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Brandt P, Gerwien F, Wagner L, Krüger T, Ramírez-Zavala B, Mirhakkak MH, Schäuble S, Kniemeyer O, Panagiotou G, Brakhage AA, Morschhäuser J, Vylkova S. Candida albicans SR-Like Protein Kinases Regulate Different Cellular Processes: Sky1 Is Involved in Control of Ion Homeostasis, While Sky2 Is Important for Dipeptide Utilization. Front Cell Infect Microbiol 2022; 12:850531. [PMID: 35601106 PMCID: PMC9121809 DOI: 10.3389/fcimb.2022.850531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/24/2022] [Indexed: 01/21/2023] Open
Abstract
Protein kinases play a crucial role in regulating cellular processes such as growth, proliferation, environmental adaptation and stress responses. Serine-arginine (SR) protein kinases are highly conserved in eukaryotes and regulate fundamental processes such as constitutive and alternative splicing, mRNA processing and ion homeostasis. The Candida albicans genome encodes two (Sky1, Sky2) and the Candida glabrata genome has one homolog (Sky1) of the human SR protein kinase 1, but their functions have not yet been investigated. We used deletion strains of the corresponding genes in both fungi to study their cellular functions. C. glabrata and C. albicans strains lacking SKY1 exhibited higher resistance to osmotic stress and toxic polyamine concentrations, similar to Saccharomyces cerevisiae sky1Δ mutants. Deletion of SKY2 in C. albicans resulted in impaired utilization of various dipeptides as the sole nitrogen source. Subsequent phosphoproteomic analysis identified the di- and tripeptide transporter Ptr22 as a potential Sky2 substrate. Sky2 seems to be involved in Ptr22 regulation since overexpression of PTR22 in the sky2Δ mutant restored the ability to grow on dipeptides and made the cells more susceptible to the dipeptide antifungals Polyoxin D and Nikkomycin Z. Altogether, our results demonstrate that C. albicans and C. glabrata Sky1 protein kinases are functionally similar to Sky1 in S. cerevisiae, whereas C. albicans Sky2, a unique kinase of the CTG clade, likely regulates dipeptide uptake via Ptr22.
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Affiliation(s)
- Philipp Brandt
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Franziska Gerwien
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Lysett Wagner
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Krüger
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | | | - Mohammad H. Mirhakkak
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Sascha Schäuble
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Olaf Kniemeyer
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Axel A. Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Joachim Morschhäuser
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- *Correspondence: Slavena Vylkova,
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Wu M, Feng G, Zhang B, Xu K, Wang Z, Cheng S, Chang C, Vyas A, Tang Z, Liu X. Phosphoproteomics Reveals Novel Targets and Phosphoprotein Networks in Cell Cycle Mediated by Dsk1 Kinase. J Proteome Res 2020; 19:1776-1787. [DOI: 10.1021/acs.jproteome.0c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mei Wu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gang Feng
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, Fujian Medical University, Fuzhou 350122, China
| | - Buyu Zhang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kaikun Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing 102206, P.R. China
| | - Zhen Wang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Sen Cheng
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing 102206, P.R. China
| | - Aditi Vyas
- W.M. Keck Science Center, 925 North Mills Avenue, The Claremont Colleges, Claremont, California 91711, United States
| | - Zhaohua Tang
- W.M. Keck Science Center, 925 North Mills Avenue, The Claremont Colleges, Claremont, California 91711, United States
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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The SR-protein FgSrp2 regulates vegetative growth, sexual reproduction and pre-mRNA processing by interacting with FgSrp1 in Fusarium graminearum. Curr Genet 2020; 66:607-619. [PMID: 32040734 DOI: 10.1007/s00294-020-01054-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/22/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
Serine/arginine (SR) proteins play significant roles in pre-mRNA splicing in eukaryotes. To investigate how gene expression influences fungal development and pathogenicity in Fusarium graminearum, a causal agent of Fusarium head blight (FHB) of wheat and barley, our previous study identified a SR protein FgSrp1 in F. graminearum, and showed that it is important for conidiation, plant infection and pre-mRNA processing. In this study, we identified another SR protein FgSrp2 in F. graminearum, which is orthologous to Schizosaccharomyces pombe Srp2. Our data showed that, whereas yeast Srp2 is essential for growth, deletion of FgSRP2 resulted in only slight defects in vegetative growth and perithecia melanization. FgSrp2 localized to the nucleus and both its N- and C-terminal regions were important for the localization to the nucleus. FgSrp2 interacted with FgSrp1 to form a complex in vivo. Double deletion of FgSRP1 and FgSRP2 revealed that they had overlapping functions in vegetative growth and sexual reproduction. RNA-seq analysis revealed that, although deletion of FgSRP2 alone had minimal effects, deletion of both FgSRP1 and FgSRP2 caused significant changes in gene transcription and RNA splicing. Overall, our results indicated that FgSrp2 regulates vegetative growth, sexual reproduction and pre-mRNA processing by interacting with FgSrp1.
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Comparative Genomic Screen in Two Yeasts Reveals Conserved Pathways in the Response Network to Phenol Stress. G3-GENES GENOMES GENETICS 2019; 9:639-650. [PMID: 30647105 PMCID: PMC6404616 DOI: 10.1534/g3.118.201000] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Living organisms encounter various perturbations, and response mechanisms to such perturbations are vital for species survival. Defective stress responses are implicated in many human diseases including cancer and neurodegenerative disorders. Phenol derivatives, naturally occurring and synthetic, display beneficial as well as detrimental effects. The phenol derivatives in this study, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), and bisphenol A (BPA), are widely used as food preservatives and industrial chemicals. Conflicting results have been reported regarding their biological activity and correlation with disease development; understanding the molecular basis of phenol action is a key step for addressing issues relevant to human health. This work presents the first comparative genomic analysis of the genetic networks for phenol stress response in an evolutionary context of two divergent yeasts, Schizosaccharomyces pombe and Saccharomyces cerevisiae. Genomic screening of deletion strain libraries of the two yeasts identified genes required for cellular response to phenol stress, which are enriched in human orthologs. Functional analysis of these genes uncovered the major signaling pathways involved. The results provide a global view of the biological events constituting the defense process, including cell cycle arrest, DNA repair, phenol detoxification by V-ATPases, reactive oxygen species alleviation, and endoplasmic reticulum stress relief through ergosterol and the unfolded protein response, revealing novel roles for these cellular pathways.
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Wang G, Sun P, Gong Z, Gu L, Lou Y, Fang W, Zhang L, Su L, Yang T, Wang B, Zhou J, Xu JR, Wang Z, Zheng W. Srk1 kinase, a SR protein-specific kinase, is important for sexual reproduction, plant infection and pre-mRNA processing in Fusarium graminearum. Environ Microbiol 2018; 20:3261-3277. [DOI: 10.1111/1462-2920.14299] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Guanghui Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Oceanography; Minjiang University; Fuzhou China
| | - Peng Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Ziwen Gong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center (BFPC), Haixia Institute of Science and Technology; Fujian Agriculture and Forestry University; Fuzhou China
| | - Yi Lou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Wenqin Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Lianhu Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Li Su
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Baohua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Jie Zhou
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins; College of Life Sciences, Fujian Agriculture and Forestry University; Fuzhou China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University; Yangling Shaanxi China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Oceanography; Minjiang University; Fuzhou China
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
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6
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Zhang Y, Gao X, Sun M, Liu H, Xu JR. The FgSRP1 SR-protein gene is important for plant infection and pre-mRNA processing in Fusarium graminearum. Environ Microbiol 2017; 19:4065-4079. [PMID: 28654215 DOI: 10.1111/1462-2920.13844] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022]
Abstract
The versatile functions of SR (serine/arginine-rich) proteins in pre-mRNA splicing and processing are modulated by reversible phosphorylation. Previous studies showed that FgPrp4, the only protein kinase among spliceosome components, is important for intron splicing and the FgSrp1 SR protein is phosphorylated at five conserved sites in Fusarium graminearum. In this study, we showed that the Fgsrp1 deletion mutant rarely produced conidia and caused only limited symptoms on wheat heads and corn silks. Deletion of FgSRP1 also reduced ascospore ejection and deoxynivalenol (DON) production. Interestingly, FgSRP1 had two transcript isoforms due to alternative splicing and both of them were required for its normal functions in growth and DON biosynthesis. FgSrp1 localized to the nucleus and interacted with FgPrp4 in vivo. Deletion of all four conserved phosphorylation sites but not individual ones affected the FgSRP1 function, suggesting their overlapping functions. RNA-seq analysis showed that the expression of over thousands of genes and splicing efficiency in over 140 introns were affected. Taken together, FgSRP1 is important for conidiation, and pathogenesis and alternative splicing is important for its normal functions. The FgSrp1 SR protein is likely important for pre-mRNA processing or splicing of various genes in different developmental and infection processes.
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Affiliation(s)
- Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuli Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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7
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Ariyachet C, Beißel C, Li X, Lorrey S, Mackenzie O, Martin PM, O'Brien K, Pholcharee T, Sim S, Krebber H, McBride AE. Post-translational modification directs nuclear and hyphal tip localization of Candida albicans mRNA-binding protein Slr1. Mol Microbiol 2017; 104:499-519. [PMID: 28187496 PMCID: PMC5405739 DOI: 10.1111/mmi.13643] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 12/21/2022]
Abstract
The morphological transition of the opportunistic fungal pathogen Candida albicans from budding to hyphal growth has been implicated in its ability to cause disease in animal models. Absence of SR‐like RNA‐binding protein Slr1 slows hyphal formation and decreases virulence in a systemic candidiasis model, suggesting a role for post‐transcriptional regulation in these processes. SR (serine–arginine)‐rich proteins influence multiple steps in mRNA metabolism and their localization and function are frequently controlled by modification. We now demonstrate that Slr1 binds to polyadenylated RNA and that its intracellular localization is modulated by phosphorylation and methylation. Wildtype Slr1‐GFP is predominantly nuclear, but also co‐fractionates with translating ribosomes. The non‐phosphorylatable slr1‐6SA‐GFP protein, in which six serines in SR/RS clusters are substituted with alanines, primarily localizes to the cytoplasm in budding cells. Intriguingly, hyphal cells display a slr1‐6SA‐GFP focus at the tip near the Spitzenkörper, a vesicular structure involved in molecular trafficking to the tip. The presence of slr1‐6SA‐GFP hyphal tip foci is reduced in the absence of the mRNA‐transport protein She3, suggesting that unphosphorylated Slr1 associates with mRNA–protein complexes transported to the tip. The impact of SLR1 deletion on hyphal formation and function thus may be partially due to a role in hyphal mRNA transport.
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Affiliation(s)
| | - Christian Beißel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August Universität Göttingen, Göttingen, Germany
| | - Xiang Li
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | - Selena Lorrey
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | | | | | | | | | - Sue Sim
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August Universität Göttingen, Göttingen, Germany
| | - Anne E McBride
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
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Majeská Čudejková M, Vojta P, Valík J, Galuszka P. Quantitative and qualitative transcriptome analysis of four industrial strains of Claviceps purpurea with respect to ergot alkaloid production. N Biotechnol 2016; 33:743-754. [PMID: 26827914 DOI: 10.1016/j.nbt.2016.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 01/14/2023]
Abstract
The fungus Claviceps purpurea is a biotrophic phytopathogen widely used in the pharmaceutical industry for its ability to produce ergot alkaloids (EAs). The fungus attacks unfertilized ovaries of grasses and forms sclerotia, which represent the only type of tissue where the synthesis of EAs occurs. The biosynthetic pathway of EAs has been extensively studied; however, little is known concerning its regulation. Here, we present the quantitative transcriptome analysis of the sclerotial and mycelial tissues providing a comprehensive view of transcriptional differences between the tissues that produce EAs and those that do not produce EAs and the pathogenic and non-pathogenic lifestyle. The results indicate metabolic changes coupled with sclerotial differentiation, which are likely needed as initiation factors for EA biosynthesis. One of the promising factors seems to be oxidative stress. Here, we focus on the identification of putative transcription factors and regulators involved in sclerotial differentiation, which might be involved in EA biosynthesis. To shed more light on the regulation of EA composition, whole transcriptome analysis of four industrial strains differing in their alkaloid spectra was performed. The results support the hypothesis proposing the composition of the amino acid pool in sclerotia to be an important factor regulating the final structure of the ergopeptines produced by Claviceps purpurea.
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Affiliation(s)
- Mária Majeská Čudejková
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
| | - Petr Vojta
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 1333/5, 779 00 Olomouc, Czech Republic
| | - Josef Valík
- Teva Czech Industries s.r.o., Ostravská 305/29, 747 70 Opava-Komárov, Czech Republic
| | - Petr Galuszka
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Cheng Y, Wang X, Yao J, Voegele RT, Zhang Y, Wang W, Huang L, Kang Z. Characterization of protein kinase PsSRPKL, a novel pathogenicity factor in the wheat stripe rust fungus. Environ Microbiol 2015; 17:2601-17. [PMID: 25407954 DOI: 10.1111/1462-2920.12719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/09/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
Abstract
As in other eukaryotes, protein kinases (PKs) are generally evolutionarily conserved and play major regulatory roles in plant pathogenic fungi. Many PKs have been proven to be important for pathogenesis in model fungal plant pathogens, but little is currently known about their roles in the pathogenesis of cereal rust fungi, devastating pathogens in agriculture worldwide. Here, we report on an in planta highly induced PK gene PsSRPKL from the wheat stripe rust fungus Puccinia striiformis f. sp. tritici (Pst), one of the most important cereal rust fungi. PsSRPKL belongs to a group of PKs that are evolutionarily specific to cereal rust fungi. It shows a high level of intraspecies polymorphism in the kinase domains and directed green fluorescent protein chimers to plant nuclei. Overexpression of PsSRPKL in fission yeast induces aberrant cell morphology and a decreased resistance to environmental stresses. Most importantly, PsSRPKL is proven to be an important pathogenicity factor responsible for fungal growth and responses to environmental stresses, therefore contributing significantly to Pst virulence in wheat. We hypothesize that cereal rust fungi have developed specific PKs as pathogenicity factors for adaptation to their host species during evolution. Thus, our findings provide significant insights into pathogenicity and virulence evolution in cereal rust fungi.
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Affiliation(s)
- Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juanni Yao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ralf T Voegele
- Fachgebiet Phytopathologie, Fakultät Agrarwissenschaften, Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Yanru Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wumei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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10
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Tang Z, Luca M, Taggart-Murphy L, Portillio J, Chang C, Guven A, Lin RJ, Murray J, Carr A. Interacting factors and cellular localization of SR protein-specific kinase Dsk1. Exp Cell Res 2012; 318:2071-84. [PMID: 22683458 DOI: 10.1016/j.yexcr.2012.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/06/2012] [Accepted: 05/23/2012] [Indexed: 01/10/2023]
Abstract
Schizosaccharomyces pombe Dsk1 is an SR protein-specific kinase (SRPK), whose homologs have been identified in every eukaryotic organism examined. Although discovered as a mitotic regulator with protein kinase activity toward SR splicing factors, it remains largely unknown about what and how Dsk1 contributes to cell cycle and pre-mRNA splicing. In this study, we investigated the Dsk1 function by determining interacting factors and cellular localization of the kinase. Consistent with its reported functions, we found that pre-mRNA processing and cell cycle factors are prominent among the proteins co-purified with Dsk1. The identification of these factors led us to find Rsd1 as a novel Dsk1 substrate, as well as the involvement of Dsk1 in cellular distribution of poly(A)(+) RNA. In agreement with its role in nuclear events, we also found that Dsk1 is mainly localized in the nucleus during G(2) phase and at mitosis. Furthermore, we revealed the oscillation of Dsk1 protein in a cell cycle-dependent manner. This paper marks the first comprehensive analysis of in vivo Dsk1-associated proteins in fission yeast. Our results reflect the conserved role of SRPK family in eukaryotic organisms, and provide information about how Dsk1 functions in pre-mRNA processing and cell-division cycle.
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Affiliation(s)
- Zhaohua Tang
- W.M. Keck Science Center, The Claremont Colleges, Claremont, CA 91711, USA.
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11
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LAMMER kinase Kic1 is involved in pre-mRNA processing. Exp Cell Res 2011; 317:2308-20. [PMID: 21745468 DOI: 10.1016/j.yexcr.2011.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 06/22/2011] [Accepted: 06/23/2011] [Indexed: 01/03/2023]
Abstract
The LAMMER kinases are conserved through evolution. They play vital roles in cell growth/differentiation, development, and metabolism. One of the best known functions of the kinases in animal cells is the regulation of pre-mRNA splicing. Kic1 is the LAMMER kinase in fission yeast Schizosaccharomyces pombe. Despite the reported pleiotropic effects of kic1+ deletion/overexpression on various cellular processes the involvement of Kic1 in splicing remains elusive. In this study, we demonstrate for the first time that Kic1 not only is required for efficient splicing but also affects mRNA export, providing evidence for the conserved roles of LAMMER kinases in the unicellular context of fission yeast. Consistent with the hypothesis of its direct participation in multiple steps of pre-mRNA processing, Kic1 is predominantly present in the nucleus during interphase. In addition, the kinase activity of Kic1 plays a role in modulating its own cellular partitioning. Interestingly, Kic1 expression oscillates in a cell cycle-dependent manner and the peak level coincides with mitosis and cytokinesis, revealing a potential mechanism for controlling the kinase activity during the cell cycle. The novel information about the in vivo functions and regulation of Kic1 offers insights into the conserved biological roles fundamental to LAMMER kinases in eukaryotes.
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Giannakouros T, Nikolakaki E, Mylonis I, Georgatsou E. Serine-arginine protein kinases: a small protein kinase family with a large cellular presence. FEBS J 2011; 278:570-86. [DOI: 10.1111/j.1742-4658.2010.07987.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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13
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Liu X, Tang WH, Zhao XM, Chen L. A network approach to predict pathogenic genes for Fusarium graminearum. PLoS One 2010; 5:e13021. [PMID: 20957229 PMCID: PMC2949387 DOI: 10.1371/journal.pone.0013021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 08/17/2010] [Indexed: 11/18/2022] Open
Abstract
Fusarium graminearum is the pathogenic agent of Fusarium head blight (FHB), which is a destructive disease on wheat and barley, thereby causing huge economic loss and health problems to human by contaminating foods. Identifying pathogenic genes can shed light on pathogenesis underlying the interaction between F. graminearum and its plant host. However, it is difficult to detect pathogenic genes for this destructive pathogen by time-consuming and expensive molecular biological experiments in lab. On the other hand, computational methods provide an alternative way to solve this problem. Since pathogenesis is a complicated procedure that involves complex regulations and interactions, the molecular interaction network of F. graminearum can give clues to potential pathogenic genes. Furthermore, the gene expression data of F. graminearum before and after its invasion into plant host can also provide useful information. In this paper, a novel systems biology approach is presented to predict pathogenic genes of F. graminearum based on molecular interaction network and gene expression data. With a small number of known pathogenic genes as seed genes, a subnetwork that consists of potential pathogenic genes is identified from the protein-protein interaction network (PPIN) of F. graminearum, where the genes in the subnetwork are further required to be differentially expressed before and after the invasion of the pathogenic fungus. Therefore, the candidate genes in the subnetwork are expected to be involved in the same biological processes as seed genes, which imply that they are potential pathogenic genes. The prediction results show that most of the pathogenic genes of F. graminearum are enriched in two important signal transduction pathways, including G protein coupled receptor pathway and MAPK signaling pathway, which are known related to pathogenesis in other fungi. In addition, several pathogenic genes predicted by our method are verified in other pathogenic fungi, which demonstrate the effectiveness of the proposed method. The results presented in this paper not only can provide guidelines for future experimental verification, but also shed light on the pathogenesis of the destructive fungus F. graminearum.
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Affiliation(s)
- Xiaoping Liu
- Institute of Systems Biology, Shanghai University, Shanghai, China
- School of Communication and Information Engineering, Shanghai University, Shanghai, China
| | - Wei-Hua Tang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xing-Ming Zhao
- Institute of Systems Biology, Shanghai University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Institute of Systems Biology, Shanghai University, Shanghai, China
- Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Nieratschker V, Schubert A, Jauch M, Bock N, Bucher D, Dippacher S, Krohne G, Asan E, Buchner S, Buchner E. Bruchpilot in ribbon-like axonal agglomerates, behavioral defects, and early death in SRPK79D kinase mutants of Drosophila. PLoS Genet 2009; 5:e1000700. [PMID: 19851455 PMCID: PMC2759580 DOI: 10.1371/journal.pgen.1000700] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 09/23/2009] [Indexed: 12/18/2022] Open
Abstract
Defining the molecular structure and function of synapses is a central theme in brain research. In Drosophila the Bruchpilot (BRP) protein is associated with T-shaped ribbons ("T-bars") at presynaptic active zones (AZs). BRP is required for intact AZ structure and normal evoked neurotransmitter release. By screening for mutations that affect the tissue distribution of Bruchpilot, we have identified a P-transposon insertion in gene CG11489 (location 79D) which shows high homology to mammalian genes for SR protein kinases (SRPKs). SRPKs phosphorylate serine-arginine rich splicing factors (SR proteins). Since proteins expressed from CG11489 cDNAs phosphorylate a peptide from a human SR protein in vitro, we name CG11489 the Drosophila Srpk79D gene. We have characterized Srpk79D transcripts and generated a null mutant. Mutation of the Srpk79D gene causes conspicuous accumulations of BRP in larval and adult nerves. At the ultrastructural level, these correspond to extensive axonal agglomerates of electron-dense ribbons surrounded by clear vesicles. Basic synaptic structure and function at larval neuromuscular junctions appears normal, whereas life expectancy and locomotor behavior of adult mutants are significantly impaired. All phenotypes of the mutant can be largely or completely rescued by panneural expression of SRPK79D isoforms. Isoform-specific antibodies recognize panneurally overexpressed GFP-tagged SRPK79D-PC isoform co-localized with BRP at presynaptic active zones while the tagged -PB isoform is found in spots within neuronal perikarya. SRPK79D concentrations in wild type apparently are too low to be revealed by these antisera. We propose that the Drosophila Srpk79D gene characterized here may be expressed at low levels throughout the nervous system to prevent the assembly of BRP containing agglomerates in axons and maintain intact brain function. The discovery of an SR protein kinase required for normal BRP distribution calls for the identification of its substrate and the detailed analysis of SRPK function for the maintenance of nervous system integrity.
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Affiliation(s)
- Vanessa Nieratschker
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Alice Schubert
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Mandy Jauch
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Nicole Bock
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Daniel Bucher
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Sonja Dippacher
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Georg Krohne
- Department of Electron Microscopy, Julius-Maximilians-University, Würzburg, Germany
| | - Esther Asan
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Sigrid Buchner
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
| | - Erich Buchner
- Department of Genetics and Neurobiology, Julius-Maximilians-University, Würzburg, Germany
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Liu S, Zhou Z, Lin Z, Ouyang Q, Zhang J, Tian S, Xing M. Identification of a nuclear localization motif in the serine/arginine protein kinase PSRPK of physarum polycephalum. BMC BIOCHEMISTRY 2009; 10:22. [PMID: 19703313 PMCID: PMC2754491 DOI: 10.1186/1471-2091-10-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 08/25/2009] [Indexed: 11/13/2022]
Abstract
Background Serine/arginine (SR) protein-specific kinases (SRPKs) are conserved in a wide range of organisms, from humans to yeast. Studies showed that SRPKs can regulate the nuclear import of SR proteins in cytoplasm, and regulate the sub-localization of SR proteins in the nucleus. But no nuclear localization signal (NLS) of SRPKs was found. We isolated an SRPK-like protein PSRPK (GenBank accession No. DQ140379) from Physarum polycephalum previously, and identified a NLS of PSRPK in this study. Results We carried out a thorough molecular dissection of the different domains of the PSRPK protein involved in its nuclear localization. By truncation of PSRPK protein, deletion of and single amino acid substitution in a putative NLS and transfection of mammalian cells, we observed the distribution of PSRPK fluorescent fusion protein in mammalian cells using confocal microscopy and found that the protein was mainly accumulated in the nucleus; this indicated that the motif contained a nuclear localization signal (NLS). Further investigation with truncated PSPRK peptides showed that the NLS (318PKKGDKYDKTD328) was localized in the alkaline Ω-loop of a helix-loop-helix motif (HLHM) of the C-terminal conserved domain. If the 318PKKGDK322 sequence was deleted from the loop or K320 was mutated to T320, the PSRPK fluorescent fusion protein could not enter and accumulate in the nucleus. Conclusion This study demonstrated that the 318PKKGDKYDKTD328 peptides localized in the C-terminal conserved domain of PSRPK with the Ω-loop structure could play a crucial role in the NLS function of PSRPK.
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Affiliation(s)
- Shide Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering and College of Life Science, Shenzhen University, Shenzhen, PR China.
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Tardos JG, Eisenreich A, Deikus G, Bechhofer DH, Chandradas S, Zafar U, Rauch U, Bogdanov VY. SR proteins ASF/SF2 and SRp55 participate in tissue factor biosynthesis in human monocytic cells. J Thromb Haemost 2008; 6:877-84. [PMID: 18315555 DOI: 10.1111/j.1538-7836.2008.02946.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
BACKGROUND Human monocytes express two naturally occurring forms of circulating tissue factor (TF) - full-length TF, a membrane-spanning protein, and alternatively spliced TF, a soluble molecule. Presence of the variable exon 5 in TF mRNA determines whether the encoded TF protein is transmembrane, or soluble. Recently, an essential SR protein ASF/SF2 was implicated in TF pre-mRNA processing in human platelets. OBJECTIVE To examine molecular mechanisms governing regulated processing of TF pre-mRNA in human monocytic cells. METHODS AND RESULTS In silico analysis of the human TF exon 5, present only in full-length TF mRNA, revealed putative binding motifs termed exonic splicing enhancers (ESE) for the SR proteins ASF/SF2 and SRp55, which were found to be abundantly expressed in monocytic cell lines THP-1 and SC, as well as monocyte-enriched peripheral blood mononuclear cells (PBMC). Using a splice competent mini-gene reporter system transiently expressed in monocytic cells, it was determined that weakening of either five closely positioned ASF/SF2 ESE (bases 87-117) or a single conserved SRp55 ESE (base 39) results in severe skipping of exon 5. ASF/SF2 and SRp55 were found to physically associate with the identified ESE. CONCLUSIONS SR proteins ASF/SF2 and SRp55 appear to interact with the variable TF exon 5 through ESE at bases 39 and 87-117. Weakening of the above ESE modulates splicing of TF exon 5. This study is the first to identify and experimentally characterize cis-acting splicing elements involved in regulated biosynthesis of human TF.
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Affiliation(s)
- J G Tardos
- Division of Hematology and Medical Oncology, The Samuel Bronfman Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029-6754, USA
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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