis revealed a pectin methylesterase, RferCE8u02, and a cellulase, GH45c34485, which showed the highest gut enriched expression. Comparison of PCWDE expression patterns revealed that cellulases and pectinases are significantly upregulated in the adult stages, and we observed specific high expression of the hemicellulase RferGH16c4170. Overall, our study revealed the potential of PCWDEs from R. ferrugineus, which may be useful in biotechnological applications and may represent new tools in R. ferrugineus pest management strategies.
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Affiliation(s)
- B Antony
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - J Johny
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - S A Aldosari
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M M Abdelazim
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Jones RW, Perez FG. A Small Cellulose-Binding-Domain Protein (CBD1) in Phytophthora is Highly Variable in the Non-binding Amino Terminus. Curr Microbiol 2017; 74:1287-1293. [PMID: 28748272 PMCID: PMC5640731 DOI: 10.1007/s00284-017-1315-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/19/2017] [Indexed: 01/05/2023]
Abstract
The small cellulose-binding-domain protein CBD1 is tightly bound to the cellulosic cell wall of the plant pathogenic stramenopile Phytophthora infestans. Transgene expression of the protein in potato plants also demonstrated binding to plant cell walls. A study was undertaken using 47 isolates of P. infestans from a worldwide collection, along with 17 other Phytophthora species and a related pathogen Plasmopara halstedii, to determine if the critical cell wall protein is subject to amino acid variability. Within the amino acid sequence of the secreted portion of CBD 1, encoded by the P. infestans isolates, 30 were identical with each other, and with P. mirabilis. Four isolates had one amino acid difference, each in a different location, while one isolate had two amino acid substitutions. The remaining 13 isolates had five amino acid changes that were each in identical locations (D17/G, D31/G, I32/S, T43/A, and G50/A), suggesting a single origin. Comparison of P. infestans CBD1 with other Phytophthora species identified extensive amino acid variation among the 60 amino acids at the amino terminus of the protein, and a high level of conservation from G61, where the critical cellulose-binding domain sequences begin, to the end of the protein (L110). While the region needed to bind to cellulose is conserved, the region that is available to interact with other cell wall components is subject to considerable variation, a feature that is evident even in the related genus Plasmopara. Specific changes can be used in determining intra- and inter-species relatedness. Application of this information allowed for the design of species-specific primers for PCR detection of P. infestans and P. sojae, by combining primers from the highly conserved and variable regions of the CBD1 gene.
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Affiliation(s)
- Richard W Jones
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA.
| | - Frances G Perez
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA
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Abstract
The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
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Ah-Fong AMV, Kim KS, Judelson HS. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics 2017; 18:198. [PMID: 28228125 PMCID: PMC5322657 DOI: 10.1186/s12864-017-3585-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis. CONCLUSIONS Spore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Kyoung Su Kim
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
- Present address: Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Korea
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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Raaymakers TM, Van den Ackerveken G. Extracellular Recognition of Oomycetes during Biotrophic Infection of Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:906. [PMID: 27446136 PMCID: PMC4915311 DOI: 10.3389/fpls.2016.00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/08/2016] [Indexed: 05/23/2023]
Abstract
Extracellular recognition of pathogens by plants constitutes an important early detection system in plant immunity. Microbe-derived molecules, also named patterns, can be recognized by pattern recognition receptors (PRRs) on the host cell membrane that trigger plant immune responses. Most knowledge on extracellular pathogen detection by plants comes from research on bacterial and fungal pathogens. For oomycetes, that comprise some of the most destructive plant pathogens, mechanisms of extracellular pattern recognition have only emerged recently. These include newly recognized patterns, e.g., cellulose-binding elicitor lectin, necrosis and ethylene-inducing peptide 1-like proteins (NLPs), and glycoside hydrolase 12, as well as their receptors, e.g., the putative elicitin PRR elicitin response and the NLP PRR receptor-like protein 23. Immunity can also be triggered by the release of endogenous host-derived patterns, as a result of oomycete enzymes or damage. In this review we will describe the types of patterns, both pathogen-derived exogenous and plant-derived endogenous ones, and what is known about their extracellular detection during (hemi-)biotrophic oomycete infection of plants.
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36
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Kirsch R, Heckel DG, Pauchet Y. How the rice weevil breaks down the pectin network: Enzymatic synergism and sub-functionalization. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 71:72-82. [PMID: 26899322 DOI: 10.1016/j.ibmb.2016.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 05/19/2023]
Abstract
Pectin is the most complex polysaccharide in nature and highly abundant in plant cell walls and middle lamellae, where it functions in plant growth and development. Phytopathogens utilize plant pectin as an energy source through enzyme-mediated degradation. These pectolytic enzymes include polygalacturonases (PGs) of the GH28 family and pectin methylesterases (PMEs) of the CE8 family. Recently, PGs were also identified in herbivorous insects of the distantly related plant bug, stick insect and Phytophaga beetle lineages. Unlike all other insects, weevils possess PMEs in addition to PGs. To investigate pectin digestion in insects and the role of PMEs in weevils, all PME and PG family members of the rice weevil Sitophilus oryzae were heterologously expressed and functionally characterized. Enzymatically active and inactive PG and PME family members were identified. The loss of activity can be explained by a lack of substrate binding correlating with substitutions of functionally important amino acid residues. We found subfunctionalization in both enzyme families, supported by expression pattern and substrate specificities as well as evidence for synergistic pectin breakdown. Our data suggest that the rice weevil might be able to use pectin as an energy source, and illustrates the potential of both PG and PME enzyme families to functionally diversify after horizontal gene transfer.
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Affiliation(s)
- Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany.
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany.
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Zhang S, Hu B, Wei W, Xiong Y, Zhu W, Peng F, Yu Y, Zheng Y, Chen P. De Novo Analysis of Wolfiporia cocos Transcriptome to Reveal the Differentially Expressed Carbohydrate-Active Enzymes (CAZymes) Genes During the Early Stage of Sclerotial Growth. Front Microbiol 2016; 7:83. [PMID: 26870032 PMCID: PMC4738778 DOI: 10.3389/fmicb.2016.00083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
The sclerotium of Wolfiporia cocos has been used as an edible mushroom and/or a traditional herbal medicine for centuries. W. cocos sclerotial formation is dependent on parasitism of the wood of Pinus species. Currently, the sclerotial development mechanisms of W. cocos remain largely unknown and the lack of pine resources limit the commercial production. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of the plant cell wall to provide carbohydrates for fungal growth, development, and reproduction. In this study, the transcript profiles from W. cocos mycelium and 2-months-old sclerotium, the early stage of sclerotial growth, were specially analyzed using de novo sequencing technology. A total of 142,428,180 high-quality reads of mycelium and 70,594,319 high-quality reads of 2-months-old sclerotium were obtained. Additionally, differentially expressed genes from the W. cocos mycelium and 2-months-old sclerotium stages were analyzed, resulting in identification of 69 CAZymes genes which were significantly up-regulated during the early stage of sclerotial growth compared to that of in mycelium stage, and more than half of them belonged to glycosyl hydrolases (GHs) family, indicating the importance of W. cocos GHs family for degrading the pine woods. And qRT-PCR was further used to confirm the expression pattern of these up-regulated CAZymes genes. Our results will provide comprehensive CAZymes genes expression information during W. cocos sclerotial growth at the transcriptional level and will lay a foundation for functional genes studies in this fungus. In addition, our study will also facilitate the efficient use of limited pine resources, which is significant for promoting steady development of Chinese W. cocos industry.
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Affiliation(s)
- Shaopeng Zhang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Bingxiong Hu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Wei Wei
- Institute for Interdisciplinary Research, Jianghan University Wuhan, China
| | - Ying Xiong
- Hefei Enzyme Information Technology Co., Ltd Wuhan, China
| | - Wenjun Zhu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Fang Peng
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Yang Yu
- College of Plant Protection, Southwest University Chongqing, China
| | - Yonglian Zheng
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Ping Chen
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
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