1
|
Srikant S, Gaudet R, Murray AW. Extending the reach of homology by using successive computational filters to find yeast pheromone genes. Curr Biol 2023; 33:4098-4110.e3. [PMID: 37699395 PMCID: PMC10592104 DOI: 10.1016/j.cub.2023.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
Collapse
Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA.
| |
Collapse
|
2
|
Zhang Y, Zhuang X, Meng J, Zan F, Liu Z, Qin C, Hao L, Wang Z, Wang L, Li H, Li H, Ding S. A Putative Zn(II) 2Cys 6-Type Transcription Factor FpUme18 Is Required for Development, Conidiation, Cell Wall Integrity, Endocytosis and Full Virulence in Fusarium pseudograminearum. Int J Mol Sci 2023; 24:10987. [PMID: 37446163 PMCID: PMC10341630 DOI: 10.3390/ijms241310987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Fusarium pseudograminearum is one of the major fungal pathogens that cause Fusarium crown rot (FCR) worldwide and can lead to a substantially reduced grain yield and quality. Transcription factors play an important role in regulating growth and pathogenicity in plant pathogens. In this study, we identified a putative Zn(II)2Cys6 fungal-type domain-containing transcription factor and named it FpUme18. The expression of FpUME18 was induced during the infection of wheat by F. pseudograminearum. The ΔFpume18 deletion mutant showed defects in growth, conidial production, and conidial germination. In the responses to the cell wall, salt and oxidative stresses, the ΔFpume18 mutant inhibited the rate of mycelial growth at a higher rate compared with the wild type. The staining of conidia and mycelia with lipophilic dye FM4-64 revealed a delay in endocytosis when FpUME18 was deleted. FpUME18 also positively regulated the expression of phospholipid-related synthesis genes. The deletion of FpUME18 attenuated the pathogenicity of wheat coleoptiles. FpUME18 also participated in the production of the DON toxin by regulating the expression of TRI genes. Collectively, FpUme18 is required for vegetative growth, conidiation, stress response, endocytosis, and full virulence in F. pseudograminearum.
Collapse
Affiliation(s)
- Yuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Xunyu Zhuang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Jiaxing Meng
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Feifei Zan
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Zheran Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Cancan Qin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Lingjun Hao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Zhifang Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Limin Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Haiyang Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| | - Shengli Ding
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
- National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, China
| |
Collapse
|
3
|
Padilla-Roji I, Ruiz-Jiménez L, Bakhat N, Vielba-Fernández A, Pérez-García A, Fernández-Ortuño D. RNAi Technology: A New Path for the Research and Management of Obligate Biotrophic Phytopathogenic Fungi. Int J Mol Sci 2023; 24:ijms24109082. [PMID: 37240427 DOI: 10.3390/ijms24109082] [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: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Powdery mildew and rust fungi are major agricultural problems affecting many economically important crops and causing significant yield losses. These fungi are obligate biotrophic parasites that are completely dependent on their hosts for growth and reproduction. Biotrophy in these fungi is determined by the presence of haustoria, specialized fungal cells that are responsible for nutrient uptake and molecular dialogue with the host, a fact that undoubtedly complicates their study under laboratory conditions, especially in terms of genetic manipulation. RNA interference (RNAi) is the biological process of suppressing the expression of a target gene through double-stranded RNA that induces mRNA degradation. RNAi technology has revolutionized the study of these obligate biotrophic fungi by enabling the analysis of gene function in these fungal. More importantly, RNAi technology has opened new perspectives for the management of powdery mildew and rust diseases, first through the stable expression of RNAi constructs in transgenic plants and, more recently, through the non-transgenic approach called spray-induced gene silencing (SIGS). In this review, the impact of RNAi technology on the research and management of powdery mildew and rust fungi will be addressed.
Collapse
Affiliation(s)
- Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Laura Ruiz-Jiménez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Nisrine Bakhat
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandra Vielba-Fernández
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| |
Collapse
|
4
|
Lyu X, Wang Q, Liu A, Liu F, Meng L, Wang P, Zhang Y, Wang L, Li Z, Wang W. The transcription factor Ste12-like increases the mycelial abiotic stress tolerance and regulates the fruiting body development of Flammulina filiformis. Front Microbiol 2023; 14:1139679. [PMID: 37213522 PMCID: PMC10192742 DOI: 10.3389/fmicb.2023.1139679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/14/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Flammulina filiformis is one of the most commercially important edible fungi worldwide, with its nutritional value and medicinal properties. It becomes a good model species to study the tolerance of abiotic stress during mycelia growth in edible mushroom cultivation. Transcription factor Ste12 has been reported to be involved in the regulation of stress tolerance and sexual reproduction in fungi. Methods In this study, identification and phylogenetic analysis of ste12-like was performed by bioinformatics methods. Four ste12-like overexpression transformants of F. filiformis were constructed by Agrobacterium tumefaciens-mediated transformation. Results and Discussion Phylogenetic analysis showed that Ste12-like contained conserved amino acid sequences. All the overexpression transformants were more tolerant to salt stress, cold stress and oxidative stress than wild-type strains. In the fruiting experiment, the number of fruiting bodies of overexpression transformants increased compared with wild-type strains, but the growth rate of stipes slowed down. It suggested that gene ste12-like was involved in the regulation of abiotic stress tolerance and fruiting body development in F. filiformis.
Collapse
Affiliation(s)
- Xiaomeng Lyu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingji Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Ao Liu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Fang Liu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Meng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Panmeng Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan Zhang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Li Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Li Wang,
| | - Zhuang Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
- Zhuang Li,
| | - Wei Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
- Wei Wang,
| |
Collapse
|
5
|
Zhan C, Li Y, Li H, Wang M, Gong S, Ma D, Li Y. Phylogenomic analysis of phenylalanine ammonia-lyase (PAL) multigene family and their differential expression analysis in wheat ( Triticum aestivum L.) suggested their roles during different stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:982457. [PMID: 36247561 PMCID: PMC9561908 DOI: 10.3389/fpls.2022.982457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 05/24/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is a key enzyme in the phenylalanine metabolism pathway and plays an important role in plant growth and stress response. It has been widely reported in plants, but less studied in wheat. In this study, 54 PAL genes were identified in the wheat genome. Based on phylogenetic analysis, the 54 TaPAL genes were divided into four groups (I, II, III, and IV). Then, the expression levels of TaPALs under biotic stresses were analyzed by transcriptome data analysis. The results showed that 31 genes were up-regulated and one gene was down-regulated after inoculation with Fusarium graminearum, 11 genes were up-regulated and 14 genes were down-regulated after inoculation with Puccinia striiformis, and 32 up-regulated and three down-regulated genes after inoculation with powdery mildew. The expression patterns of the five TaPALs were further analyzed by qRT-PCR. After inoculation with F. graminearum, the expression levels of five TaPALs were up-regulated. However, the TaPALs (expect TaPAL49) were down-regulated when inoculated with P. striiformis. Finally, the functions of TaPAL32 and TaPAL42 in resistance of wheat to the stripe rust were further analyzed by virus induced gene silencing (VIGS) assays. The results showed that the disease severity of TaPAL32 and TaPAL42 silenced plants was higher than that of control plants at 14 days after inoculation. It indicated that these two genes played a positive role in wheat stripe rust resistance. This study provided new evidence support for the functional study of PAL genes in wheat, and provided potential application value for the breeding of wheat resistant varieties.
Collapse
Affiliation(s)
- Chuang Zhan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiting Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Han Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Mengru Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yan Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
6
|
Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence. Fungal Genet Biol 2022; 161:103712. [PMID: 35667520 DOI: 10.1016/j.fgb.2022.103712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/18/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022]
Abstract
Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, yet relatively few virulence-specific regulators are characterised in detail and their evolutionary trajectories are not well understood. Hence, this study compared the full range of TFs across taxonomically-diverse fungal proteomes and classified their lineages through an orthology analysis. The primary aims were to characterise differences in the range and profile of TF lineages broadly linked to plant-host association or pathogenic lifestyles, and to better characterise the evolutionary origin and trajectory of experimentally-validated virulence regulators. We observed significantly fewer TFs among obligate, host-associated pathogens, largely attributed to contractions in several Zn2Cys6 TF-orthogroup lineages. We also present novel insight into the key virulence-regulating TFs Ste12, Pf2 and EBR1, providing evidence for their ancestral origins, expansion and/or loss. Ultimately, the analysis presented here provides both primary evidence for TF evolution in fungal phytopathogenicity, as well as a practical phylogenetic resource to guide further detailed investigation on the regulation of virulence within key pathogen lineages.
Collapse
|
7
|
Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
Collapse
Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | |
Collapse
|
8
|
John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
Collapse
Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| |
Collapse
|
9
|
Zhou X, Zhu X, Shao W, Song J, Jiang W, He Y, Yin J, Ma D, Qiao Y. Genome-Wide Mining of Wheat DUF966 Gene Family Provides New Insights Into Salt Stress Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:569838. [PMID: 32983219 PMCID: PMC7483657 DOI: 10.3389/fpls.2020.569838] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/14/2020] [Indexed: 05/24/2023]
Abstract
Domain of unknown function (DUF) proteins constitute a great deal of families of functionally uncharacterized proteins in eukaryotes. The DUF966 gene family is found in monocotyledons, dicotyledons, mosses, and other species. However, little is known about the functions of DUF966 genes in wheat (Triticum aestivum L.). In this study, we identified and characterized the TaDUF966 gene family members in wheat by in silico analysis. A total of 28 TaDUF966 proteins were identified in wheat. Phylogenetic analysis divided these proteins into two groups (Groups I and II). Proteins in each group showed a highly conserved DUF966 domain and conserved motif distribution, implying their functional conservation. Analysis of gene expression profiling data showed that some TaDUF966 genes were induced by salt stress. We further confirmed the role of TaDUF966-9B in salt stress using virus induced gene silencing (VIGS) assay. Compared with the empty vector control, the TaDUF966-9B knockdown plants exhibited severe leaf curling at 10 days post-inoculation with BSMV under salt stress, suggesting that TaDUF966 genes play a vital role in salt stress tolerance in wheat. Taken together, these results expand our knowledge of the evolution of the DUF966 gene family in wheat and promote the potential application of these genes in wheat genetic improvement.
Collapse
Affiliation(s)
- Xiaoyi Zhou
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoguo Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenna Shao
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinghan Song
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Wenqiang Jiang
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiqin He
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| |
Collapse
|
10
|
Koch A, Höfle L, Werner BT, Imani J, Schmidt A, Jelonek L, Kogel K. SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. MOLECULAR PLANT PATHOLOGY 2019; 20:1636-1644. [PMID: 31603277 PMCID: PMC6859480 DOI: 10.1111/mpp.12866] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CYP3RNA, a double-stranded (ds)RNA designed to concomitantly target the two sterol 14α-demethylase genes FgCYP51A and FgCYP51B and the fungal virulence factor FgCYP51C, inhibits the growth of the ascomycete fungus Fusarium graminearum (Fg) in vitro and in planta. Here we compare two different methods (setups) of dsRNA delivery, viz. transgene expression (host-induced gene silencing, HIGS) and spray application (spray-induced gene silencing, SIGS), to assess the activity of CYP3RNA and novel dsRNA species designed to target one or two FgCYP51 genes. Using Arabidopsis and barley, we found that dsRNA designed to target two FgCYP51 genes inhibited fungal growth more efficiently than dsRNA targeting a single gene, although both dsRNA species reduced fungal infection. Either dsRNA delivery method reduced fungal growth stronger than anticipated from previous mutational knock-out (KO) strategies, where single gene KO had no significant effect on fungal viability. Consistent with the strong inhibitory effects of the dsRNAs on fungal development in both setups, we detected to a large extent dsRNA-mediated co-silencing of respective non-target FgCYP51 genes. Together, our data further support the valuation that dsRNA applications have an interesting potential for pesticide target validation and gene function studies, apart from their potential for crop protection.
Collapse
Affiliation(s)
- Aline Koch
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Lisa Höfle
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Bernhard Timo Werner
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Jafargholi Imani
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Alexandra Schmidt
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems BiologyJustus Liebig UniversityHeinrich‐Buff‐Ring 58D‐35392GiessenGermany
| | - Karl‐Heinz Kogel
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| |
Collapse
|
11
|
Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1190 I. Introduction 1190 II. Rust fungi: a diverse and serious threat to agriculture 1191 III. The different facets of rust life cycles and unresolved questions about their evolution 1191 IV. The biology of rust infection 1192 V. Rusts in the genomics era: the ever-expanding list of candidate effector genes 1195 VI. Functional characterization of rust effectors 1197 VII. Putting rusts to sleep: Pucciniales research outlooks 1201 Acknowledgements 1202 References 1202 SUMMARY: Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure, largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts. Thousands of genes encoding secreted proteins highly expressed during host infection have been reported for different rust species, which represents significant potential towards understanding rust effector function. Recent high-throughput in planta expression screen approaches (effectoromics) have pushed the field ahead even further towards predicting high-priority effectors and identifying avirulence genes. These new insights into rust effector biology promise to inform future research and spur the development of effective and sustainable strategies for managing rust diseases.
Collapse
Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| |
Collapse
|
12
|
Qi T, Guo J, Peng H, Liu P, Kang Z, Guo J. Host-Induced Gene Silencing: A Powerful Strategy to Control Diseases of Wheat and Barley. Int J Mol Sci 2019; 20:E206. [PMID: 30626050 PMCID: PMC6337638 DOI: 10.3390/ijms20010206] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/31/2018] [Accepted: 01/03/2019] [Indexed: 12/15/2022] Open
Abstract
Wheat and barley are the most highly produced and consumed grains in the world. Various pathogens-viruses, bacteria, fungi, insect pests, and nematode parasites-are major threats to yield and economic losses. Strategies for the management of disease control mainly depend on resistance or tolerance breeding, chemical control, and biological control. The discoveries of RNA silencing mechanisms provide a transgenic approach for disease management. Host-induced gene silencing (HIGS) employing RNA silencing mechanisms and, specifically, silencing the targets of invading pathogens, has been successfully applied in crop disease prevention. Here, we cover recent studies that indicate that HIGS is a valuable tool to protect wheat and barley from diseases in an environmentally friendly way.
Collapse
Affiliation(s)
- Tuo Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Huan Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
13
|
Zhu X, Guo J, He F, Zhang Y, Tan C, Yang Q, Huang C, Kang Z, Guo J. Silencing PsKPP4, a MAP kinase kinase kinase gene, reduces pathogenicity of the stripe rust fungus. MOLECULAR PLANT PATHOLOGY 2018; 19:2590-2602. [PMID: 30047240 PMCID: PMC6638076 DOI: 10.1111/mpp.12731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many obligately parasitic pathogens absorb nutrients from host plants via specialized infection structures, called haustoria and infection hyphae, to further colonization and growth in the host plant. In the wheat (Triticum aestivum) stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), the mitogen-activated protein kinase kinase (MAPKK) PsFUZ7 is involved in the regulation of haustorium formation and invasive growth. Here, we functionally characterized PsKPP4 of Pst, which is homologous to the yeast MAPKKK STE11. Similar to the silencing of PsFUZ7, the knockdown of PsKPP4 was detected in the vegetative hyphae and haustoria, resulting in the reduced pathogenicity of Pst. Pst urediniospores treated with the STE11 MAPKKK activation inhibitor produced deformed germ tubes. In addition, overexpression of PsKPP4 in fission yeast resulted in the production of fusiform cells and increased tolerance of yeast cells to oxidative stress. The transformation of PsKPP4 into the mst11 mutant of Magnaporthe oryzae partially restored mst11 function. The PsKPP4 protein contains a sterile alpha motif (SAM), Ras association (RA) and kinase domains, similar to its homologues in other fungi. Yeast two-hybrid assays revealed that the SAM domain is essential for the interaction between PsKPP4 and PsUBC2, a homologue of Ustilago maydis UBC2, known to interact with KPP4, which is associated with the regulation of the Fus3 cascade. Host-induced gene silencing of PsUBC2 reduced the pathogenicity of Pst slightly, indicating that PsUBC2 also plays a minor role in the regulation of the infection pathway of Pst. These observations indicate that PsKPP4, interacting with PsUBC2, may play an important role in the regulation of infection-related morphogenesis in Pst.
Collapse
Affiliation(s)
- Xiaoguo Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Fuxin He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Yang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Chenglong Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Qian Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Chuanming Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant ProtectionNorthwest A&F UniversityYangling712100ShaanxiChina
| |
Collapse
|