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Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
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Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
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Azizullah, Noman M, Gao Y, Wang H, Xiong X, Wang J, Li D, Song F. The SUMOylation pathway regulates the pathogenicity of Fusarium oxysporum f. sp. niveum in watermelon through stabilizing the pH regulator FonPalC via SUMOylation. Microbiol Res 2024; 281:127632. [PMID: 38310728 DOI: 10.1016/j.micres.2024.127632] [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: 10/21/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
SUMOylation is a key post-translational modification, where small ubiquitin-related modifier (SUMO) proteins regulate crucial biological processes, including pathogenesis, in phytopathogenic fungi. Here, we investigated the function and mechanism of the SUMOylation pathway in the pathogenicity of Fusarium oxysporum f. sp. niveum (Fon), the fungal pathogen that causes watermelon Fusarium wilt. Disruption of key SUMOylation pathway genes, FonSMT3, FonAOS1, FonUBC9, and FonMMS21, significantly reduced pathogenicity, impaired penetration ability, and attenuated invasive growth capacity of Fon. Transcription and proteomic analyses identified a diverse set of SUMOylation-regulated differentially expressed genes and putative FonSMT3-targeted proteins, which are predicted to be involved in infection, DNA damage repair, programmed cell death, reproduction, growth, and development. Among 155 putative FonSMT3-targeted proteins, FonPalC, a Pal/Rim-pH signaling regulator, was confirmed to be SUMOylated. The FonPalC protein accumulation was significantly decreased in SUMOylation-deficient mutant ∆Fonsmt3. Deletion of FonPalC resulted in impaired mycelial growth, decreased pathogenicity, enhanced osmosensitivity, and increased intracellular vacuolation in Fon. Importantly, mutations in conserved SUMOylation sites of FonPalC failed to restore the defects in ∆Fonpalc mutant, indicating the critical function of the SUMOylation in FonPalC stability and Fon pathogenicity. Identifying key SUMOylation-regulated pathogenicity-related proteins provides novel insights into the molecular mechanisms underlying Fon pathogenesis regulated by SUMOylation.
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Affiliation(s)
- Azizullah
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Muhammad Noman
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yizhou Gao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Xiong
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiajing Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dayong Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fengming Song
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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3
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Matkovic R, Morel M, Lanciano S, Larrous P, Martin B, Bejjani F, Vauthier V, Hansen MMK, Emiliani S, Cristofari G, Gallois-Montbrun S, Margottin-Goguet F. TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV. Nat Commun 2022; 13:66. [PMID: 35013187 PMCID: PMC8748822 DOI: 10.1038/s41467-021-27650-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
The Human Silencing Hub (HUSH) complex constituted of TASOR, MPP8 and Periphilin recruits the histone methyl-transferase SETDB1 to spread H3K9me3 repressive marks across genes and transgenes in an integration site-dependent manner. The deposition of these repressive marks leads to heterochromatin formation and inhibits gene expression, but the underlying mechanism is not fully understood. Here, we show that TASOR silencing or HIV-2 Vpx expression, which induces TASOR degradation, increases the accumulation of transcripts derived from the HIV-1 LTR promoter at a post-transcriptional level. Furthermore, using a yeast 2-hybrid screen, we identify new TASOR partners involved in RNA metabolism including the RNA deadenylase CCR4-NOT complex scaffold CNOT1. TASOR and CNOT1 synergistically repress HIV expression from its LTR. Similar to the RNA-induced transcriptional silencing complex found in fission yeast, we show that TASOR interacts with the RNA exosome and RNA Polymerase II, predominantly under its elongating state. Finally, we show that TASOR facilitates the association of RNA degradation proteins with RNA polymerase II and is detected at transcriptional centers. Altogether, we propose that HUSH operates at the transcriptional and post-transcriptional levels to repress HIV proviral expression.
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Affiliation(s)
- Roy Matkovic
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France.
| | - Marina Morel
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | | | - Pauline Larrous
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Benjamin Martin
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Fabienne Bejjani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Virginie Vauthier
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525 AM, Nijmegen, The Netherlands
| | - Stéphane Emiliani
- Université de Paris, Institut Cochin, INSERM, CNRS, 75014, Paris, France
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Vélez N, Monteoliva L, Sánchez-Quitian ZA, Amador-García A, García-Rodas R, Ceballos-Garzón A, Gil C, Escandón P, Zaragoza Ó, Parra-Giraldo CM. The Combination of Iron and Copper Increases Pathogenicity and Induces Proteins Related to the Main Virulence Factors in Clinical Isolates of Cryptococcus neoformans var. grubii. J Fungi (Basel) 2022; 8:jof8010057. [PMID: 35049997 PMCID: PMC8778102 DOI: 10.3390/jof8010057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/31/2021] [Indexed: 01/09/2023] Open
Abstract
In fungi, metals are associated with the expression of virulence factors. However, it is unclear whether the uptake of metals affects their pathogenicity. This study aimed to evaluate the effect of iron/copper in modulating pathogenicity and proteomic response in two clinical isolates of C. neoformans with high and low pathogenicity. Methods: In both isolates, the effect of 50 µM iron and 500 µM copper on pathogenicity, capsule induction, and melanin production was evaluated. We then performed a quantitative proteomic analysis of cytoplasmic extracts exposed to that combination. Finally, the effect on pathogenicity by iron and copper was evaluated in eight additional isolates. Results: In both isolates, the combination of iron and copper increased pathogenicity, capsule size, and melanin production. Regarding proteomic data, proteins with increased levels after iron and copper exposure were related to biological processes such as cell stress, vesicular traffic (Ap1, Vps35), cell wall structure (Och1, Ccr4, Gsk3), melanin biosynthesis (Hem15, Mln2), DNA repair (Chk1), protein transport (Mms2), SUMOylation (Uba2), and mitochondrial transport (Atm1). Increased pathogenicity by exposure to metal combination was also confirmed in 90% of the eight isolates. Conclusions: The combination of these metals enhances pathogenicity and increases the abundance of proteins related to the main virulence factors.
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Affiliation(s)
- Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Zilpa-Adriana Sánchez-Quitian
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
| | - Ahinara Amador-García
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Rocío García-Rodas
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, 28013 Madrid, Spain; (R.G.-R.); (Ó.Z.)
| | - Andrés Ceballos-Garzón
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
- Department of Parasitology and Medical Mycology, Faculty of Pharmacy, University of Nantes, 44200 Nantes, France
| | - Concha Gil
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia;
| | - Óscar Zaragoza
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, 28013 Madrid, Spain; (R.G.-R.); (Ó.Z.)
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
- Correspondence:
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5
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Rana A, Gupta N, Thakur A. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens. Mol Aspects Med 2021; 81:101017. [PMID: 34497025 DOI: 10.1016/j.mam.2021.101017] [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: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Host-pathogen interactions at the molecular level are the key to fungal pathogenesis. Fungal pathogens utilize several mechanisms such as adhesion, invasion, phenotype switching and metabolic adaptations, to survive in the host environment and respond. Post-transcriptional and translational regulations have emerged as key regulatory mechanisms ensuring the virulence and survival of fungal pathogens. Through these regulations, fungal pathogens effectively alter their protein pool, respond to various stress, and undergo morphogenesis, leading to efficient and comprehensive changes in fungal physiology. The regulation of virulence through post-transcriptional and translational regulatory mechanisms is mediated through mRNA elements (cis factors) or effector molecules (trans factors). The untranslated regions upstream and downstream of the mRNA, as well as various RNA-binding proteins involved in translation initiation or circularization of the mRNA, play pivotal roles in the regulation of morphology and virulence by influencing protein synthesis, protein isoforms, and mRNA stability. Therefore, post-transcriptional and translational mechanisms regulating the morphology, virulence and drug-resistance processes in fungal pathogens can be the target for new therapeutics. With improved "omics" technologies, these regulatory mechanisms are increasingly coming to the forefront of basic biology and drug discovery. This review aims to discuss various modes of post-transcriptional and translation regulations, and how these mechanisms exert influence in the virulence and morphogenesis of fungal pathogens.
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Affiliation(s)
- Aishwarya Rana
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Nidhi Gupta
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Anil Thakur
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India.
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Escobar-Niño A, Morano Bermejo IM, Carrasco Reinado R, Fernandez-Acero FJ. Deciphering the Dynamics of Signaling Cascades and Virulence Factors of B. cinerea during Tomato Cell Wall Degradation. Microorganisms 2021; 9:microorganisms9091837. [PMID: 34576732 PMCID: PMC8466851 DOI: 10.3390/microorganisms9091837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/24/2021] [Indexed: 11/30/2022] Open
Abstract
The ascomycete Botrytis cinerea is one of the most relevant plant pathogenic fungi, affecting fruits, flowers, and greenhouse-grown crops. The infection strategy used by the fungus comprises a magnificent set of tools to penetrate and overcome plant defenses. In this context, the plant-pathogen communication through membrane receptors and signal transduction cascades is essential to trigger specific routes and the final success of the infection. In previous reports, proteomics approaches to B. cinerea signal transduction cascades changes in response to different carbon source and plant-based elicitors have been performed. Analyzing the secretome, membranome, phosphoproteome, and the phosphomembranome. Moreover, phenotypic changes in fungal biology was analyzed, specifically toxin production. To obtain the whole picture of the process and reveal the network from a system biology approach, this proteomic information has been merged with the phenotypic characterization, to be analyzed using several bioinformatics algorithms (GO, STRING, MCODE) in order to unravel key points in the signal transduction regulation crucial to overcome plant defenses, as well as new virulence/pathogenicity factors that could be used as therapeutic targets in the control of the gray mold rot disease. A total of 1721 and 663 exclusive or overexpressed proteins were identified under glucose (GLU) and deproteinized tomato cell walls (TCW), summarizing all of the protein identifications under phenotypic characterized stages. Under GO analysis, there are more biological process and molecular functions described in GLU, highlighting the increase in signaling related categories. These results agree with the high number of total identified proteins in GLU, probably indicating a more varied and active metabolism of the fungus. When analyzing only GO annotations related with signal transduction, it was revealed that there were proteins related to TOR signaling, the phosphorelay signal transduction system, and inositol lipid-mediated signaling, only under GLU conditions. On the contrary, calcium-mediated signaling GO annotation is only present between the proteins identified under TCW conditions. To establish a potential relationship between expressed proteins, cluster analyses showed 41 and 14 clusters under GLU and TCW conditions, confirming an increase in biological activity in GLU, where we identified a larger number of clusters related to transcription, translation, and cell division, between others. From these analyses, clusters related to signal transduction and clusters related to mycotoxin production were found, which correlated with the phenotypic characterization. The identification of the proteins encompassed in each condition and signal transduction cascade would provide the research community with new information about the B. cinerea infection process and potential candidates of pathogenicity/virulence factors, overcoming plant defenses, and new therapeutic targets.
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The Protein Kinase A-Dependent Phosphoproteome of the Human Pathogen Aspergillus fumigatus Reveals Diverse Virulence-Associated Kinase Targets. mBio 2020; 11:mBio.02880-20. [PMID: 33323509 PMCID: PMC7773993 DOI: 10.1128/mbio.02880-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PKA is essential for the virulence of eukaryotic human pathogens. Understanding PKA signaling mechanisms is therefore fundamental to deciphering pathogenesis and developing novel therapies. Protein kinase A (PKA) signaling plays a critical role in the growth and development of all eukaryotic microbes. However, few direct targets have been characterized in any organism. The fungus Aspergillus fumigatus is a leading infectious cause of death in immunocompromised patients, but the specific molecular mechanisms responsible for its pathogenesis are poorly understood. We used this important pathogen as a platform for a comprehensive and multifaceted interrogation of both the PKA-dependent whole proteome and phosphoproteome in order to elucidate the mechanisms through which PKA signaling regulates invasive microbial disease. Employing advanced quantitative whole-proteomic and phosphoproteomic approaches with two complementary phosphopeptide enrichment strategies, coupled to an independent PKA interactome analysis, we defined distinct PKA-regulated pathways and identified novel direct PKA targets contributing to pathogenesis. We discovered three previously uncharacterized virulence-associated PKA effectors, including an autophagy-related protein, Atg24; a CCAAT-binding transcriptional regulator, HapB; and a CCR4-NOT complex-associated ubiquitin ligase, Not4. Targeted mutagenesis, combined with in vitro kinase assays, multiple murine infection models, structural modeling, and molecular dynamics simulations, was employed to characterize the roles of these new PKA targets in growth, environmental and antimicrobial stress responses, and pathogenesis in a mammalian system. We also elucidated the molecular mechanisms of PKA regulation for these effectors by defining the functionality of phosphorylation at specific PKA target sites. We have comprehensively characterized the PKA-dependent phosphoproteome and validated PKA targets as direct regulators of infectious disease for the first time in any pathogen, providing new insights into PKA signaling and control over microbial pathogenesis.
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Abstract
The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland.
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland
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9
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Collart MA, Kassem S, Villanyi Z. Mutations in the NOT Genes or in the Translation Machinery Similarly Display Increased Resistance to Histidine Starvation. Front Genet 2017; 8:61. [PMID: 28588606 PMCID: PMC5439007 DOI: 10.3389/fgene.2017.00061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/04/2017] [Indexed: 11/18/2022] Open
Abstract
The NOT genes encode subunits of the conserved Ccr4-Not complex, a global regulator of gene expression, and in particular of mRNA metabolism. They were originally identified in a selection for increased resistance to histidine starvation in the yeast S. cerevisiae. Recent work indicated that the Not5 subunit, ortholog of mammalian CNOT3, determines global translation levels by defining binding of the Ccr4-Not scaffold protein Not1 to ribosomal mRNAs during transcription. This is needed for optimal translation of ribosomal proteins. In this work we searched for mutations in budding yeast that were resistant to histidine starvation using the same selection that originally led to the isolation of the NOT genes. We thereby isolated mutations in ribosome-related genes. This common phenotype of ribosome mutants and not mutants is in good agreement with the positive role of the Not proteins for translation. In this regard, it is interesting that frequent mutations in RPL5 and RPL10 or in CNOT3 have been observed to accumulate in adult T-cell acute lymphoblastic leukemia (T-ALL). This suggests that in metazoans a common function implicating ribosome subunits and CNOT3 plays a role in the development of cancer. In this perspective we suggest that the Ccr4-Not complex, according to translation levels and fidelity, could itself be involved in the regulation of amino acid biosynthesis levels. We discuss how this could explain why mutations have been identified in many cancers.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire (CMU), Faculty of Medicine, University of GenevaGeneva, Switzerland
| | - Sari Kassem
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire (CMU), Faculty of Medicine, University of GenevaGeneva, Switzerland
| | - Zoltan Villanyi
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire (CMU), Faculty of Medicine, University of GenevaGeneva, Switzerland
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10
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Dai Y, Cao Z, Huang L, Liu S, Shen Z, Wang Y, Wang H, Zhang H, Li D, Song F. CCR4-Not Complex Subunit Not2 Plays Critical Roles in Vegetative Growth, Conidiation and Virulence in Watermelon Fusarium Wilt Pathogen Fusarium oxysporum f. sp. niveum. Front Microbiol 2016; 7:1449. [PMID: 27695445 PMCID: PMC5025516 DOI: 10.3389/fmicb.2016.01449] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 11/24/2022] Open
Abstract
CCR4-Not complex is a multifunctional regulator that plays important roles in multiple cellular processes in eukaryotes. In the present study, the biological function of FonNot2, a core subunit of the CCR4-Not complex, was explored in Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon wilt disease. FonNot2 was expressed at higher levels in conidia and germinating conidia and during infection in Fon-inoculated watermelon roots than in mycelia. Targeted disruption of FonNot2 resulted in retarded vegetative growth, reduced conidia production, abnormal conidial morphology, and reduced virulence on watermelon. Scanning electron microscopy observation of infection behaviors and qRT-PCR analysis of in planta fungal growth revealed that the ΔFonNot2 mutant was defective in the ability to penetrate watermelon roots and showed reduced fungal biomass in root and stem of the inoculated plants. Phenotypic and biochemical analyses indicated that the ΔFonNot2 mutant displayed hypersensitivity to cell wall perturbing agents (e.g., Congo Red and Calcofluor White) and oxidative stress (e.g., H2O2 and paraquat), decreased fusaric acid content, and reduced reactive oxygen species (ROS) production during spore germination. Our data demonstrate that FonNot2 plays critical roles in regulating vegetable growth, conidiogenesis and conidia morphology, and virulence on watermelon via modulating cell wall integrity, oxidative stress response, ROS production and FA biosynthesis through the regulation of transcription of genes involved in multiple pathways.
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Affiliation(s)
- Yi Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Zhongye Cao
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Lihong Huang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Shixia Liu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Zhihui Shen
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Yuyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Hui Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Huijuan Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Dayong Li
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Fengming Song
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
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Abstract
In a recent issue of Nature Communications Ukleja and co‐workers reported a cryo‐EM 3D reconstruction of the Ccr4‐Not complex from Schizosaccharomyces pombe with an immunolocalization of the different subunits. The newly gained architectural knowledge provides cues to apprehend the functional diversity of this major eukaryotic regulator. Indeed, in the cytoplasm alone, Ccr4‐Not regulates translational repression, decapping and deadenylation, and the Not module additionally plays a positive role in translation. The spatial distribution of the subunits within the structure is compatible with a model proposing that the Ccr4‐Not complex interacts with the 5′ and 3′ ends of target mRNAs, allowing different functional modules of the complex to act at different stages of the translation process, possibly within a circular constellation of the mRNA. This work opens new avenues, and reveals important gaps in our understanding regarding structure and mode of function of the Ccr4‐Not complex that need to be addressed in the future.
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Affiliation(s)
- Zoltan Villanyi
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics Geneva, Geneva, Switzerland
| | - Martine A Collart
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics Geneva, Geneva, Switzerland.
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Verma-Gaur J, Traven A. Post-transcriptional gene regulation in the biology and virulence of Candida albicans. Cell Microbiol 2016; 18:800-6. [PMID: 26999710 PMCID: PMC5074327 DOI: 10.1111/cmi.12593] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/28/2016] [Accepted: 03/16/2016] [Indexed: 11/27/2022]
Abstract
In the human fungal pathogen Candida albicans, remodelling of gene expression drives host adaptation and virulence. Recent studies revealed that in addition to transcription, post‐transcriptional mRNA control plays important roles in virulence‐related pathways. Hyphal morphogenesis, biofilm formation, stress responses, antifungal drug susceptibility and virulence in animal models require post‐transcriptional regulators. This includes RNA binding proteins that control mRNA localization, decay and translation, as well as the cytoplasmic mRNA decay pathway. Comprehensive understanding of how modulation of gene expression networks drives C. albicans virulence will necessitate integration of our knowledge on transcriptional and post‐transcriptional mRNA control.
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Affiliation(s)
- Jiyoti Verma-Gaur
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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13
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Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:438-54. [PMID: 26821858 PMCID: PMC5066686 DOI: 10.1002/wrna.1332] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 12/22/2022]
Abstract
The Ccr4‐Not complex is a multisubunit complex present in all eukaryotes that contributes to regulate gene expression at all steps, from production of messenger RNAs (mRNAs) in the nucleus to their degradation in the cytoplasm. In the nucleus it influences the post‐translational modifications of the chromatin template that has to be remodeled for transcription, it is present at sites of transcription and associates with transcription factors as well as with the elongating polymerase, it interacts with the factors that prepare the new transcript for export to the cytoplasm and finally is important for nuclear quality control and influences mRNA export. In the cytoplasm it is present in polysomes where mRNAs are translated and in RNA granules where mRNAs will be redirected upon inhibition of translation. It influences mRNA translatability, and is needed during translation, on one hand for co‐translational protein interactions and on the other hand to preserve translation that stalls. It is one of the relevant players during co‐translational quality control. It also interacts with factors that will repress translation or induce mRNA decapping when recruited to the translating template. Finally, Ccr4‐Not carries deadenylating enzymes and is a key player in mRNA decay, generic mRNA decay that follows normal translation termination, co‐translational mRNA decay of transcripts on which the ribosomes stall durably or which carry a non‐sense mutation and finally mRNA decay that is induced by external signaling for a change in genetic programming. Ccr4‐Not is a master regulator of eukaryotic gene expression. WIREs RNA 2016, 7:438–454. doi: 10.1002/wrna.1332 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Martine A Collart
- Department Microbiology and Molecular Medicine, CMU, Geneva, Switzerland.,Institute of Genetics and Genomics, Geneva, Switzerland
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14
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Bui DC, Son H, Shin JY, Kim JC, Kim H, Choi GJ, Lee YW. The FgNot3 Subunit of the Ccr4-Not Complex Regulates Vegetative Growth, Sporulation, and Virulence in Fusarium graminearum. PLoS One 2016; 11:e0147481. [PMID: 26799401 PMCID: PMC4723064 DOI: 10.1371/journal.pone.0147481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/05/2016] [Indexed: 01/23/2023] Open
Abstract
The Ccr4-Not complex is evolutionarily conserved and important for multiple cellular functions in eukaryotic cells. In this study, the biological roles of the FgNot3 subunit of this complex were investigated in the plant pathogenic fungus Fusarium graminearum. Deletion of FgNOT3 resulted in retarded vegetative growth, retarded spore germination, swollen hyphae, and hyper-branching. The ΔFgnot3 mutants also showed impaired sexual and asexual sporulation, decreased virulence, and reduced expression of genes related to conidiogenesis. Fgnot3 deletion mutants were sensitive to thermal stress, whereas NOT3 orthologs in other model eukaryotes are known to be required for cell wall integrity. We found that FgNot3 functions as a negative regulator of the production of secondary metabolites, including trichothecenes and zearalenone. Further functional characterization of other components of the Not module of the Ccr4-Not complex demonstrated that the module is conserved. Each subunit primarily functions within the context of a complex and might have distinct roles outside of the complex in F. graminearum. This is the first study to functionally characterize the Not module in filamentous fungi and provides novel insights into signal transduction pathways in fungal development.
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Affiliation(s)
- Duc-Cuong Bui
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Ji Young Shin
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hun Kim
- Eco-friendly New Materials Research Group, Research Center for Biobased Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Eco-friendly New Materials Research Group, Research Center for Biobased Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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15
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Hubstenberger A, Cameron C, Noble SL, Keenan S, Evans TC. Modifiers of solid RNP granules control normal RNP dynamics and mRNA activity in early development. J Cell Biol 2015; 211:703-16. [PMID: 26527741 PMCID: PMC4639854 DOI: 10.1083/jcb.201504044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/25/2015] [Indexed: 12/13/2022] Open
Abstract
Modifiers of aberrant solid RNP granules suggest new insights into pathways that control dynamics of large-scale RNP bodies and mRNAs during C. elegans oogenesis. Ribonucleoproteins (RNPs) often coassemble into supramolecular bodies with regulated dynamics. The factors controlling RNP bodies and connections to RNA regulation are unclear. During Caenorhabditis elegans oogenesis, cytoplasmic RNPs can transition among diffuse, liquid, and solid states linked to mRNA regulation. Loss of CGH-1/Ddx6 RNA helicase generates solid granules that are sensitive to mRNA regulators. Here, we identified 66 modifiers of RNP solids induced by cgh-1 mutation. A majority of genes promote or suppress normal RNP body assembly, dynamics, or metabolism. Surprisingly, polyadenylation factors promote RNP coassembly in vivo, suggesting new functions of poly(A) tail regulation in RNP dynamics. Many genes carry polyglutatmine (polyQ) motifs or modulate polyQ aggregation, indicating possible connections with neurodegenerative disorders induced by CAG/polyQ expansion. Several RNP body regulators repress translation of mRNA subsets, suggesting that mRNAs are repressed by multiple mechanisms. Collectively, these findings suggest new pathways of RNP modification that control large-scale coassembly and mRNA activity during development.
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Affiliation(s)
- Arnaud Hubstenberger
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 Pierre-and-Marie-Curie University, University Paris 06, 75005 Paris, France
| | - Cristiana Cameron
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Scott L Noble
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 Graduate Program in Molecular Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Sean Keenan
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Thomas C Evans
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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Harrison PF, Powell DR, Clancy JL, Preiss T, Boag PR, Traven A, Seemann T, Beilharz TH. PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA (NEW YORK, N.Y.) 2015; 21:1502-10. [PMID: 26092945 PMCID: PMC4509939 DOI: 10.1261/rna.048355.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/20/2015] [Indexed: 05/21/2023]
Abstract
A major objective of systems biology is to quantitatively integrate multiple parameters from genome-wide measurements. To integrate gene expression with dynamics in poly(A) tail length and adenylation site, we developed a targeted next-generation sequencing approach, Poly(A)-Test RNA-sequencing. PAT-seq returns (i) digital gene expression, (ii) polyadenylation site/s, and (iii) the polyadenylation-state within and between eukaryotic transcriptomes. PAT-seq differs from previous 3' focused RNA-seq methods in that it depends strictly on 3' adenylation within total RNA samples and that the full-native poly(A) tail is included in the sequencing libraries. Here, total RNA samples from budding yeast cells were analyzed to identify the intersect between adenylation state and gene expression in response to loss of the major cytoplasmic deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in the classic Crabtree-Warburg metabolic shift. Because all polyadenylated RNA is interrogated by the approach, alternative adenylation sites, noncoding RNA and RNA-decay intermediates were also identified. Most important, the PAT-seq approach uses standard sequencing procedures, supports significant multiplexing, and thus replication and rigorous statistical analyses can for the first time be brought to the measure of 3'-UTR dynamics genome wide.
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Affiliation(s)
- Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - Jennifer L Clancy
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
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17
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Valenzuela-Miranda D, Nuñez-Acuña G, Valenzuela-Muñoz V, Asgari S, Gallardo-Escárate C. MicroRNA biogenesis pathway from the salmon louse (Caligus rogercresseyi): Emerging role in delousing drug response. Gene 2015; 555:231-41. [DOI: 10.1016/j.gene.2014.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/06/2014] [Indexed: 12/20/2022]
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18
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Shirai YT, Suzuki T, Morita M, Takahashi A, Yamamoto T. Multifunctional roles of the mammalian CCR4-NOT complex in physiological phenomena. Front Genet 2014; 5:286. [PMID: 25191340 PMCID: PMC4139912 DOI: 10.3389/fgene.2014.00286] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/04/2014] [Indexed: 01/12/2023] Open
Abstract
The carbon catabolite repression 4 (CCR4)–negative on TATA-less (NOT) complex serves as one of the major deadenylases of eukaryotes. Although it was originally identified and characterized in yeast, recent studies have revealed that the CCR4–NOT complex also exerts important functions in mammals, -including humans. However, there are some differences in the composition and functions of the CCR4–NOT complex between mammals and yeast. It is noteworthy that each subunit of the CCR4–NOT complex has unique, multifunctional roles and is responsible for various physiological phenomena. This heterogeneity and versatility of the CCR4–NOT complex makes an overall understanding of this complex difficult. Here, we describe the functions of each subunit of the mammalian CCR4–NOT complex and discuss the molecular mechanisms by which it regulates homeostasis in mammals. Furthermore, a possible link between the disruption of the CCR4–NOT complex and various diseases will be discussed. Finally, we propose that the analysis of mice with each CCR4–NOT subunit knocked out is an effective strategy for clarifying its complicated functions and networks in mammals.
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Affiliation(s)
- Yo-Taro Shirai
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Toru Suzuki
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Masahiro Morita
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Goodman Cancer Research Centre, McGill University Montreal, QC, Canada
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
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