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Zhan S, Wu W, Hu J, Liu F, Qiao X, Chen L, Zhou Y. The pathogenicity and regulatory function of temperature-sensitive proteins PscTSP in Pseudofabraea citricarpa under high temperature stress. Int J Biol Macromol 2024; 270:132017. [PMID: 38697438 DOI: 10.1016/j.ijbiomac.2024.132017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Citrus fruit rich in beneficial health-promoting nutrients used for functional foods or dietary supplements production. However, its quality and yield were damaged by citrus target spot. Citrus target spot is a low-temperature fungal disease caused by Pseudofabraea citricarpa, resulting in citrus production reductions and economic losses. In this study, transcriptome and gene knockout mutant analyses were performed on the growth and pathogenicity of P. citricarpa under different temperature conditions to quantify the functions of temperature-sensitive proteins (PscTSP). The optimum growth temperature for P. citricarpa strain WZ1 was 20 °C, while it inhibited or stopped growth above 30 °C and stopped growth below 4 °C or above 30 °C. Certain PscTSP-key genes of P. citricarpa were identified under high temperature stress. qRT-PCR analysis confirmed the expression levels of PscTSPs under high temperature stress. PscTSPs were limited by temperature and deletion of the PscTSP-X gene leads to changes in the integrity of citrus cell walls, osmotic regulation, oxidative stress response, calcium regulation, chitin synthesis, and the pathogenicity of P. citricarpa. These results provide insight into the underlying mechanisms of temperature sensitivity and pathogenicity in P. citricarpa, providing a foundation for developing resistance strategies against citrus target spot disease.
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Affiliation(s)
- Shuang Zhan
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Wang Wu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Junhua Hu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; Scientific Observing and Experimental Station of Fruit Tree Science (Southwest Region), Ministry of Agriculture, Chongqing 400712, China.
| | - Fengjiao Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Xinghua Qiao
- Wanzhou District of Chongqing Plant Protection and Fruit Tree Technology Promotion Station, Wanzhou, 404000, China
| | - Li Chen
- Wanzhou District of Chongqing Plant Protection and Fruit Tree Technology Promotion Station, Wanzhou, 404000, China
| | - Yan Zhou
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; Scientific Observing and Experimental Station of Fruit Tree Science (Southwest Region), Ministry of Agriculture, Chongqing 400712, China
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Chen D, Chen J, Dai R, Zheng X, Han Y, Chen Y, Xue T. Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress. BMC Genomics 2024; 25:141. [PMID: 38311722 PMCID: PMC10840233 DOI: 10.1186/s12864-024-10043-5] [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: 06/08/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. RESULTS Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. CONCLUSIONS SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.
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Affiliation(s)
- Duo Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jing Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Rongchun Dai
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xuehai Zheng
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yuying Han
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ting Xue
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, China.
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Yan X, Tang B, Ryder LS, MacLean D, Were VM, Eseola AB, Cruz-Mireles N, Ma W, Foster AJ, Osés-Ruiz M, Talbot NJ. The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors. THE PLANT CELL 2023; 35:1360-1385. [PMID: 36808541 PMCID: PMC10118281 DOI: 10.1093/plcell/koad036] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 05/04/2023]
Abstract
The rice blast fungus Magnaporthe oryzae causes a devastating disease that threatens global rice (Oryza sativa) production. Despite intense study, the biology of plant tissue invasion during blast disease remains poorly understood. Here we report a high-resolution transcriptional profiling study of the entire plant-associated development of the blast fungus. Our analysis revealed major temporal changes in fungal gene expression during plant infection. Pathogen gene expression could be classified into 10 modules of temporally co-expressed genes, providing evidence for the induction of pronounced shifts in primary and secondary metabolism, cell signaling, and transcriptional regulation. A set of 863 genes encoding secreted proteins are differentially expressed at specific stages of infection, and 546 genes named MEP (Magnaportheeffector protein) genes were predicted to encode effectors. Computational prediction of structurally related MEPs, including the MAX effector family, revealed their temporal co-regulation in the same co-expression modules. We characterized 32 MEP genes and demonstrate that Mep effectors are predominantly targeted to the cytoplasm of rice cells via the biotrophic interfacial complex and use a common unconventional secretory pathway. Taken together, our study reveals major changes in gene expression associated with blast disease and identifies a diverse repertoire of effectors critical for successful infection.
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Affiliation(s)
- Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lauren S Ryder
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent M Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Alice Bisola Eseola
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neftaly Cruz-Mireles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Weibin Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Andrew J Foster
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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Hanano A, Blée E, Murphy DJ. Caleosin/peroxygenases: multifunctional proteins in plants. ANNALS OF BOTANY 2023; 131:387-409. [PMID: 36656070 PMCID: PMC10072107 DOI: 10.1093/aob/mcad001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/08/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Caleosin/peroxygenases (CLO/PXGs) are a family of multifunctional proteins that are ubiquitous in land plants and are also found in some fungi and green algae. CLO/PXGs were initially described as a class of plant lipid-associated proteins with some similarities to the oleosins that stabilize lipid droplets (LDs) in storage tissues, such as seeds. However, we now know that CLO/PXGs have more complex structures, distributions and functions than oleosins. Structurally, CLO/PXGs share conserved domains that confer specific biochemical features, and they have diverse localizations and functions. SCOPE This review surveys the structural properties of CLO/PXGs and their biochemical roles. In addition to their highly conserved structures, CLO/PXGs have peroxygenase activities and are involved in several aspects of oxylipin metabolism in plants. The enzymatic activities and the spatiotemporal expression of CLO/PXGs are described and linked with their wider involvement in plant physiology. Plant CLO/PXGs have many roles in both biotic and abiotic stress responses in plants and in their responses to environmental toxins. Finally, some intriguing developments in the biotechnological uses of CLO/PXGs are addressed. CONCLUSIONS It is now two decades since CLO/PXGs were first recognized as a new class of lipid-associated proteins and only 15 years since their additional enzymatic functions as a new class of peroxygenases were discovered. There are many interesting research questions that remain to be addressed in future physiological studies of plant CLO/PXGs and in their recently discovered roles in the sequestration and, possibly, detoxification of a wide variety of lipidic xenobiotics that can challenge plant welfare.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Elizabeth Blée
- Former Head of Phyto-oxylipins laboratory, Institute of Plant Molecular Biology, University of Strasbourg, France
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Treforest, UK
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), Damascus, Syria
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Peng YJ, Zhang H, Feng MG, Ying SH. Steryl Acetyl Hydrolase 1 (BbSay1) Links Lipid Homeostasis to Conidiogenesis and Virulence in the Entomopathogenic Fungus Beauveria bassiana. J Fungi (Basel) 2022; 8:jof8030292. [PMID: 35330294 PMCID: PMC8953178 DOI: 10.3390/jof8030292] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023] Open
Abstract
Beauveria bassiana, as a well-studied entomopathogenic fungus, has a great potential for the biological control of insect pests. Lipid metabolism has been linked to the life cycle of B. bassiana; however, the underlying mechanisms remain unknown. In this study, a homolog of yeast steryl acetyl hydrolase 1 (Say1) was functionally characterized. The loss of B. bassianaSAY1 (BbSAY1) impaired the lipid homeostasis in conidia, with a significant reduction in oleic acid content. The ΔBbsay1 mutant strain displayed anelevated accumulation of lipid bodies and aweakened membrane permeability. As for phenotypic aspects, gene loss resulted in significant defects in germination, conidiation, and virulence. Our findings highlight that Say1, involved in lipid homeostasis, contributes to the cytomembrane integrity, development, and virulence in B. bassiana.
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The Heterotrimeric Transcription Factor CCAAT-Binding Complex and Ca 2+-CrzA Signaling Reversely Regulate the Transition between Fungal Hyphal Growth and Asexual Reproduction. mBio 2021; 12:e0300721. [PMID: 34781745 PMCID: PMC8593669 DOI: 10.1128/mbio.03007-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The life cycle of filamentous fungi generally comprises hyphal growth and asexual reproduction. Both growth and propagation processes are critical for invasion growth, spore dissemination, and virulence in fungal pathogens and for the production of secondary metabolites or for biomass accumulation in industrial filamentous fungi. The CCAAT-binding complex (CBC) is a heterotrimeric transcription factor comprising three subunits, HapB, HapC, and HapE, and is highly conserved in fungi. Previous studies revealed that CBC regulates sterol metabolism by repressing several genes in the ergosterol biosynthetic pathway in the human fungal pathogen Aspergillus fumigatus. In the present study, we found dysfunction of CBC caused the abnormal asexual reproduction (conidiation) in submerged liquid culture. CBC suppresses the activation of the brlA gene in the central regulatory pathway for conidiation combined with its upstream regulators fluG, flbD, and flbC by binding to the 5'-CCAAT-3' motif within conidiation gene promoters, and lack of CBC member HapB results in the upregulation of these genes. Furthermore, when the expression of brlA or flbC is repressed, the submerged conidiation does not happen in the hapB mutant. Interestingly, deletion of HapB leads to enhanced transient cytosolic Ca2+ levels and activates conidiation-positive inducer Ca2+-CrzA modules to enhance submerged conidiation, demonstrating that CrzA works with CBC as a reverse regulator of fungal conidiation. To the best of our knowledge, the finding of this study is the first report for the molecular switch mechanism between vegetative hyphal growth and asexual development regulated by CBC, in concert with Ca2+-CrzA signaling in A. fumigatus. IMPORTANCE A precisely timed switch between vegetative hyphal growth and asexual development is a crucial process for the filamentous fungal long-term survival, dissemination, biomass production, and virulence. However, under the submerged culture condition, filamentous fungi would undergo constant vegetative growth whereas asexual conidiation rarely occurs. Knowledge about possible regulators is scarce, and how they could inhibit conidiation in liquid culture is poorly understood. Here, we demonstrated that the transcription factor heterotrimeric CBC dominantly maintains vegetative growth in liquid-submerged cultures by directly suppressing the conidiation-inductive signal. In contrast, calcium and the transcription factor CrzA, are positive inducers of conidiation. Our new insights into the CBC and Ca2+-CrzA regulatory system for transition control in the submerged conidiation of A. fumigatus may have broad repercussions for all filamentous fungi. Moreover, our elucidation of the molecular mechanism for submerged conidiation may support new strategies to precisely control vegetative growth and asexual conidiation in aspergilli used in industry.
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Mahfouz S, Mansour G, Murphy DJ, Hanano A. Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00347-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractDioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.
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Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR. Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects. Microbiol Res 2020; 241:126567. [PMID: 33080488 DOI: 10.1016/j.micres.2020.126567] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India; Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | | | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | - Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India.
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
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Pham TA, Schwerdt JG, Shirley NJ, Xing X, Hsieh YS, Srivastava V, Bulone V, Little A. Analysis of cell wall synthesis and metabolism during early germination of Blumeria graminis f. sp. hordei conidial cells induced in vitro. Cell Surf 2019; 5:100030. [PMID: 32743146 PMCID: PMC7389524 DOI: 10.1016/j.tcsw.2019.100030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 11/30/2022] Open
Abstract
As an obligate biotroph, Blumeria graminis f. sp. hordei (Bgh) cannot be grown in an axenic culture, and instead must be cultivated on its host species, Hordeum vulgare (barley). In this study an in vitro system utilizing n-hexacosanal, a constituent of the barley cuticle and known inducer of Bgh germination, was used to cultivate Bgh and differentiate conidia up to the appressorial germ tube stage for analysis. Transcriptomic and proteomic profiling of the appressorial germ tube stage revealed that there was a significant shift towards energy and protein production during the pre-penetrative phase of development, with an up-regulation of enzymes associated with cellular respiration and protein synthesis, modification and transport. Glycosidic linkage analysis of the cell wall polysaccharides demonstrated that during appressorial development an increase in 1,3- and 1,4-linked glucosyl residues and xylosyl residues was detected along with a significant decrease in galactosyl residues. The use of this in vitro cultivation method demonstrates that it is possible to analyse the pre-penetrative processes of Bgh development in the absence of a plant host.
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Affiliation(s)
- Trang A.T. Pham
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Julian G. Schwerdt
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Neil J. Shirley
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Xiaohui Xing
- Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Yves S.Y. Hsieh
- Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Vincent Bulone
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Alan Little
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
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Rahman F, Hassan M, Hanano A, Fitzpatrick DA, McCarthy CGP, Murphy DJ. Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi. BMC Genomics 2018; 19:976. [PMID: 30593269 PMCID: PMC6309107 DOI: 10.1186/s12864-018-5334-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim of this study was to investigate the evolution and functions of the CLO/PXGs in the Fungi and other non-plant clades and to elucidate the overall origin of this gene family. RESULTS CLO/PXG-like genes are distributed across the full range of fungal groups from the basal clades, Cryptomycota and Microsporidia, to the largest and most complex Dikarya species. However, the genes were only present in 243 out of 844 analysed fungal genomes. CLO/PXG-like genes have been retained in many pathogenic or parasitic fungi that have undergone considerable genomic and structural simplification, indicating that they have important functions in these species. Structural and functional analyses demonstrate that CLO/PXGs are multifunctional proteins closely related to similar proteins found in all major taxa of the Chlorophyte Division of the Viridiplantae. Transcriptome and physiological data show that fungal CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression and are upregulated in response to a range of biotic and abiotic stresses as well as participating in key metabolic and developmental processes such as lipid metabolism, signalling, reproduction and pathogenesis. Biochemical data also reveal that the Aspergillus flavus CLO/PXG has specific functions in sporulation and aflatoxin production as well as playing roles in lipid droplet function. CONCLUSIONS In contrast to plants, CLO/PXGs only occur in about 30% of sequenced fungal genomes but are present in all major taxa. Fungal CLO/PXGs have similar but not identical roles to those in plants, including stress-related oxylipin signalling, lipid metabolism, reproduction and pathogenesis. While the presence of CLO/PXG orthologs in all plant genomes sequenced to date would suggest that they have core housekeeping functions in plants, the selective loss of CLO/PXGs in many fungal genomes suggests more restricted functions in fungi as accessory genes useful in particular environments or niches. We suggest an ancient origin of CLO/PXG-like genes in the 'last eukaryotic common ancestor' (LECA) and their subsequent loss in ancestors of the Metazoa, after the latter had diverged from the ancestral fungal lineage.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | | | | | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
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Kusch S, Frantzeskakis L, Thieron H, Panstruga R. Small RNAs from cereal powdery mildew pathogens may target host plant genes. Fungal Biol 2018; 122:1050-1063. [PMID: 30342621 DOI: 10.1016/j.funbio.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
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12
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Hu Y, Liang Y, Zhang M, Tan F, Zhong S, Li X, Gong G, Chang X, Shang J, Tang S, Li T, Luo P. Comparative transcriptome profiling of Blumeria graminis f. sp. tritici during compatible and incompatible interactions with sister wheat lines carrying and lacking Pm40. PLoS One 2018; 13:e0198891. [PMID: 29975700 PMCID: PMC6033381 DOI: 10.1371/journal.pone.0198891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022] Open
Abstract
Blumeria graminis f. sp. tritici (Bgt) is an obligate biotrophic fungus that causes wheat powdery mildew, which is a devastating disease in wheat. However, little is known about the pathogenesis of this fungus, and differences in the pathogenesis of the same pathogen at various resistance levels in hosts have not been determined. In the present study, leaf tissues of both Pm40-expressing hexaploid wheat line L658 and its Pm40-deficient sister line L958 were harvested at 0 (without inoculation), 6, 12, 24, 48 and 72 hours post-inoculation (hpi) with Bgt race 15 and then subjected to RNA sequencing (RNA-seq). In addition, we also observed changes in fungal growth morphology at the aforementioned time points. There was a high correlation between percentage of reads mapped to the Bgt reference genome and biomass of the fungus within the leaf tissue during the growth process. The percentage of mapped reads of Bgt in compatible interactions was significantly higher (at the p<0.05 level) than that of reads in incompatible interactions from 24 to 72 hpi. Further functional annotations indicated that expression levels of genes encoding H+-transporting ATPase, putative secreted effector proteins (PSEPs) and heat shock proteins (HSPs) were significantly up-regulated in compatible interactions compared with these levels in incompatible interactions, particularly at 72 hpi. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that genes involved in the endocytosis pathway were also enriched in compatible interactions. Overall, genes encoding H+-transporting ATPase, PSEPs and HSPs possibly played crucial roles in successfully establishing the pathogenesis of compatible interactions during late stages of inoculation. The study results also indicated that endocytosis is likely to play a potential role in Bgt in establishing compatible interactions.
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Affiliation(s)
- Yuting Hu
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yinping Liang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Zhang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feiquan Tan
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengfu Zhong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoshu Gong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Chang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Shang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengwen Tang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peigao Luo
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
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13
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Lanver D, Müller AN, Happel P, Schweizer G, Haas FB, Franitza M, Pellegrin C, Reissmann S, Altmüller J, Rensing SA, Kahmann R. The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis. THE PLANT CELL 2018; 30:300-323. [PMID: 29371439 PMCID: PMC5868686 DOI: 10.1105/tpc.17.00764] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/20/2017] [Accepted: 01/24/2018] [Indexed: 05/19/2023]
Abstract
The maize smut fungus Ustilago maydis is a model organism for elucidating host colonization strategies of biotrophic fungi. Here, we performed an in depth transcriptional profiling of the entire plant-associated development of U. maydis wild-type strains. In our analysis, we focused on fungal metabolism, nutritional strategies, secreted effectors, and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy, and induction of tumors. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen assimilation are important virulence factors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules. While known components of the b-mating type cascade emerged as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role for leaf tumor formation and effector gene expression for one of these transcription factors.
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Affiliation(s)
- Daniel Lanver
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - André N Müller
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Petra Happel
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Gabriel Schweizer
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Fabian B Haas
- Philipps Universität Marburg, Fb17 Biologie, AG Zellbiologie der Pflanzen, 35043 Marburg, Germany
| | - Marek Franitza
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Clément Pellegrin
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Stefan A Rensing
- Philipps Universität Marburg, Fb17 Biologie, AG Zellbiologie der Pflanzen, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Regine Kahmann
- Max-Planck-Institut für Terrestrische Mikrobiologie, Abteilung Organismische Interaktionen, 35043 Marburg, Germany
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