1
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Huang Y, Chen J, Xia H, Gao Z, Gu Q, Liu W, Tang G. FvMbp1-Swi6 complex regulates vegetative growth, stress tolerance, and virulence in Fusarium verticillioides. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134576. [PMID: 38759405 DOI: 10.1016/j.jhazmat.2024.134576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
The mycotoxigenic fungus Fusarium verticillioides is a common pathogen of grain and medicine that contaminates the host with fumonisin B1 (FB1) mycotoxin, poses serious threats to human and animal health. Therefore, it is crucial to unravel the regulatory mechanisms of growth, and pathogenicity of F. verticillioides. Mbp1 is a component of the MluI cell cycle box binding factor complex and acts as an APSES-type transcription factor that regulates cell cycle progression. However, no information is available regarding its role in F. verticillioides. In this study, we demonstrate that FvMbp1 interacts with FvSwi6 that acts as the cell cycle transcription factor, to form the heteromeric transcription factor complexes in F. verticillioides. Our results show that ΔFvMbp1 and ΔFvSwi6 both cause a severe reduction of vegetative growth, conidiation, and increase tolerance to diverse environmental stresses. Moreover, ΔFvMbp1 and ΔFvSwi6 dramatically decrease the virulence of the pathogen on the stalk and ear of maize. Transcriptome profiling show that FvMbp1-Swi6 complex co-regulates the expression of genes associated with multiple stress responses. These results indicate the functional importance of the FvMbp1-Swi6 complex in the filamentous fungi F. verticillioides and reveal a potential target for the effective prevention and control of Fusarium diseases.
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Affiliation(s)
- Yufei Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jinfeng Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zenggui Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing 210095, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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2
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Louw NL, Wolfe BE, Uricchio LH. A phylogenomic perspective on interspecific competition. Ecol Lett 2024; 27:e14359. [PMID: 38332550 DOI: 10.1111/ele.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 02/10/2024]
Abstract
Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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3
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Lu K, Chen R, Yang Y, Xu H, Jiang J, Li L. Involvement of the Cell Wall-Integrity Pathway in Signal Recognition, Cell-Wall Biosynthesis, and Virulence in Magnaporthe oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:608-622. [PMID: 37140471 DOI: 10.1094/mpmi-11-22-0231-cr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The fungal cell wall is the first layer exposed to the external environment. The cell wall has key roles in regulating cell functions, such as cellular stability, permeability, and protection against stress. Understanding the structure of the cell wall and the mechanism of its biogenesis is important for the study of fungi. Highly conserved in fungi, including Magnaporthe oryzae, the cell wall-integrity (CWI) pathway is the primary signaling cascade regulating cell-wall structure and function. The CWI pathway has been demonstrated to correlate with pathogenicity in many phytopathogenic fungi. In the synthesis of the cell wall, the CWI pathway cooperates with multiple signaling pathways to regulate cell morphogenesis and secondary metabolism. Many questions have arisen regarding the cooperation of different signaling pathways with the CWI pathway in regulating cell-wall synthesis and pathogenicity. In this review, we summarized the latest advances in the M. oryzae CWI pathway and cell-wall structure. We discussed the CWI pathway components and their involvement in different aspects, such as virulence factors, the possibility of the pathway as a target for antifungal therapies, and crosstalk with other signaling pathways. This information will aid in better understanding the universal functions of the CWI pathway in regulating cell-wall synthesis and pathogenicity in M. oryzae. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Kailun Lu
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Rangrang Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Yi Yang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Hui Xu
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Jihong Jiang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Lianwei Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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4
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Carreras-Villaseñor N, Martínez-Rodríguez LA, Ibarra-Laclette E, Monribot-Villanueva JL, Rodríguez-Haas B, Guerrero-Analco JA, Sánchez-Rangel D. The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus. Front Microbiol 2023; 14:1224096. [PMID: 37520351 PMCID: PMC10375492 DOI: 10.3389/fmicb.2023.1224096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Luis A. Martínez-Rodríguez
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Enrique Ibarra-Laclette
- Laboratorio de Genómica y Transcriptómica, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Juan L. Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - José A. Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Diana Sánchez-Rangel
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigadora Por Mexico-CONAHCyT, Xalapa, Mexico
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5
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Afonin DA, Geras’kina OV, Loseva TV, Kirpichnikov MP, Studitsky VM, Feofanov AV. Structure and Affinity of Complexes between the DNA-Binding Domain of Swi4 and DNA. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922050037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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6
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Argüello-Miranda O, Marchand AJ, Kennedy T, Russo MAX, Noh J. Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry. J Cell Biol 2022; 221:212720. [PMID: 34694336 PMCID: PMC8548912 DOI: 10.1083/jcb.202103171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0.
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Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ashley J Marchand
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Taylor Kennedy
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX
| | - Marielle A X Russo
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
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7
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Medina EM, Walsh E, Buchler NE. Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain. Curr Opin Genet Dev 2019; 58-59:103-110. [PMID: 31600629 DOI: 10.1016/j.gde.2019.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 10/25/2022]
Abstract
Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.
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Affiliation(s)
- Edgar M Medina
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Evan Walsh
- Bioinformatics Program, North Carolina State University, Raleigh, NC 27607, USA
| | - Nicolas E Buchler
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27606, USA.
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8
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Kohler V, Goessweiner-Mohr N, Aufschnaiter A, Fercher C, Probst I, Pavkov-Keller T, Hunger K, Wolinski H, Büttner S, Grohmann E, Keller W. TraN: A novel repressor of an Enterococcus conjugative type IV secretion system. Nucleic Acids Res 2019; 46:9201-9219. [PMID: 30060171 PMCID: PMC6158623 DOI: 10.1093/nar/gky671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/18/2018] [Indexed: 11/19/2022] Open
Abstract
The dissemination of multi-resistant bacteria represents an enormous burden on modern healthcare. Plasmid-borne conjugative transfer is the most prevalent mechanism, requiring a type IV secretion system that enables bacteria to spread beneficial traits, such as resistance to last-line antibiotics, among different genera. Inc18 plasmids, like the Gram-positive broad host-range plasmid pIP501, are substantially involved in propagation of vancomycin resistance from Enterococci to methicillin-resistant strains of Staphylococcus aureus. Here, we identified the small cytosolic protein TraN as a repressor of the pIP501-encoded conjugative transfer system, since deletion of traN resulted in upregulation of transfer factors, leading to highly enhanced conjugative transfer. Furthermore, we report the complex structure of TraN with DNA and define the exact sequence of its binding motif. Targeting this protein–DNA interaction might represent a novel therapeutic approach against the spreading of antibiotic resistances.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Nikolaus Goessweiner-Mohr
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria
| | | | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Ines Probst
- Division of Infectious Diseases, University Medical Center Freiburg, Freiburg 79106, Germany
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Kristin Hunger
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 10691, Sweden
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Freiburg 79106, Germany.,Life Sciences and Technology, Beuth University of Applied Sciences, Berlin 13353, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Austria
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9
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Hu C, Inoue H, Sun W, Takeshita Y, Huang Y, Xu Y, Kanoh J, Chen Y. The Inner Nuclear Membrane Protein Bqt4 in Fission Yeast Contains a DNA-Binding Domain Essential for Telomere Association with the Nuclear Envelope. Structure 2018; 27:335-343.e3. [PMID: 30503780 DOI: 10.1016/j.str.2018.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/30/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
Abstract
Telomeres, the protective caps at the end of the chromosomes, are often associated with the nuclear envelope (NE). Telomere positioning to the NE is dynamically regulated during mitosis and meiosis. One inner nuclear membrane protein, Bqt4, in Schizosaccharomyces pombe plays essential roles in connecting telomeres to the NE. However, the structural basis of Bqt4 in mediating telomere-NE association is not clear. Here, we report the crystal structure of the N-terminal domain of Bqt4. The N-terminal domain of Bqt4 structurally resembles the APSES-family DNA-binding domain and has a moderate double-stranded DNA-binding activity. Disruption of Bqt4-DNA interaction results in telomere detachment from the NE. These data suggest that the DNA-binding activity of Bqt4 may function to prime the chromosome onto the NE and promote telomere-NE association.
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Affiliation(s)
- Chunyi Hu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Haruna Inoue
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wenqi Sun
- School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China
| | - Yumiko Takeshita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yaoguang Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Ying Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Junko Kanoh
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China.
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10
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Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B. How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome. Nucleic Acids Res 2018; 46:10514-10529. [PMID: 30252102 PMCID: PMC6212790 DOI: 10.1093/nar/gky836] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/28/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022] Open
Abstract
Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Timothy R Hughes
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - William Wiley Navarre
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jun Liu
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
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11
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Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC. Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3. Nat Commun 2018; 9:3732. [PMID: 30213934 PMCID: PMC6137059 DOI: 10.1038/s41467-018-06096-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/15/2018] [Indexed: 11/18/2022] Open
Abstract
Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK–TcpK box complex reveals a binding mode centered on and around the β-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. Additional studies highlight that the TcpK dimer is important for specific DNA binding. Conjugative transfer of antibiotic resistance plasmid pCW3 in Clostridium perfringens is mediated by the tcp locus. Here, the authors identify a wHTH-type protein, TcpK, that is essential for efficient plasmid transfer and interacts with the plasmid oriT region in a unique manner.
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Affiliation(s)
- Daouda A K Traore
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.,Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako (USTTB), BP E3206, Bamako, Mali
| | - Jessica A Wisniewski
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Paul J Conroy
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.,Australian Synchrotron, Clayton, 3168, VIC, Australia
| | - Yee-Foong Mok
- Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia
| | - Carmen Lao
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Michael D W Griffin
- Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia
| | - Vicki Adams
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.
| | - Julian I Rood
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia. .,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, 3800, VIC, Australia. .,EMBL Australia, Monash University, Clayton, 3800, VIC, Australia.
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12
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Hendler A, Medina EM, Buchler NE, de Bruin RAM, Aharoni A. The evolution of a G1/S transcriptional network in yeasts. Curr Genet 2018; 64:81-86. [PMID: 28744706 DOI: 10.1007/s00294-017-0726-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Abstract
The G1-to-S cell cycle transition is promoted by the periodic expression of a large set of genes. In Saccharomyces cerevisiae G1/S gene expression is regulated by two transcription factor (TF) complexes, the MBF and SBF, which bind to specific DNA sequences, the MCB and SCB, respectively. Despite extensive research little is known regarding the evolution of the G1/S transcription regulation including the co-evolution of the DNA binding domains with their respective DNA binding sequences. We have recently examined the co-evolution of the G1/S TF specificity through the systematic generation and examination of chimeric Mbp1/Swi4 TFs containing different orthologue DNA binding domains in S. cerevisiae (Hendler et al. in PLoS Genet 13:e1006778. doi: 10.1371/journal.pgen.1006778 , 2017). Here, we review the co-evolution of G1/S transcriptional network and discuss the evolutionary dynamics and specificity of the MBF-MCB and SBF-SCB interactions in different fungal species.
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Affiliation(s)
- Adi Hendler
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105, Beersheba, Israel
| | - Edgar M Medina
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Nicolas E Buchler
- Department of Biology, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105, Beersheba, Israel.
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Hendler A, Medina EM, Kishkevich A, Abu-Qarn M, Klier S, Buchler NE, de Bruin RAM, Aharoni A. Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness. PLoS Genet 2017; 13:e1006778. [PMID: 28505153 PMCID: PMC5448814 DOI: 10.1371/journal.pgen.1006778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/30/2017] [Accepted: 04/24/2017] [Indexed: 01/21/2023] Open
Abstract
Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 200 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. The difference in size and complexity of the G1/S transcriptional network across yeast species makes it well suited to investigate how TF paralogs (SBF and MBF) and DNA binding sequences (SCB and MCB) co-evolved after gene duplication to rewire and expand the network of G1/S target genes. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the SBF-regulated G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation.
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Affiliation(s)
- Adi Hendler
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Edgar M. Medina
- Department of Biology, Duke University, Durham, United States
- Center for Genomic and Computational Biology, Duke University, Durham, United States
| | - Anastasiya Kishkevich
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Mehtap Abu-Qarn
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Steffi Klier
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Nicolas E. Buchler
- Department of Biology, Duke University, Durham, United States
- Center for Genomic and Computational Biology, Duke University, Durham, United States
| | - Robertus A. M. de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
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14
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Medina EM, Turner JJ, Gordân R, Skotheim JM, Buchler NE. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. eLife 2016; 5. [PMID: 27162172 PMCID: PMC4862756 DOI: 10.7554/elife.09492] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast. DOI:http://dx.doi.org/10.7554/eLife.09492.001 Living cells grow and divide with remarkable precision to ensure that their genetic material is faithfully duplicated and distributed equally to the newly formed daughter cells. This precision is achieved through a series of steps known as the cell cycle. The cell cycle is ancient and conserved across all Eukaryotes, including plants, animals and fungi. However, some of the core proteins present in animals and fungi are unrelated. This raises the question as to how a drastic change could have occurred and been tolerated over evolution. In animals and plants, a protein called E2F controls the expression of genes that are needed to begin the cell cycle. In most fungi, an equivalent protein called SBF performs the same role as E2F, but the two proteins are very different and do not appear to share a common ancestor. This is unexpected given that fungi and animals are more closely related to one another than either is to plants. Medina et al. searched the genomes of many animals, fungi, plants, algae, and their closest relatives for genes that encoded proteins like E2F and SBF. SBF-like proteins were only found in fungi, yet some fungal groups had cell cycle regulators like those found in animals. Zoosporic fungi, which diverged early from the fungal ancestor, had both SBF- and E2F-like proteins, while many fungi later lost E2F during evolution. So how did fungi acquire SBF? Medina et al. observed that part of the SBF protein is similar to proteins found in many viruses. The broad distribution of these viral SBF-like proteins suggests that they arose first in viruses, and a fungal ancestor acquired one such protein during a viral infection. As SBF and E2F bind similar DNA sequences, Medina et al. hypothesized that this viral SBF hijacked control of the cell cycle in the fungal ancestor by controlling expression of genes that were originally controlled only by E2F. In support of this idea, experiments showed that many E2F binding sites in modern genes are also SBF binding sites, and that E2F sites can substitute for SBF sites in SBF-controlled genes. Future experiments in zoosporic fungi, which have animal-like and fungal-like features, would provide a glimpse of how a fungal ancestor may have used both SBF and E2F. These experiments may also reveal why most fungi have retained the newer SBF but lost the ancestral and widely conserved E2F protein. DOI:http://dx.doi.org/10.7554/eLife.09492.002
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Affiliation(s)
- Edgar M Medina
- Department of Biology, Duke University, Durham, United States.,Center for Genomic and Computational Biology, Duke University, Durham, United States
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University, Durham, United States.,Department of Biostatistics and Bioinformatics, Duke University, Durham, United States
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, United States
| | - Nicolas E Buchler
- Department of Biology, Duke University, Durham, United States.,Center for Genomic and Computational Biology, Duke University, Durham, United States
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15
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Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors. Nat Struct Mol Biol 2016; 23:147-54. [PMID: 26727490 PMCID: PMC4973471 DOI: 10.1038/nsmb.3150] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/25/2015] [Indexed: 02/07/2023]
Abstract
Heat Shock Transcription Factor (HSF) family members function in stress protection and in human disease including proteopathies, neurodegeneration and cancer. The mechanisms that drive distinct post-translational modifications, co-factor recruitment and target gene activation for specific HSF paralogs are unknown. We present high-resolution crystal structures of the human HSF2 DNA-binding domain (DBD) bound to DNA, revealing an unprecedented view of HSFs that provides insights into their unique biology. The HSF2 DBD structures resolve a novel carboxyl-terminal helix that directs the coiled-coil domain to wrap around DNA, exposing paralog-specific sequences of the DBD surface, for differential post-translational modifications and co-factor interactions. We further demonstrate a direct interaction between HSF1 and HSF2 through their coiled-coil domains. Together, these features provide a new model for HSF structure as the basis for differential and combinatorial regulation to influence the transcriptional response to cellular stress.
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Allen MD, Freund SMV, Zinzalla G, Bycroft M. The SWI/SNF Subunit INI1 Contains an N-Terminal Winged Helix DNA Binding Domain that Is a Target for Mutations in Schwannomatosis. Structure 2015; 23:1344-9. [PMID: 26073604 PMCID: PMC4509781 DOI: 10.1016/j.str.2015.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation. Mutations in SWI/SNF subunits are among the most frequent gene alterations in cancer. The INI1/hSNF5/SMARCB1 subunit is mutated in both malignant rhabdoid tumor, a highly aggressive childhood cancer, and schwannomatosis, a tumor-predisposing syndrome characterized by mostly benign tumors of the CNS. Here, we show that mutations in INI1 that cause schwannomatosis target a hitherto unidentified N-terminal winged helix DNA binding domain that is also present in the BAF45a/PHF10 subunit of the SWI/SNF complex. The domain is structurally related to the SKI/SNO/DAC domain, which is found in a number of metazoan chromatin-associated proteins. INI1 and its metazoan homologs contain a variant winged helix DNA binding domain A homologous domain is present in the BAF45a/PHF10 subunit of the SWI/SNF complex Structurally related domains are found in other metazoan chromatin-associated proteins INI1 mutations that cause schwannomatosis map to the winged helix domain
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Affiliation(s)
- Mark D Allen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Giovanna Zinzalla
- Centre for Advanced Cancer Therapies, Department of Microbiology, Cell and Tumour Biology and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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