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Cerav EN, Wu N, Akkaya MS. Transcriptome-Wide N6-Methyladenosine (m 6A) Methylation Analyses in a Compatible Wheat- Puccinia striiformis f. sp. tritici Interaction. PLANTS (BASEL, SWITZERLAND) 2024; 13:982. [PMID: 38611510 PMCID: PMC11013425 DOI: 10.3390/plants13070982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant-pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat's response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens.
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Affiliation(s)
| | | | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China; (E.N.C.); (N.W.)
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Wang J, Chen T, Tang Y, Zhang S, Xu M, Liu M, Zhang J, Loake GJ, Jiang J. The Biological Roles of Puccinia striiformis f. sp. tritici Effectors during Infection of Wheat. Biomolecules 2023; 13:889. [PMID: 37371469 DOI: 10.3390/biom13060889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Puccinia striiformis f. sp. tritici (Pst) is the causative agent of wheat stripe rust, which can lead to a significant loss in annual wheat yields. Therefore, there is an urgent need for a deeper comprehension of the basic mechanisms underlying Pst infection. Effectors are known as the agents that plant pathogens deliver into host tissues to promote infection, typically by interfering with plant physiology and biochemistry. Insights into effector activity can significantly aid the development of future strategies to generate disease-resistant crops. However, the functional analysis of Pst effectors is still in its infancy, which hinders our understanding of the molecular mechanisms of the interaction between Pst and wheat. In this review, we summarize the potential roles of validated and proposed Pst effectors during wheat infection, including proteinaceous effectors, non-coding RNAs (sRNA effectors), and secondary metabolites (SMs effectors). Further, we suggest specific countermeasures against Pst pathogenesis and future research directions, which may promote our understanding of Pst effector functions during wheat immunity attempts.
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Affiliation(s)
- Junjuan Wang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Tongtong Chen
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Yawen Tang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Sihan Zhang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengyao Xu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Meiyan Liu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Jian Zhang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Gary J Loake
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Jihong Jiang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
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Emir M, Ozketen AC, Andac Ozketen A, Çelik Oğuz A, Huang M, Karakaya A, Rampitsch C, Gunel A. Increased levels of cell wall degrading enzymes and peptidases are associated with aggressiveness in a virulent isolate of Pyrenophora teres f. maculata. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153839. [PMID: 36370615 DOI: 10.1016/j.jplph.2022.153839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Pyrenophora teres f. maculata (Ptm) is a fungal pathogen that causes the spot form of net blotch on barley and leads to economic losses in many of the world's barley-growing regions. Isolates of Ptm exhibit varying levels of aggressiveness that result in quantifiable changes in the severity of the disease. Previous research on plant-pathogen interactions has shown that such divergence is reflected in the proteome and secretome of the pathogen, with certain classes of proteins more prominent in aggressive isolates. Here we have made a detailed comparative analysis of the secretomes of two Ptm isolates, GPS79 and E35 (highly and mildly aggressive, respectively) using a proteomics-based approach. The secretomes were obtained in vitro using media amended with barley leaf sections. Secreted proteins therein were harvested, digested with trypsin, and fractionated offline by HPLC prior to LC-MS in a high-resolution instrument to obtain deep coverage of the proteome. The subsequent analysis used a label-free quantitative proteomics approach with relative quantification of proteins based on precursor ion intensities. A total of 1175 proteins were identified, 931 from Ptm and 244 from barley. Further analysis revealed 160 differentially abundant proteins with at least a two-fold abundance difference between the isolates, with the most enriched in the aggressive GPS79 secretome. These proteins were mainly cell-wall (carbohydrate) degrading enzymes and peptidases, with some oxidoreductases and other pathogenesis-related proteins also identified, suggesting that aggressiveness is associated with an improved ability of GPS79 to overcome cell wall barriers and neutralize host defense responses.
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Affiliation(s)
- Mahmut Emir
- Kirsehir-Ahi Evran University, Faculty of Arts and Sciences, Department of Chemistry, Kirsehir, Turkey
| | | | | | - Arzu Çelik Oğuz
- Ankara University Faculty of Agriculture, Department of Plant Protection, Dışkapı, Ankara, Turkey
| | - Mei Huang
- Agriculture and Agrifood Canada, Morden Research and Development Centre, Morden MB, Canada
| | - Aziz Karakaya
- Ankara University Faculty of Agriculture, Department of Plant Protection, Dışkapı, Ankara, Turkey
| | - Christof Rampitsch
- Agriculture and Agrifood Canada, Morden Research and Development Centre, Morden MB, Canada.
| | - Aslihan Gunel
- Kirsehir-Ahi Evran University, Faculty of Arts and Sciences, Department of Chemistry, Kirsehir, Turkey.
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Wu N, Ozketen AC, Cheng Y, Jiang W, Zhou X, Zhao X, Guan Y, Xiang Z, Akkaya MS. Puccinia striiformis f. sp. tritici effectors in wheat immune responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1012216. [PMID: 36420019 PMCID: PMC9677129 DOI: 10.3389/fpls.2022.1012216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The obligate biotrophic fungus Puccinia striiformis f. sp. tritici, which causes yellow (stripe) rust disease, is among the leading biological agents resulting in tremendous yield losses on global wheat productions per annum. The combatting strategies include, but are not limited to, fungicide applications and the development of resistant cultivars. However, evolutionary pressure drives rapid changes, especially in its "effectorome" repertoire, thus allowing pathogens to evade and breach resistance. The extracellular and intracellular effectors, predominantly secreted proteins, are tactical arsenals aiming for many defense processes of plants. Hence, the identity of the effectors and the molecular mechanisms of the interactions between the effectors and the plant immune system have long been targeted in research. The obligate biotrophic nature of P. striiformis f. sp. tritici and the challenging nature of its host, the wheat, impede research on this topic. Next-generation sequencing and novel prediction algorithms in bioinformatics, which are accompanied by in vitro and in vivo validation approaches, offer a speedy pace for the discovery of new effectors and investigations of their biological functions. Here, we briefly review recent findings exploring the roles of P. striiformis f. sp. tritici effectors together with their cellular/subcellular localizations, host responses, and interactors. The current status and the challenges will be discussed. We hope that the overall work will provide a broader view of where we stand and a reference point to compare and evaluate new findings.
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Affiliation(s)
- Nan Wu
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | | | - Yu Cheng
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Wanqing Jiang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xuan Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinran Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yaorong Guan
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhaoxia Xiang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, Dalian, China
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Petre B, Duplessis S. A decade after the first Pucciniales genomes: A bibliometric snapshot of (post) genomics studies in three model rust fungi. Front Microbiol 2022; 13:989580. [PMID: 36187960 PMCID: PMC9515648 DOI: 10.3389/fmicb.2022.989580] [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] [Received: 07/08/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pucciniales (rust fungi) are one of the largest fungal order of plant pathogens. They collectively infect key crops such as wheat and soybean, and threaten global food security. In the early 2010s, the genome sequences of three rust fungi were released: Melampsora larici-populina (the poplar leaf rust fungus), Puccinia graminis f. sp. tritici (the wheat stem rust fungus), and Puccinia striiformis f. sp. triciti (the wheat stripe rust or wheat yellow rust fungus). The availability of those genomes has forwarded rust biology into the post-genomic era, sparking a series of genomics, transcriptomics, in silico, and functional studies. Here, we snapshot the last 10 years of post-genomics studies addressing M. larici-populina, P. graminis f. sp. tritici, and/or P. striiformis f. sp. tritici. This mini-review notably reveals the model species-centered structure of the research community, and highlights the drastic increase of the number of functional studies focused on effectors since 2014, which notably revealed chloroplasts as a central host compartment targeted by rust fungi. This mini-review also discusses genomics-facilitated studies in other rust species, and emerging post-genomic research trends related to fully-phased rust genomes.
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