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Wang Z, Zhong S, Zhang S, Zhang B, Zheng Y, Sun Y, Zhang Q, Liu X. A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription. PLoS Pathog 2024; 20:e1012138. [PMID: 38640110 PMCID: PMC11062530 DOI: 10.1371/journal.ppat.1012138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/01/2024] [Accepted: 03/20/2024] [Indexed: 04/21/2024] Open
Abstract
Proper transcription orchestrated by RNA polymerase II (RNPII) is crucial for cellular development, which is rely on the phosphorylation state of RNPII's carboxyl-terminal domain (CTD). Sporangia, developed from mycelia, are essential for the destructive oomycetes Phytophthora, remarkable transcriptional changes are observed during the morphological transition. However, how these changes are rapidly triggered and their relationship with the versatile RNPII-CTD phosphorylation remain enigmatic. Herein, we found that Phytophthora capsici undergone an elevation of Ser5-phosphorylation in its uncanonical heptapeptide repeats of RNPII-CTD during sporangia development, which subsequently changed the chromosomal occupation of RNPII and primarily activated transcription of certain genes. A cyclin-dependent kinase, PcCDK7, was highly induced and phosphorylated RNPII-CTD during this morphological transition. Mechanistically, a novel DCL1-dependent microRNA, pcamiR1, was found to be a feedback modulator for the precise phosphorylation of RNPII-CTD by complexing with PcAGO1 and regulating the accumulation of PcCDK7. Moreover, this study revealed that the pcamiR1-CDK7-RNPII regulatory module is evolutionarily conserved and the impairment of the balance between pcamiR1 and PcCDK7 could efficiently reduce growth and virulence of P. capsici. Collectively, this study uncovers a novel and evolutionary conserved mechanism of transcription regulation which could facilitate correct development and identifies pcamiR1 as a promising target for disease control.
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Affiliation(s)
- Zhiwen Wang
- China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Shan Zhong
- China Agricultural University, Beijing, China
| | | | - Borui Zhang
- China Agricultural University, Beijing, China
| | - Yang Zheng
- China Agricultural University, Beijing, China
| | - Ye Sun
- China Agricultural University, Beijing, China
| | | | - Xili Liu
- China Agricultural University, Beijing, China
- State Key Laboratory or Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, China
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2
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Xu J, Li Y, Jia J, Xiong W, Zhong C, Huang G, Gou X, Meng Y, Shan W. Mutations in PpAGO3 Lead to Enhanced Virulence of Phytophthora parasitica by Activation of 25-26 nt sRNA-Associated Effector Genes. Front Microbiol 2022; 13:856106. [PMID: 35401482 PMCID: PMC8989244 DOI: 10.3389/fmicb.2022.856106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/03/2022] [Indexed: 12/04/2022] Open
Abstract
Oomycetes represent a unique group of plant pathogens that are destructive to a wide range of crops and natural ecosystems. Phytophthora species possess active small RNA (sRNA) silencing pathways, but little is known about the biological roles of sRNAs and associated factors in pathogenicity. Here we show that an AGO gene, PpAGO3, plays a major role in the regulation of effector genes hence the pathogenicity of Phytophthora parasitica. PpAGO3 was unique among five predicted AGO genes in P. parasitica, showing strong mycelium stage-specific expression. Using the CRISPR-Cas9 technology, we generated PpAGO3ΔRGG1-3 mutants that carried a deletion of 1, 2, or 3 copies of the N-terminal RGG motif (QRGGYD) but failed to obtain complete knockout mutants, which suggests its vital role in P. parasitica. These mutants showed increased pathogenicity on both Nicotiana benthamiana and Arabidopsis thaliana plants. Transcriptome and sRNA sequencing of PpAGO3ΔRGG1 and PpAGO3ΔRGG3 showed that these mutants were differentially accumulated with 25–26 nt sRNAs associated with 70 predicted cytoplasmic effector genes compared to the wild-type, of which 13 exhibited inverse correlation between gene expression and 25–26 nt sRNA accumulation. Transient overexpression of the upregulated RXLR effector genes, PPTG_01869 and PPTG_15425 identified in the mutants PpAGO3ΔRGG1 and PpAGO3ΔRGG3, strongly enhanced N. benthamiana susceptibility to P. parasitica. Our results suggest that PpAGO3 functions together with 25–26 nt sRNAs to confer dynamic expression regulation of effector genes in P. parasitica, thereby contributing to infection and pathogenicity of the pathogen.
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Affiliation(s)
- Junjie Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yilin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Jinbu Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wenjing Xiong
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Chengcheng Zhong
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Guiyan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiuhong Gou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
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3
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Dunker F, Oberkofler L, Lederer B, Trutzenberg A, Weiberg A. An Arabidopsis downy mildew non-RxLR effector suppresses induced plant cell death to promote biotroph infection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:718-732. [PMID: 33063828 PMCID: PMC7853606 DOI: 10.1093/jxb/eraa472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 05/11/2023]
Abstract
Our understanding of obligate biotrophic pathogens is limited by lack of knowledge concerning the molecular function of virulence factors. We established Arabidopsis host-induced gene silencing (HIGS) to explore gene functions of Hyaloperonospora arabidopsidis, including CYSTEINE-RICH PROTEIN (HaCR)1, a potential secreted effector gene of this obligate biotrophic pathogen. HaCR1 HIGS resulted in H. arabidopsidis-induced local plant cell death and reduced pathogen reproduction. We functionally characterized HaCR1 by ectopic expression in Nicotiana benthamiana. HaCR1 was capable of inhibiting effector-triggered plant cell death. Consistent with this, HaCR1 expression in N. benthamiana led to stronger disease symptoms caused by the hemibiotrophic oomycete pathogen Phytophthora capsici, but reduced disease symptoms caused by the necrotrophic fungal pathogen Botrytis cinerea. Expressing HaCR1 in transgenic Arabidopsis confirmed higher susceptibility to H. arabidopsidis and to the bacterial hemibiotrophic pathogen Pseudomonas syringae. Increased H. arabidopsidis infection was in accordance with reduced PATHOGENESIS RELATED (PR)1 induction. Expression of full-length HaCR1 was required for its function, which was lost if the signal peptide was deleted, suggesting its site of action in the plant apoplast. This study provides phytopathological and molecular evidence for the importance of this widespread, but largely unexplored class of non-RxLR effectors in biotrophic oomycetes.
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Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Lorenz Oberkofler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Bernhard Lederer
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
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4
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Dubey H, Kiran K, Jaswal R, Bhardwaj SC, Mondal TK, Jain N, Singh NK, Kayastha AM, Sharma TR. Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat. Funct Integr Genomics 2020; 20:711-721. [PMID: 32705366 DOI: 10.1007/s10142-020-00745-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
Abstract
Puccinia triticina (P. triticina) is one of the most devastating fungal pathogens of wheat which causes significant annual yield loss to the crop. Understanding the gene regulatory mechanism of the biotrophic pathogen is one of the important aspects of host-pathogen interaction studies. Dicer-like genes are considered as important mediators of RNAi-based gene regulation. In this study, we report the presence of three Dicer-like genes (Pt-DCL1, Pt-DCL2, Pt-DCL3) in P. triticina genome identified through computational and biological analyses. Quantitative real-time PCR studies revealed an increase in the expression of these genes in germinating spore stages. Heterologous expression combined with mass spectrometry analysis of Pt-DCL2 confirmed the presence of a canonical Dicer-like gene in P. triticina. Phylogenetic analysis of the Pt-DCLs with the Dicer-like proteins from other organisms showed a distinct cluster of rust pathogens from the order Pucciniales. The results indicated a species-specific duplication of Dicer-like genes within the wheat rust pathogens. This study, for the first time, reports the presence of Dicer-dependent RNAi pathway in P. triticina that may play a role in gene regulatory mechanism of the pathogen during its development. Our study serves as a vital source of information for further RNAi-based molecular studies for better understanding and management of the wheat leaf rust disease.
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Affiliation(s)
- Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India.,School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.,Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, Karnataka, 560035, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Rajdeep Jaswal
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Subhash C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, 171009, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Neha Jain
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India. .,Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India.
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5
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Panabières F, Rancurel C, da Rocha M, Kuhn ML. Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica. Front Genet 2020; 11:557. [PMID: 32582290 PMCID: PMC7290008 DOI: 10.3389/fgene.2020.00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Satellite DNA is a class of repetitive sequences that are organized in long arrays of tandemly repeated units in most eukaryotes. Long considered as selfish DNA, satellite sequences are now proposed to contribute to genome integrity. Despite their potential impact on the architecture and evolution of the genome, satellite DNAs have not been investigated in oomycetes due to the paucity of genomic data and the difficulty of assembling highly conserved satellite arrays. Yet gaining knowledge on the structure and evolution of genomes of oomycete pathogens is crucial to understanding the mechanisms underlying adaptation to their environment and to proposing efficient disease control strategies. A de novo assembly of the genome of Phytophthora parasitica, an important oomycete plant pathogen, led to the identification of several families of tandemly repeated sequences varying in size, copy number, and sequence conservation. Among them, two abundant families, designated as PpSat1 and PpSat2, displayed typical features of satellite DNA and were collectively designated as PpSat. These two satellite families differ by their length, sequence, organization, genomic environment, and evolutionary dynamics. PpSat1, but not PpSat2, presented homologs among oomycetes. This observation, as well as the characterization of transcripts of PpSat families, suggested that these satellite DNA families likely play a conserved role within this important group of pathogens.
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6
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Dunker F, Trutzenberg A, Rothenpieler JS, Kuhn S, Pröls R, Schreiber T, Tissier A, Kemen A, Kemen E, Hückelhoven R, Weiberg A. Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. eLife 2020; 9:56096. [PMID: 32441255 PMCID: PMC7297541 DOI: 10.7554/elife.56096] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant’s Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitatively enhanced susceptibility.
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Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Jan S Rothenpieler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Sarah Kuhn
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Reinhard Pröls
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Ariane Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
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7
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Bollmann SR, Press CM, Tyler BM, Grünwald NJ. Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora. Front Microbiol 2018; 9:2841. [PMID: 30555430 PMCID: PMC6284064 DOI: 10.3389/fmicb.2018.02841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/05/2018] [Indexed: 01/17/2023] Open
Abstract
Modulation of gene expression through RNA interference is well conserved in eukaryotes and is involved in many cellular processes. In the oomycete Phytophthora, research on the small RNA machinery and function has started to reveal potential roles in the pathogen, but much is still unknown. We examined Argonaute (AGO) homologs within oomycete genome sequences, especially among Phytophthora species, to gain a clearer understanding of the evolution of this well-conserved protein family. We identified AGO homologs across many representative oomycete and stramenopile species, and annotated representative homologs in P. sojae. Furthermore, we demonstrate variable transcript levels of all identified AGO homologs in comparison to previously identified Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) homologs. Our phylogenetic analysis further refines the relationship of the AGO homologs in oomycetes and identifies a conserved tandem duplication of AGO homologs in a subset of Phytophthora species.
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Affiliation(s)
- Stephanie R Bollmann
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Caroline M Press
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
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Waldron FM, Stone GN, Obbard DJ. Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes. PLoS Genet 2018; 14:e1007533. [PMID: 30059538 PMCID: PMC6085071 DOI: 10.1371/journal.pgen.1007533] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/09/2018] [Accepted: 07/04/2018] [Indexed: 11/24/2022] Open
Abstract
RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.
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Affiliation(s)
- Fergal M. Waldron
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Graham N. Stone
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Darren J. Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- Centre for Immunity Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
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9
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Ali SS, Shao J, Lary DJ, Kronmiller BA, Shen D, Strem MD, Amoako-Attah I, Akrofi AY, Begoude BD, ten Hoopen GM, Coulibaly K, Kebe BI, Melnick RL, Guiltinan MJ, Tyler BM, Meinhardt LW, Bailey BA. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biol Evol 2017; 9:2982378. [PMID: 28186564 PMCID: PMC5381587 DOI: 10.1093/gbe/evx021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta . Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.
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Affiliation(s)
- Shahin S. Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Jonathan Shao
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, China
| | - Mary D. Strem
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - B.A. Didier Begoude
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
| | - G. Martijn ten Hoopen
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
- CIRAD, UPR 106 Bioagresseurs, Montpellier, France
| | | | | | - Rachel L. Melnick
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | - Brett M. Tyler
- Center for Genome Research and Biocomputing, Oregon State University
- Department of Botany and Plant Pathology, Oregon State University
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
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10
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Wang Q, Li T, Xu K, Zhang W, Wang X, Quan J, Jin W, Zhang M, Fan G, Wang MB, Shan W. The tRNA-Derived Small RNAs Regulate Gene Expression through Triggering Sequence-Specific Degradation of Target Transcripts in the Oomycete Pathogen Phytophthora sojae. FRONTIERS IN PLANT SCIENCE 2016; 7:1938. [PMID: 28066490 PMCID: PMC5177647 DOI: 10.3389/fpls.2016.01938] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/07/2016] [Indexed: 05/05/2023]
Abstract
Along with the well-studied microRNA (miRNA) and small interfering RNA (siRNA) is a new class of transfer RNA-derived small RNA (tsRNA), which has recently been detected in multiple organisms and is implicated in gene regulation. However, while miRNAs and siRNAs are known to repress gene expression through sequence-specific RNA cleavage or translational repression, how tsRNAs regulate gene expression remains unclear. Here we report the identification and functional characterization of tsRNAs in the oomycete pathogen Phytophthora sojae. We show that multiple tRNAs are processed into abundant tsRNAs, which accumulate in a similar developmental stage-specific manner and are negatively correlated with the expression of predicted target genes. Degradome sequencing and 5' RLM RACE experiments indicate tsRNAs can trigger degradation of target transcripts. Transient expression assays using GUS sensor constructs confirmed the requirement of sequence complementarity in tsRNA-mediated RNA degradation in P. sojae. Our results show that the tsRNA are a class of functional endogenous sRNAs and suggest that tsRNA regulate gene expression through inducing sequence-specific degradation of target RNAs in oomycetes.
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Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Tingting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Ke Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Wei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Xiaolong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Junli Quan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Weibo Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Meixiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Guangjin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Ming-Bo Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- CSIRO AgricultureCanberra, ACT, Australia
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Weixing Shan,
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