1
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Yang H, Kim X, Skłenar J, Aubourg S, Sancho-Andrés G, Stahl E, Guillou MC, Gigli-Bisceglia N, Tran Van Canh L, Bender KW, Stintzi A, Reymond P, Sánchez-Rodríguez C, Testerink C, Renou JP, Menke FLH, Schaller A, Rhodes J, Zipfel C. Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES. NATURE PLANTS 2023; 9:2085-2094. [PMID: 38049516 DOI: 10.1038/s41477-023-01583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 11/03/2023] [Indexed: 12/06/2023]
Abstract
Plant signalling peptides are typically released from larger precursors by proteolytic cleavage to regulate plant growth, development and stress responses. Recent studies reported the characterization of a divergent family of Brassicaceae-specific peptides, SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs), and their perception by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2). Here, we reveal that the SCOOP family is highly expanded, containing at least 50 members in the Columbia-0 reference Arabidopsis thaliana genome. Notably, perception of these peptides is strictly MIK2-dependent. How bioactive SCOOP peptides are produced, and to what extent their perception is responsible for the multiple physiological roles associated with MIK2 are currently unclear. Using N-terminomics, we validate the N-terminal cleavage site of representative PROSCOOPs. The cleavage sites are determined by conserved motifs upstream of the minimal SCOOP bioactive epitope. We identified subtilases necessary and sufficient to process PROSCOOP peptides at conserved cleavage motifs. Mutation of these subtilases, or their recognition motifs, suppressed PROSCOOP cleavage and associated overexpression phenotypes. Furthermore, we show that higher-order mutants of these subtilases show phenotypes reminiscent of mik2 null mutant plants, consistent with impaired PROSCOOP biogenesis, and demonstrating biological relevance of SCOOP perception by MIK2. Together, this work provides insights into the molecular mechanisms underlying the functions of the recently identified SCOOP peptides and their receptor MIK2.
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Affiliation(s)
- Huanjie Yang
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xeniya Kim
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Jan Skłenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sébastien Aubourg
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Elia Stahl
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Nora Gigli-Bisceglia
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Loup Tran Van Canh
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Kyle W Bender
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Annick Stintzi
- Institute of Biology, Plant Physiology and Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Jean-Pierre Renou
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andreas Schaller
- Institute of Biology, Plant Physiology and Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Jack Rhodes
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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2
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Hafiz FB, Geistlinger J, Al Mamun A, Schellenberg I, Neumann G, Rozhon W. Tissue-Specific Hormone Signalling and Defence Gene Induction in an In Vitro Assembly of the Rapeseed Verticillium Pathosystem. Int J Mol Sci 2023; 24:10489. [PMID: 37445666 DOI: 10.3390/ijms241310489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/11/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Priming plants with beneficial microbes can establish rapid and robust resistance against numerous pathogens. Here, compelling evidence is provided that the treatment of rapeseed plants with Trichoderma harzianum OMG16 and Bacillus velezensis FZB42 induces defence activation against Verticillium longisporum infection. The relative expressions of the JA biosynthesis genes LOX2 and OPR3, the ET biosynthesis genes ACS2 and ACO4 and the SA biosynthesis and signalling genes ICS1 and PR1 were analysed separately in leaf, stem and root tissues using qRT-PCR. To successfully colonize rapeseed roots, the V. longisporum strain 43 pathogen suppressed the biosynthesis of JA, ET and SA hormones in non-primed plants. Priming led to fast and strong systemic responses of JA, ET and SA biosynthesis and signalling gene expression in each leaf, stem and root tissue. Moreover, the quantification of plant hormones via UHPLC-MS analysis revealed a 1.7- and 2.6-fold increase in endogenous JA and SA in shoots of primed plants, respectively. In roots, endogenous JA and SA levels increased up to 3.9- and 2.3-fold in Vl43-infected primed plants compared to non-primed plants, respectively. Taken together, these data indicate that microbial priming stimulates rapeseed defence responses against Verticillium infection and presumably transduces defence signals from the root to the upper parts of the plant via phytohormone signalling.
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Affiliation(s)
- Fatema Binte Hafiz
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Abdullah Al Mamun
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Günter Neumann
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Germany
| | - Wilfried Rozhon
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
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3
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Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
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Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
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4
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Jiang M, Zhang Y, Yang X, Li X, Lang H. Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1135684. [PMID: 36909380 PMCID: PMC9998908 DOI: 10.3389/fpls.2023.1135684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Yuting Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Yang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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5
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Wang L, Calabria J, Chen HW, Somssich M. The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6052-6067. [PMID: 35709954 PMCID: PMC9578349 DOI: 10.1093/jxb/erac263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Fusarium oxysporum is a soil-borne fungal pathogen of several major food crops. Research on understanding the molecular details of fungal infection and the plant's defense mechanisms against this pathogen has long focused mainly on the tomato-infecting F. oxysporum strains and their specific host plant. However, in recent years, the Arabidopsis thaliana-Fusarium oxysporum strain 5176 (Fo5176) pathosystem has additionally been established to study this plant-pathogen interaction with all the molecular biology, genetic, and genomic tools available for the A. thaliana model system. Work on this system has since produced several new insights, especially with regards to the role of phytohormones involved in the plant's defense response, and the receptor proteins and peptide ligands involved in pathogen detection. Furthermore, work with the pathogenic strain Fo5176 and the related endophytic strain Fo47 has demonstrated the suitability of this system for comparative studies of the plant's specific responses to general microbe- or pathogen-associated molecular patterns. In this review, we highlight the advantages of this specific pathosystem, summarize the advances made in studying the molecular details of this plant-fungus interaction, and point out open questions that remain to be answered.
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Affiliation(s)
- Liu Wang
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jacob Calabria
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hsiang-Wen Chen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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6
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Jiang M, Li X, Dong X, Zu Y, Zhan Z, Piao Z, Lang H. Research Advances and Prospects of Orphan Genes in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:947129. [PMID: 35874010 PMCID: PMC9305701 DOI: 10.3389/fpls.2022.947129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Ye Zu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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7
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Moon H, Jeong AR, Kwon OK, Park CJ. Oryza-Specific Orphan Protein Triggers Enhanced Resistance to Xanthomonas oryzae pv. oryzae in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:859375. [PMID: 35360326 PMCID: PMC8961030 DOI: 10.3389/fpls.2022.859375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/17/2022] [Indexed: 05/27/2023]
Abstract
All genomes carry lineage-specific orphan genes lacking homology in their closely related species. Identification and functional study of the orphan genes is fundamentally important for understanding lineage-specific adaptations including acquirement of resistance to pathogens. However, most orphan genes are of unknown function due to the difficulties in studying them using helpful comparative genomics. Here, we present a defense-related Oryza-specific orphan gene, Xio1, specifically induced by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) in an immune receptor XA21-dependent manner. Salicylic acid (SA) and ethephon (ET) also induced its expression, but methyl jasmonic acid (MeJA) reduced its basal expression. C-terminal green fluorescent protein (GFP) tagged Xio1 (Xio1-GFP) was visualized in the nucleus and the cytosol after polyethylene glycol (PEG)-mediated transformation in rice protoplasts and Agrobacterium-mediated infiltration in tobacco leaves. Transgenic rice plants overexpressing Xio1-GFP showed significantly enhanced resistance to Xoo with reduced lesion lengths and bacterial growth, in company with constitutive expression of defense-related genes. However, all of the transgenic plants displayed severe growth retardation and premature death. Reactive oxygen species (ROS) was significantly produced in rice protoplasts constitutively expressing Xio1-GFP. Overexpression of Xio1-GFP in non-Oryza plant species, Arabidopsis thaliana, failed to induce growth retardation and enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000. Our results suggest that the defense-related orphan gene Xio1 plays an important role in distinctive mechanisms evolved within the Oryza and provides a new source of Oryza-specific genes for crop-breeding programs.
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Affiliation(s)
- Hyeran Moon
- Department of Molecular Biology, Sejong University, Seoul, South Korea
| | - A-Ram Jeong
- Department of Molecular Biology, Sejong University, Seoul, South Korea
| | - Oh-Kyu Kwon
- Department of Molecular Biology, Sejong University, Seoul, South Korea
| | - Chang-Jin Park
- Department of Molecular Biology, Sejong University, Seoul, South Korea
- Department of Bioresources Engineering, Sejong University, Seoul, South Korea
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8
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Omidvar R, Vosseler N, Abbas A, Gutmann B, Grünwald-Gruber C, Altmann F, Siddique S, Bohlmann H. Analysis of a gene family for PDF-like peptides from Arabidopsis. Sci Rep 2021; 11:18948. [PMID: 34556705 PMCID: PMC8460643 DOI: 10.1038/s41598-021-98175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/31/2021] [Indexed: 11/09/2022] Open
Abstract
Plant defensins are small, basic peptides that have a characteristic three-dimensional folding pattern which is stabilized by four disulfide bridges. We show here that Arabidopsis contains in addition to the proper plant defensins a group of 9 plant defensin-like (PdfL) genes. They are all expressed at low levels while GUS fusions of the promoters showed expression in most tissues with only minor differences. We produced two of the encoded peptides in E. coli and tested the antimicrobial activity in vitro. Both were highly active against fungi but had lower activity against bacteria. At higher concentrations hyperbranching and swollen tips, which are indicative of antimicrobial activity, were induced in Fusarium graminearum by both peptides. Overexpression lines for most PdfL genes were produced using the 35S CaMV promoter to study their possible in planta function. With the exception of PdfL4.1 these lines had enhanced resistance against F. oxysporum. All PDFL peptides were also transiently expressed in Nicotiana benthamiana leaves with agroinfiltration using the pPZP3425 vector. In case of PDFL1.4 this resulted in complete death of the infiltrated tissues after 7 days. All other PDFLs resulted only in various degrees of small necrotic lesions. In conclusion, our results show that at least some of the PdfL genes could function in plant resistance.
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Affiliation(s)
- Reza Omidvar
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Nadine Vosseler
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria
| | - Amjad Abbas
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Birgit Gutmann
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria
- RIVIERA Pharma and Cosmetics GmbH, Holzhackerstraße 1, Tulln, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Shahid Siddique
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences Vienna, UFT Tulln, Konrad Lorenz Str. 24, 3430, Tulln, Austria.
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9
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Dossa K, Zhou R, Li D, Liu A, Qin L, Mmadi MA, Su R, Zhang Y, Wang J, Gao Y, Zhang X, You J. A novel motif in the 5'-UTR of an orphan gene 'Big Root Biomass' modulates root biomass in sesame. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1065-1079. [PMID: 33369837 PMCID: PMC8131042 DOI: 10.1111/pbi.13531] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 05/06/2023]
Abstract
Developing crops with improved root system is crucial in current global warming scenario. Underexploited crops are valuable reservoirs of unique genes that can be harnessed for the improvement of major crops. In this study, we performed genome-wide association studies on seven root traits in sesame (Sesamum indicum L.) and uncovered 409 significant signals, 19 quantitative trait loci containing 32 candidate genes. A peak SNP significantly associated with root number and root dry weight traits was located in the promoter of the gene named 'Big Root Biomass' (BRB), which was subsequently validated in a bi-parental population. BRB has no functional annotation and is restricted to the Lamiales order. We detected the presence of a novel motif 'AACACACAC' located in the 5'-UTR of BRB in single and duplicated copy in accessions with high and small root biomass, respectively. A strong expression level of BRB was negatively correlated with high root biomass, and this was attributed to the gene SiMYB181 which represses the activity of BRB by binding specifically to the single motif but not to the duplicated one. Curiously, the allele that enhanced BRB expression has been intensively selected by modern breeding. Overexpression of BRB in Arabidopsis modulates auxin pathway leading to reduced root biomass, improved yield parameters under normal growth conditions and increased drought stress sensitivity. Overall, BRB represents a solid gene model for improving the performance of sesame and other crops.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
- Laboratory of Genetics, Horticulture and Seed SciencesFaculty of Agronomic SciencesUniversity of Abomey‐CalaviCotonouBenin
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Lu Qin
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Marie A. Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Ruqi Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Yujuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
- Cotton Research CenterShandong Academy of Agricultural SciencesJinanChina
| | - Jianqiang Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
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Brennan CJ, Zhou B, Benbow HR, Ajaz S, Karki SJ, Hehir JG, O’Driscoll A, Feechan A, Mullins E, Doohan FM. Taxonomically Restricted Wheat Genes Interact With Small Secreted Fungal Proteins and Enhance Resistance to Septoria Tritici Blotch Disease. FRONTIERS IN PLANT SCIENCE 2020; 11:433. [PMID: 32477375 PMCID: PMC7236048 DOI: 10.3389/fpls.2020.00433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Understanding the nuances of host/pathogen interactions are paramount if we wish to effectively control cereal diseases. In the case of the wheat/Zymoseptoria tritici interaction that leads to Septoria tritici blotch (STB) disease, a 10,000-year-old conflict has led to considerable armaments being developed on both sides which are not reflected in conventional model systems. Taxonomically restricted genes (TRGs) have evolved in wheat to better allow it to cope with stress caused by fungal pathogens, and Z. tritici has evolved specialized effectors which allow it to manipulate its' host. A microarray focused on the latent phase response of a resistant wheat cultivar (cv. Stigg) and susceptible wheat cultivar (cv. Gallant) to Z. tritici infection was mined for TRGs within the Poaceae. From this analysis, we identified two TRGs that were significantly upregulated in response to Z. tritici infection, Septoria-responsive TRG6 and 7 (TaSRTRG6 and TaSRTRG7). Virus induced silencing of these genes resulted in an increased susceptibility to STB disease in cvs. Gallant and Stigg, and significantly so in the latter (2.5-fold increase in STB disease). In silico and localization studies categorized TaSRTRG6 as a secreted protein and TaSRTRG7 as an intracellular protein. Yeast two-hybrid analysis and biofluorescent complementation studies demonstrated that both TaSRTRG6 and TaSRTRG7 can interact with small proteins secreted by Z. tritici (potential effector candidates). Thus we conclude that TRGs are an important part of the wheat-Z. tritici co-evolution story and potential candidates for modulating STB resistance.
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Affiliation(s)
- Ciarán J. Brennan
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Binbin Zhou
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Harriet R. Benbow
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Sobia Ajaz
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Sujit J. Karki
- School of Agriculture and Food Science, University College Dublin, Belfield, Ireland
| | | | | | - Angela Feechan
- School of Agriculture and Food Science, University College Dublin, Belfield, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc, Carlow, Ireland
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
- *Correspondence: Fiona M. Doohan,
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11
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Wu L, Du G, Bao R, Li Z, Gong Y, Liu F. De novo assembly and discovery of genes involved in the response of Solanum sisymbriifolium to Verticillium dahlia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1009-1027. [PMID: 31402823 PMCID: PMC6656901 DOI: 10.1007/s12298-019-00666-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/20/2019] [Accepted: 04/02/2019] [Indexed: 05/27/2023]
Abstract
Verticillium wilt, caused by the soil-borne fungus Verticillium dahliae, is a devastating disease of eggplant (Solanum spp.) and causes substantial losses worldwide. Although some genes or biological processes involved in the interaction between eggplant and V. dahliae have been identified in some studies, the underlying molecular mechanism is not yet clear. Here, we monitored the transcriptomic profiles of the roots of resistant S. sisymbriifolium plants challenged with V. dahliae. Based on the measurements of physiological indexes (T-SOD, POD and SSs), three time points were selected and subsequently divided into two stages (S_12 h vs. S_0 h and S_48 h vs. S_12 h). KEGG enrichment analysis of the DEGs revealed several genes putatively involved in regulating plant-V. dahliae interactions, including mitogen-activated protein kinase (MAPK) genes (MEKK1 and MAP2K1), WRKY genes (WRKY22 and WRKY33) and cytochrome P450 (CYP) genes (CYP73A/C4H, CYP98A/C3'H and CYP84A/F5H). In addition, a subset of genes that play an important role in activating V. dahliae defence responses, including Ve genes as well as genes encoding PR proteins and TFs, were screened and are discussed. These results will help to identify key resistance genes and will contribute to a further understanding of molecular mechanisms of the S. sisymbriifolium resistance response to V. dahliae.
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Affiliation(s)
- Liyan Wu
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205 Yunnan China
| | - Guanghui Du
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
| | - Rui Bao
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205 Yunnan China
| | - Zhibin Li
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205 Yunnan China
| | - Yaju Gong
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205 Yunnan China
| | - Feihu Liu
- Plant Improvement and Utilization Lab, Yunnan University, Kunming, 650091 Yunnan China
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12
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Jiang M, Dong X, Lang H, Pang W, Zhan Z, Li X, Piao Z. Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa. Int J Mol Sci 2018; 19:ijms19072064. [PMID: 30012965 PMCID: PMC6073354 DOI: 10.3390/ijms19072064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 11/16/2022] Open
Abstract
Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.
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Affiliation(s)
- Mingliang Jiang
- College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, China.
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming 650504, China.
| | - Hong Lang
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China.
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, China.
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, China.
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, China.
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, China.
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13
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Depotter JRL, Deketelaere S, Inderbitzin P, Tiedemann AV, Höfte M, Subbarao KV, Wood TA, Thomma BPHJ. Verticillium longisporum, the invisible threat to oilseed rape and other brassicaceous plant hosts. MOLECULAR PLANT PATHOLOGY 2016; 17:1004-16. [PMID: 26663851 PMCID: PMC6638321 DOI: 10.1111/mpp.12350] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 05/21/2023]
Abstract
INTRODUCTION The causal agents of Verticillium wilts are globally distributed pathogens that cause significant crop losses every year. Most Verticillium wilts are caused by V. dahliae, which is pathogenic on a broad range of plant hosts, whereas other pathogenic Verticillium species have more restricted host ranges. In contrast, V. longisporum appears to prefer brassicaceous plants and poses an increasing problem to oilseed rape production. TAXONOMY Kingdom Fungi; Phylum Ascomycota; Class Sordariomycetes; Subclass Hypocreomycetida; Family Plectosphaerellaceae; genus Verticillium. DISEASE SYMPTOMS Dark unilateral stripes appear on the stems of apparently healthy looking oilseed rape plants at the end of the growing season. Microsclerotia are subsequently formed in the stem cortex beneath the epidermis. GENOME Verticillium longisporum is the only non-haploid species in the Verticillium genus, as it is an amphidiploid hybrid that carries almost twice as much genetic material as the other Verticillium species as a result of interspecific hybridization. DISEASE MANAGEMENT There is no effective fungicide treatment to control Verticillium diseases, and resistance breeding is the preferred strategy for disease management. However, only a few Verticillium wilt resistance genes have been identified, and monogenic resistance against V. longisporum has not yet been found. Quantitative resistance exists mainly in the Brassica C-genome of parental cabbage lines and may be introgressed in oilseed rape breeding lines. COMMON NAME Oilseed rape colonized by V. longisporum does not develop wilting symptoms, and therefore the common name of Verticillium wilt is unsuitable for this crop. Therefore, we propose 'Verticillium stem striping' as the common name for Verticillium infections of oilseed rape.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Silke Deketelaere
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, B-9000, Ghent, Belgium
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Andreas Von Tiedemann
- Department of Crop Sciences, Plant Pathology and Crop Protection Division, Georg-August University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, B-9000, Ghent, Belgium
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
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Perochon A, Jianguang J, Kahla A, Arunachalam C, Scofield SR, Bowden S, Wallington E, Doohan FM. TaFROG Encodes a Pooideae Orphan Protein That Interacts with SnRK1 and Enhances Resistance to the Mycotoxigenic Fungus Fusarium graminearum. PLANT PHYSIOLOGY 2015; 169:2895-906. [PMID: 26508775 PMCID: PMC4677899 DOI: 10.1104/pp.15.01056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/26/2015] [Indexed: 05/18/2023]
Abstract
All genomes encode taxonomically restricted orphan genes, and the vast majority are of unknown function. There is growing evidence that such genes play an important role in the environmental adaptation of taxa. We report the functional characterization of an orphan gene (Triticum aestivum Fusarium Resistance Orphan Gene [TaFROG]) as a component of resistance to the globally important wheat (T. aestivum) disease, Fusarium head blight. TaFROG is taxonomically restricted to the grass subfamily Pooideae. Gene expression studies showed that it is a component of the early wheat response to the mycotoxin deoxynivalenol (DON), which is a virulence factor produced by the causal fungal agent of Fusarium head blight, Fusarium graminearum. The temporal induction of TaFROG by F. graminearum in wheat spikelets correlated with the activation of the defense Triticum aestivum Pathogenesis-Related-1 (TaPR1) gene. But unlike TaPR1, TaFROG induction by F. graminearum was toxin dependent, as determined via comparative analysis of the effects of wild-type fungus and a DON minus mutant derivative. Using virus-induced gene silencing and overexpressing transgenic wheat lines, we present evidence that TaFROG contributes to host resistance to both DON and F. graminearum. TaFROG is an intrinsically disordered protein, and it localized to the nucleus. A wheat alpha subunit of the Sucrose Non-Fermenting1-Related Kinase1 was identified as a TaFROG-interacting protein based on a yeast two-hybrid study. In planta bimolecular fluorescence complementation assays confirmed the interaction. Thus, we conclude that TaFROG encodes a new Sucrose Non-Fermenting1-Related Kinase1-interacting protein and enhances biotic stress resistance.
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Affiliation(s)
- Alexandre Perochon
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Jia Jianguang
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Amal Kahla
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Chanemougasoundharam Arunachalam
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Steven R Scofield
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Sarah Bowden
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Emma Wallington
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
| | - Fiona M Doohan
- University College Dublin Earth Institute and School of Biology and Environmental Science, College of Science, University College Dublin, Belfield, Dublin 4, Ireland (A.P., J.J., A.K., C.A., F.M.D.);United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, and Purdue University, Department of Agronomy, West Lafayette, Indiana 47907-2054 (S.R.S.); andNational Institute of Agricultural Botany, Cambridge, CB3 0LE, United Kingdom (S.B., E.W.)
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15
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Arendsee ZW, Li L, Wurtele ES. Coming of age: orphan genes in plants. TRENDS IN PLANT SCIENCE 2014; 19:698-708. [PMID: 25151064 DOI: 10.1016/j.tplants.2014.07.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/27/2014] [Accepted: 07/17/2014] [Indexed: 05/19/2023]
Abstract
Sizable minorities of protein-coding genes from every sequenced eukaryotic and prokaryotic genome are unique to the species. These so-called ‘orphan genes’ may evolve de novo from non-coding sequence or be derived from older coding material. They are often associated with environmental stress responses and species-specific traits or regulatory patterns. However, difficulties in studying genes where comparative analysis is impossible, and a bias towards broadly conserved genes, have resulted in underappreciation of their importance. We review here the identification, possible origins, evolutionary trends, and functions of orphans with an emphasis on their role in plant biology. We exemplify several evolutionary trends with an analysis of Arabidopsis thaliana and present QQS as a model orphan gene.
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16
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Zhang B, Tremousaygue D, Denancé N, van Esse HP, Hörger AC, Dabos P, Goffner D, Thomma BPHJ, van der Hoorn RAL, Tuominen H. PIRIN2 stabilizes cysteine protease XCP2 and increases susceptibility to the vascular pathogen Ralstonia solanacearum in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:1009-19. [PMID: 24947605 PMCID: PMC4321228 DOI: 10.1111/tpj.12602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 05/18/2023]
Abstract
PIRIN (PRN) is a member of the functionally diverse cupin protein superfamily. There are four members of the Arabidopsis thaliana PRN family, but the roles of these proteins are largely unknown. Here we describe a function of the Arabidopsis PIRIN2 (PRN2) that is related to susceptibility to the bacterial plant pathogen Ralstonia solanacearum. Two prn2 mutant alleles displayed decreased disease development and bacterial growth in response to R. solanacearum infection. We elucidated the underlying molecular mechanism by analyzing PRN2 interactions with the papain-like cysteine proteases (PLCPs) XCP2, RD21A, and RD21B, all of which bound to PRN2 in yeast two-hybrid assays and in Arabidopsis protoplast co-immunoprecipitation assays. We show that XCP2 is stabilized by PRN2 through inhibition of its autolysis on the basis of PLCP activity profiling assays and enzymatic assays with recombinant protein. The stabilization of XCP2 by PRN2 was also confirmed in planta. Like prn2 mutants, an xcp2 single knockout mutant and xcp2 prn2 double knockout mutant displayed decreased susceptibility to R. solanacearum, suggesting that stabilization of XCP2 by PRN2 underlies susceptibility to R. solanacearum in Arabidopsis.
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Affiliation(s)
- Bo Zhang
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University901 87, Umeå, Sweden
| | - Dominique Tremousaygue
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, Unité Mixte de Recherche 44131326 Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 259431326 Castanet-Tolosan, France
| | - Nicolas Denancé
- Laboratoire de Recherche en Sciences Végétales, Unité Mixte de Recherche 5546, Université de Toulouse, UPS31326 Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 554631326 Castanet-Tolosan, France
| | - H Peter van Esse
- Laboratory of Phytopathology, Wageningen UniversityDroevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Anja C Hörger
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research50829, Cologne, Germany
| | - Patrick Dabos
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, Unité Mixte de Recherche 44131326 Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 259431326 Castanet-Tolosan, France
| | - Deborah Goffner
- Laboratoire de Recherche en Sciences Végétales, Unité Mixte de Recherche 5546, Université de Toulouse, UPS31326 Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 554631326 Castanet-Tolosan, France
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen UniversityDroevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research50829, Cologne, Germany
| | - Hannele Tuominen
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University901 87, Umeå, Sweden
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