1
|
Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [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: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
Collapse
Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
2
|
Kan Y, He Z, Keyhani NO, Li N, Huang S, Zhao X, Liu P, Zeng F, Li M, Luo Z, Zhang Y. A network of transcription factors in complex with a regulating cell cycle cyclin orchestrates fungal oxidative stress responses. BMC Biol 2024; 22:81. [PMID: 38609978 PMCID: PMC11015564 DOI: 10.1186/s12915-024-01884-3] [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: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Response to oxidative stress is universal in almost all organisms and the mitochondrial membrane protein, BbOhmm, negatively affects oxidative stress responses and virulence in the insect fungal pathogen, Beauveria bassiana. Nothing further, however, is known concerning how BbOhmm and this phenomenon is regulated. RESULTS Three oxidative stress response regulating Zn2Cys6 transcription factors (BbOsrR1, 2, and 3) were identified and verified via chromatin immunoprecipitation (ChIP)-qPCR analysis as binding to the BbOhmm promoter region, with BbOsrR2 showing the strongest binding. Targeted gene knockout of BbOsrR1 or BbOsrR3 led to decreased BbOhmm expression and consequently increased tolerances to free radical generating compounds (H2O2 and menadione), whereas the ΔBbOsrR2 strain showed increased BbOhmm expression with concomitant decreased tolerances to these compounds. RNA and ChIP sequencing analysis revealed that BbOsrR1 directly regulated a wide range of antioxidation and transcription-associated genes, negatively affecting the expression of the BbClp1 cyclin and BbOsrR2. BbClp1 was shown to localize to the cell nucleus and negatively mediate oxidative stress responses. BbOsrR2 and BbOsrR3 were shown to feed into the Fus3-MAPK pathway in addition to regulating antioxidation and detoxification genes. Binding motifs for the three transcription factors were found to partially overlap in the promoter region of BbOhmm and other target genes. Whereas BbOsrR1 appeared to function independently, co-immunoprecipitation revealed complex formation between BbClp1, BbOsrR2, and BbOsrR3, with BbClp1 partially regulating BbOsrR2 phosphorylation. CONCLUSIONS These findings reveal a regulatory network mediated by BbOsrR1 and the formation of a BbClp1-BbOsrR2-BbOsrR3 complex that orchestrates fungal oxidative stress responses.
Collapse
Affiliation(s)
- Yanze Kan
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Zhangjiang He
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
- Biochemical Engineering Center of Guizhou Province, Guizhou University, Guiyang, 50025, People's Republic of China
| | - Nemat O Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, 60607, USA
| | - Ning Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Shuaishuai Huang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Xin Zhao
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Pengfei Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Fanqin Zeng
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Min Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Zhibing Luo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Yongjun Zhang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China.
| |
Collapse
|
3
|
Haase MAB, Steenwyk JL, Boeke JD. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics 2024; 226:iyae008. [PMID: 38271560 PMCID: PMC10917516 DOI: 10.1093/genetics/iyae008] [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: 08/28/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here, we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation-mediated by the trans-regulator Spt10-is ancient, likely emerging between 320 and 380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage, which coincided with the loss of 1 copy of its paralogous core histone genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora fast-evolving lineage.
Collapse
Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
| |
Collapse
|
4
|
Hoang CQ, Duong GHT, Tran MH, Vu TX, Tran TB, Pham HTN. Molecular mechanisms underlying phenotypic degeneration in Cordyceps militaris: insights from transcriptome reanalysis and osmotic stress studies. Sci Rep 2024; 14:2231. [PMID: 38278834 PMCID: PMC10817986 DOI: 10.1038/s41598-024-51946-3] [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: 09/05/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Phenotypic degeneration in Cordyceps militaris poses a significant concern for producers, yet the mechanisms underlying this phenomenon remain elusive. To address this concern, we isolated two strains that differ in their abilities to form fruiting bodies. Our observations revealed that the degenerated strain lost the capacity to develop fruiting bodies, exhibited limited radial expansion, increased spore density, and elevated intracellular glycerol levels. Transcriptome reanalysis uncovered dysregulation of genes involved in the MAPK signaling pathway in the degenerate strain. Our RT-qPCR results demonstrated reduced expression of sexual development genes, along with upregulation of genes involved in asexual sporulation, glycerol synthesis, and MAPK regulation, when compared to the wild-type strain. Additionally, we discovered that osmotic stress reduced radial growth but increased conidia sporulation and glycerol accumulation in all strains. Furthermore, hyperosmotic stress inhibited fruiting body formation in all neutralized strains. These findings indicate dysregulation of the MAPK signaling pathway, the possibility of the activation of the high-osmolarity glycerol and spore formation modules, as well as the downregulation of the pheromone response and filamentous growth cascades in the degenerate strain. Overall, our study sheds light on the mechanisms underlying Cordyceps militaris degeneration and identifies potential targets for improving cultivation practices.
Collapse
Affiliation(s)
- Chinh Q Hoang
- Center of Experimental Biology, National Center for Technical Progress, C6 Thanh Xuan Bac, Thanh Xuan, Hanoi, Vietnam.
| | - Giang H T Duong
- Center of Experimental Biology, National Center for Technical Progress, C6 Thanh Xuan Bac, Thanh Xuan, Hanoi, Vietnam
- Department of Molecular Biotechnology, Institute of New Technology, Academy of Military Science and Technology, 17 Hoang Sam, Cau Giay, Hanoi, Vietnam
| | - Mai H Tran
- Center for Biomedical Informatics, Vingroup Big Data Institute, and GeneStory JSC, 458 Minh Khai, Hai Ba Trung, Hanoi, Vietnam
- GeneStory JSC, 458 Minh Khai, Hai Ba Trung, Hanoi, Vietnam
| | - Tao X Vu
- Center of Experimental Biology, National Center for Technical Progress, C6 Thanh Xuan Bac, Thanh Xuan, Hanoi, Vietnam
| | - Tram B Tran
- Center of Experimental Biology, National Center for Technical Progress, C6 Thanh Xuan Bac, Thanh Xuan, Hanoi, Vietnam
| | - Hang T N Pham
- Department of Pharmacology and Biochemistry, National Institute of Medicinal Materials, 3B Quang Trung, Hoan Kiem District, Hanoi, 100000, Vietnam
- University of Medicine and Pharmacy, Vietnam National University, 144 Xuan Thuy, Cau Giay District, Hanoi, 100000, Vietnam
| |
Collapse
|
5
|
Zhao L, Shu Y, Quan S, Dhanasekaran S, Zhang X, Zhang H. Screening and Regulation Mechanism of Key Transcription Factors of Penicillium expansum Infecting Postharvest Pears by ATAC-Seq Analysis. Foods 2022; 11:foods11233855. [PMID: 36496662 PMCID: PMC9738651 DOI: 10.3390/foods11233855] [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: 10/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Transcription factors play a key role in Penicillium expansum infection process. Although the crucial characteristics of some transcription factors of pathogenic fungi have been found, many transcription factors involved in P. expansum infections have not been explored and studied. This study aimed to screen the transcription factors of P. expansum involved in postharvest pear infections by ATAC-seq analysis and to analyze the differentially expressed peak-related genes by GO enrichment and KEGG pathway analysis. Our results found the up-regulation of differentially expressed peak-related genes involved in the MAPK signaling pathway, pentose phosphate pathway, starch and sucrose metabolism, and pentose and glucuronate interconversions. Our study especially confirmed the differential regulation of transcription factors MCM1, Ste12 and gene WSC in the MAPK signaling pathway and PG1, RPE1 in the pentose and glucuronate interconversions pathway. These transcription factors and related genes might play an essential role in pear fruit infection by P. expansum. RT-qPCR validation of twelve expressed peak-related genes in P. expansum showed that the expression levels of these twelve genes were compatible with the ATAC-Seq. Our findings might shed some light on the regulatory molecular networks consisting of transcription factors that engaged in P. expansum invasion and infection of pear fruits.
Collapse
|
6
|
Liu KX, Jia JQ, Chen N, Fu DD, Sun JY, Zhao JM, Li JY, Xiao SQ, Xue CS. Mating-Type Genes Control Sexual Reproduction, Conidial Germination, and Virulence in Cochliobolus lunatus. PHYTOPATHOLOGY 2022; 112:1055-1062. [PMID: 34738831 DOI: 10.1094/phyto-02-21-0063-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cochliobolus lunatus (anamorph: Curvularia lunata) is a major pathogenic fungus that causes the Curvularia leaf spot of maize. ClMAT1-1-1 and ClMAT1-2-1, the C. lunatus orthologs of C. heterostrophus ChMAT1-1-1 and ChMAT1-2-1, were investigated in the present study to uncover their functions in C. lunatus. Southern blot analysis showed that these mating-type MAT genes exist in the C. lunatus genome as a single copy. ClMAT1-1-1 and ClMAT1-2-1 were knocked out and complemented to generate ΔClmat1-1-1 and ΔClmat1-2-1 and ΔClmat1-1-1-C and ΔClmat1-2-1-C, respectively. The mutant strains had defective sexual development and failed to produce pseudothecia. There were no significant differences in growth rate or conidia production between the mutant and wild-type strains. However, the aerial mycelia and mycelial dry weight of ΔClmat1-1-1 and ΔClmat1-2-1 were lower than those of wild type, suggesting that MAT genes affect asexual development. ClMAT genes were involved in the responses to cell wall integrity and osmotic adaptation. ΔClmat1-2-1 had a lower conidial germination rate than the wild-type strain CX-3. The virulence of ΔClmat1-2-1 and ΔClmat1-1-1 was also reduced compared with the wild-type. Complementary strains could restore all the phenotypes.
Collapse
Affiliation(s)
- K X Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - J Q Jia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - N Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - D D Fu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - J Y Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - J M Zhao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - J Y Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - S Q Xiao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - C S Xue
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, P.R. China
| |
Collapse
|
7
|
Ayra L, Reyero-Saavedra MDR, Isidra-Arellano MC, Lozano L, Ramírez M, Leija A, Fuentes SI, Girard L, Valdés-López O, Hernández G. Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors. FRONTIERS IN PLANT SCIENCE 2021; 12:679463. [PMID: 34163511 PMCID: PMC8216239 DOI: 10.3389/fpls.2021.679463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/25/2023]
Abstract
Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.
Collapse
Affiliation(s)
- Litzy Ayra
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María del Rocio Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Luis Lozano
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara-Isabel Fuentes
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
8
|
Belcher MS, Vuu KM, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loqué D, Shih PM. Design of orthogonal regulatory systems for modulating gene expression in plants. Nat Chem Biol 2020; 16:857-865. [PMID: 32424304 DOI: 10.1038/s41589-020-0547-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/09/2020] [Indexed: 11/08/2022]
Abstract
Agricultural biotechnology strategies often require the precise regulation of multiple genes to effectively modify complex plant traits. However, most efforts are hindered by a lack of characterized tools that allow for reliable and targeted expression of transgenes. We have successfully engineered a library of synthetic transcriptional regulators that modulate expression strength in planta. By leveraging orthogonal regulatory systems from Saccharomyces spp., we have developed a strategy for the design of synthetic activators, synthetic repressors, and synthetic promoters and have validated their use in Nicotiana benthamiana and Arabidopsis thaliana. This characterization of contributing genetic elements that dictate gene expression represents a foundation for the rational design of refined synthetic regulators. Our findings demonstrate that these tools provide variation in transcriptional output while enabling the concerted expression of multiple genes in a tissue-specific and environmentally responsive manner, providing a basis for generating complex genetic circuits that process endogenous and environmental stimuli.
Collapse
Affiliation(s)
- Michael S Belcher
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Khanh M Vuu
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andy Zhou
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Nasim Mansoori
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Agosto Ramos
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mitchell G Thompson
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Henrik V Scheller
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick M Shih
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
| |
Collapse
|
9
|
Zhou W, Dorrity MW, Bubb KL, Queitsch C, Fields S. Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes. Genetics 2020; 214:397-407. [PMID: 31810988 PMCID: PMC7017024 DOI: 10.1534/genetics.119.302929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Amino acid substitutions are commonly found in human transcription factors, yet the functional consequences of much of this variation remain unknown, even in well-characterized DNA-binding domains. Here, we examine how six single-amino acid variants in the DNA-binding domain of Ste12-a yeast transcription factor regulating mating and invasion-alter Ste12 genome binding, motif recognition, and gene expression to yield markedly different phenotypes. Using a combination of the "calling-card" method, RNA sequencing, and HT-SELEX (high throughput systematic evolution of ligands by exponential enrichment), we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors. Mating-defective variants led to decreased expression of distinct subsets of genes necessary for mating. Hyper-invasive variants also decreased expression of subsets of genes involved in mating, but increased the expression of other subsets of genes associated with the cellular response to osmotic stress. While single-amino acid changes in the coding region of this transcription factor result in complex regulatory reconfiguration, the major phenotypic consequences for the cell appear to depend on changes in the expression of a small number of genes with related functions.
Collapse
Affiliation(s)
- Wei Zhou
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| |
Collapse
|
10
|
Zhao X, Yang X, Lu Z, Wang H, He Z, Zhou G, Luo Z, Zhang Y. MADS-box transcription factor Mcm1 controls cell cycle, fungal development, cell integrity and virulence in the filamentous insect pathogenic fungus Beauveria bassiana. Environ Microbiol 2019; 21:3392-3416. [PMID: 30972885 DOI: 10.1111/1462-2920.14629] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/09/2019] [Indexed: 12/15/2022]
Abstract
MADS-box transcription factor Mcm1 plays crucial roles in regulating mating processes and pathogenesis in some fungi. However, its roles are varied in fungal species, and its function remains unclear in entomopathogenic fungi. Here, Mcm1 orthologue, Bbmcm1, was characterized in a filamentous entomopathogenic fungus, Beauveria bassiana. Disruption of Bbmcm1 resulted in a distinct reduction in growth with abnormal conidiogenesis, and a significant decrease in conidial viability with abnormal germination. ΔBbmcm1 displayed impaired cell integrity, with distorted cell wall structure and altered cell wall component. Abnormal cell cycle was detected in ΔBbmcm1 with longer G2 /M phase but shorter G1 /G0 and S phases in unicellular blastospores, and sparser septa in multicellular hyphae, which might be responsible for defects in development and differentiation due to the regulation of cell cycle-involved genes, as well as the corresponding cellular events-associated genes. Dramatically decreased virulence was examined in ΔBbmcm1, with impaired ability to escape haemocyte encapsulation, which was consistent with markedly reduced cuticle-degrading enzyme production by repressing their coding genes, and downregulated fungal effector protein-coding genes, suggesting a novel role of Mcm1 in interaction with host insect. These data indicate that Mcm1 is a crucial regulator of development, cell integrity, cell cycle and virulence in insect fungal pathogens.
Collapse
Affiliation(s)
- Xin Zhao
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xingju Yang
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Zhuoyue Lu
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Huifang Wang
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Zhangjiang He
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Guangyan Zhou
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Zhibing Luo
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Yongjun Zhang
- Biotechnology Research Center, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| |
Collapse
|
11
|
Zhu X, Jiao M, Guo J, Liu P, Tan C, Yang Q, Zhang Y, Thomas Voegele R, Kang Z, Guo J. A novel MADS-box transcription factor PstMCM1-1 is responsible for full virulence of Puccinia striiformis f. sp. tritici. Environ Microbiol 2018; 20:1452-1463. [PMID: 29393562 DOI: 10.1111/1462-2920.14054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/27/2017] [Accepted: 01/21/2018] [Indexed: 11/26/2022]
Abstract
In many eukaryotes, transcription factor MCM1 gene plays crucial roles in regulating mating processes and pathogenesis by interacting with other co-factors. However, little is known about the role of MCM1 in rust fungi. Here, we identified two MCM1 orthologs, PstMCM1-1 and PstMCM1-2, in the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). Sequence analysis indicated that both PstMCM1-1 and PstMCM1-2 contain conserved MADS domains and that PstMCM1-1 belongs to a group of SRF-like proteins that are evolutionarily specific to rust fungi. Yeast two-hybrid assays indicated that PstMCM1-1 interacts with transcription factors PstSTE12 and PstbE1. PstMCM1-1 was found to be highly induced during early infection stages in wheat and during pycniospore formation on the alternate host barberry (Berberis shensiana). PstMCM1-1 could complement the lethal phenotype and mating defects in a mcm1 mutant of Saccharomyces cerevisiae. In addition, it partially complemented the defects in appressorium formation and plant infection in a Magnaporthe oryzae Momcm1 mutant. Knock down of PstMCM1-1 resulted in a significant reduction of hyphal extension and haustorium formation and the virulence of Pst on wheat. Our results suggest that PstMCM1-1 plays important roles in the regulation of mating and pathogenesis of Pst most likely by interacting with co-factors.
Collapse
Affiliation(s)
- Xiaoguo Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Min Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Peng Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chenglong Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qian Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ralf Thomas Voegele
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, 70599, Germany
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
12
|
Xiong D, Wang Y, Tian L, Tian C. MADS-Box Transcription Factor VdMcm1 Regulates Conidiation, Microsclerotia Formation, Pathogenicity, and Secondary Metabolism of Verticillium dahliae. Front Microbiol 2016; 7:1192. [PMID: 27536281 PMCID: PMC4971026 DOI: 10.3389/fmicb.2016.01192] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
Verticillium dahliae, a notorious phytopathogenic fungus, causes vascular wilt diseases in many plant species resulting in devastating yield losses worldwide. Due to its ability to colonize plant xylem and form microsclerotia, V. dahliae is highly persistent and difficult to control. In this study, we show that the MADS-box transcription factor VdMcm1 is a key regulator of conidiation, microsclerotia formation, virulence, and secondary metabolism of V. dahliae. In addition, our findings suggest that VdMcm1 is involved in cell wall integrity. Finally, comparative RNA-Seq analysis reveals 823 significantly downregulated genes in the VdMcm1 deletion mutant, with diverse biological functions in transcriptional regulation, plant infection, cell adhesion, secondary metabolism, transmembrane transport activity, and cell secretion. When taken together, these data suggest that VdMcm1 performs pleiotropic functions in V. dahliae.
Collapse
Affiliation(s)
- Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Longyan Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| |
Collapse
|
13
|
Valiante V, Baldin C, Hortschansky P, Jain R, Thywißen A, Straßburger M, Shelest E, Heinekamp T, Brakhage AA. TheAspergillus fumigatusconidial melanin production is regulated by the bifunctional bHLH DevR and MADS-box RlmA transcription factors. Mol Microbiol 2016; 102:321-335. [DOI: 10.1111/mmi.13462] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 02/02/2023]
Affiliation(s)
- Vito Valiante
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
| | - Clara Baldin
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University Jena; Adolf-Reichwein-Str. 23 Jena 07745 Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
| | - Radhika Jain
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University Jena; Adolf-Reichwein-Str. 23 Jena 07745 Germany
| | - Andreas Thywißen
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University Jena; Adolf-Reichwein-Str. 23 Jena 07745 Germany
| | - Maria Straßburger
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
| | - Ekaterina Shelest
- Research Group Bioinformatics/Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University Jena; Adolf-Reichwein-Str. 23 Jena 07745 Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI); Adolf-Reichwein-Str. 23 Jena 07745 Germany
- Department of Microbiology and Molecular Biology; Institute of Microbiology, Friedrich Schiller University Jena; Adolf-Reichwein-Str. 23 Jena 07745 Germany
| |
Collapse
|
14
|
Li N, Kunitake E, Endo Y, Aoyama M, Kanamaru K, Kimura M, Kato M, Kobayashi T. Involvement of an SRF-MADS protein McmA in regulation of extracellular enzyme production and asexual/sexual development in Aspergillus nidulans. Biosci Biotechnol Biochem 2016; 80:1820-8. [PMID: 26967516 DOI: 10.1080/09168451.2016.1146074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SRF-MADS proteins are transcription factors conserved among eukaryotes that regulate a variety of cellular functions; however, their physiological roles are still not well understood in filamentous fungi. Effects of a mutation in mcmA gene that encodes the sole SRF-MADS protein in the fungus Aspergillus nidulans were examined by RNA sequencing. Sequencing data revealed that expression levels of cellulase genes were significantly decreased by the mutation as reported previously. However, expression levels of various hemicellulolytic enzyme genes, several extracellular protease genes, the nosA and rosA genes involved in sexual development, and AN4394 encoding an ortholog of EcdR involved in Aspergillus oryzae conidiation, were also significantly decreased by the mutation. As expected from the RNA sequencing data, the mcmA mutant had reduced protease production, cleistothecial development, and conidiation. This is the first report describing the involvement of SRF-MADS proteins in protease production in fungi, and asexual and sexual development in Aspergillus.
Collapse
Affiliation(s)
| | - Emi Kunitake
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Yoshikazu Endo
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Miki Aoyama
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Kyoko Kanamaru
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Makoto Kimura
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Masashi Kato
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Tetsuo Kobayashi
- a Department of Biological Mechanisms and Functions , Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| |
Collapse
|
15
|
Becker K, Beer C, Freitag M, Kück U. Genome-wide identification of target genes of a mating-type α-domain transcription factor reveals functions beyond sexual development. Mol Microbiol 2015; 96:1002-22. [DOI: 10.1111/mmi.12987] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Kordula Becker
- Christian Doppler Laboratory for Fungal Biotechnology; Lehrstuhl für Allgemeine und Molekulare Botanik; Ruhr-Universität Bochum; Universitätsstr. 150 D-44780 Bochum Germany
| | - Christina Beer
- Christian Doppler Laboratory for Fungal Biotechnology; Lehrstuhl für Allgemeine und Molekulare Botanik; Ruhr-Universität Bochum; Universitätsstr. 150 D-44780 Bochum Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics; Oregon State University; Corvallis Oregon 97331-7305 USA
| | - Ulrich Kück
- Christian Doppler Laboratory for Fungal Biotechnology; Lehrstuhl für Allgemeine und Molekulare Botanik; Ruhr-Universität Bochum; Universitätsstr. 150 D-44780 Bochum Germany
| |
Collapse
|
16
|
Yang C, Liu H, Li G, Liu M, Yun Y, Wang C, Ma Z, Xu JR. The MADS-box transcription factor FgMcm1 regulates cell identity and fungal development in Fusarium graminearum. Environ Microbiol 2015; 17:2762-76. [PMID: 25627073 DOI: 10.1111/1462-2920.12747] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, MADS-box genes are known to play major regulatory roles in various biological processes by combinatorial interactions with other transcription factors. In this study, we functionally characterized the FgMCM1 MADS-box gene in Fusarium graminearum, the causal agent of wheat and barley head blight. Deletion of FgMCM1 resulted in the loss of perithecium production and phialide formation. The Fgmcm1 mutant was significantly reduced in virulence, deoxynivalenol biosynthesis and conidiation. In yeast two-hybrid assays, FgMcm1 interacted with Mat1-1-1 and Fst12, two transcription factors important for sexual reproduction. Whereas Fgmcm1 mutants were unstable and produced stunted subcultures, Fgmcm1 mat1-1-1 but not Fgmcm1 fst12 double mutants were stable. Furthermore, spontaneous suppressor mutations occurred frequently in stunted subcultures to recover growth rate. Ribonucleic acid sequencing analysis indicated that a number of sexual reproduction-related genes were upregulated in stunted subcultures compared with the Fgmcm1 mutant, which was downregulated in the expression of genes involved in pathogenesis, secondary metabolism and conidiation. We also showed that culture instability was not observed in the Fvmcm1 mutants of the heterothallic Fusarium verticillioides. Overall, our data indicate that FgMcm1 plays a critical role in the regulation of cell identity, sexual and asexual reproduction, secondary metabolism and pathogenesis in F. graminearum.
Collapse
Affiliation(s)
- Cui Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwestern A&F University, Yangling, Shaanxi, 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwestern A&F University, Yangling, Shaanxi, 712100, China
| | - Guotian Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Meigang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwestern A&F University, Yangling, Shaanxi, 712100, China
| | - Yingzi Yun
- Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Chenfang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwestern A&F University, Yangling, Shaanxi, 712100, China
| | - Zhonghua Ma
- Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwestern A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
17
|
Baker CR, Hanson-Smith V, Johnson AD. Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science 2013; 342:104-8. [PMID: 24092741 PMCID: PMC3911913 DOI: 10.1126/science.1240810] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can therefore be neatly partitioned between descendant paralogs. However, many gene products, such as transcriptional regulators, are components within cooperative assemblies; here, we show that a natural consequence of duplication and divergence of such proteins can be competitive interference between the paralogs. Our example is based on the duplication of the essential MADS-box transcriptional regulator Mcm1, which is found in all fungi and regulates a large set of genes. We show that a set of historical amino acid sequence substitutions minimized paralog interference in contemporary species and, in doing so, increased the molecular complexity of this gene regulatory network. We propose that paralog interference is a common constraint on gene duplicate evolution, and its resolution, which can generate additional regulatory complexity, is needed to stabilize duplicated genes in the genome.
Collapse
Affiliation(s)
- Christopher R. Baker
- Department of Immunology and Microbiology, University of California, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Victor Hanson-Smith
- Department of Immunology and Microbiology, University of California, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Alexander D. Johnson
- Department of Immunology and Microbiology, University of California, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| |
Collapse
|
18
|
Ortiz CS, Shim WB. The role of MADS-box transcription factors in secondary metabolism and sexual development in the maize pathogen Fusarium verticillioides. MICROBIOLOGY-SGM 2013; 159:2259-2268. [PMID: 23985144 DOI: 10.1099/mic.0.068775-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MADS-box transcription factors (TFs) regulate functionally diverse gene targets in eukaryotes. In select ascomycetes, MADS-box TFs have been shown to play a role in virulence, and vegetative and sexual development. Here, we characterized Fusarium verticillioides MADS-box TFs, Mads1 and Mads2, in terms of their roles in secondary metabolism and sexual mating. Sequence analyses showed that MADS1 and MADS2 encode TFs with a SRF-type dimerization domain and a MEF2-type dimerization domain, respectively. The MADS1 and MADS2 knockout mutants (Fmt1 and Fmt2 strains, respectively) exhibited decreased vegetative growth and FB1 production when compared to the wild-type. Fmt1 showed reduced expression of 14 polyketide synthase (PKS) genes present in the organism, whereas Fmt2 did not display a change in PKS gene expression. Significantly, the deletion of MADS1 and MADS2 in the MAT1-2 genotype (Fmt4 and Fmt5 strains, respectively) led to strains that failed to produce perithecia and ascospores when crossed with the MAT1-1 wild-type strain. Notably, deletion of either gene did not have an effect on the ability of the fungus to colonize maize stalk or kernels. FB1 production and PKS expression data suggest that Mads1 is a broad regulator of secondary metabolism in F. verticillioides, and may target regulons upstream of Mads2 to influence FB1 production. In addition, MADS-box TFs in F. verticillioides play a critical role in the perithecia development.
Collapse
Affiliation(s)
- Carlos S Ortiz
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
| |
Collapse
|
19
|
Matveenko AG, Zemlyanko OM, Zhouravleva GA. Identification of Saccharomyces cerevisiae genes leading to synthetic lethality of prion [PSI +] with SUP45 mutations. Mol Biol 2013. [DOI: 10.1134/s0026893313040110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
20
|
Bastajian N, Friesen H, Andrews BJ. Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast. PLoS Genet 2013; 9:e1003507. [PMID: 23675312 PMCID: PMC3649975 DOI: 10.1371/journal.pgen.1003507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 03/27/2013] [Indexed: 11/19/2022] Open
Abstract
The Bck2 protein is a potent genetic regulator of cell-cycle-dependent gene expression in budding yeast. To date, most experiments have focused on assessing a potential role for Bck2 in activation of the G1/S-specific transcription factors SBF (Swi4, Swi6) and MBF (Mbp1, Swi6), yet the mechanism of gene activation by Bck2 has remained obscure. We performed a yeast two-hybrid screen using a truncated version of Bck2 and discovered six novel Bck2-binding partners including Mcm1, an essential protein that binds to and activates M/G1 promoters through Early Cell cycle Box (ECB) elements as well as to G2/M promoters. At M/G1 promoters Mcm1 is inhibited by association with two repressors, Yox1 or Yhp1, and gene activation ensues once repression is relieved by an unknown activating signal. Here, we show that Bck2 interacts physically with Mcm1 to activate genes during G1 phase. We used chromatin immunoprecipitation (ChIP) experiments to show that Bck2 localizes to the promoters of M/G1-specific genes, in a manner dependent on functional ECB elements, as well as to the promoters of G1/S and G2/M genes. The Bck2-Mcm1 interaction requires valine 69 on Mcm1, a residue known to be required for interaction with Yox1. Overexpression of BCK2 decreases Yox1 localization to the early G1-specific CLN3 promoter and rescues the lethality caused by overexpression of YOX1. Our data suggest that Yox1 and Bck2 may compete for access to the Mcm1-ECB scaffold to ensure appropriate activation of the initial suite of genes required for cell cycle commitment.
Collapse
Affiliation(s)
- Nazareth Bastajian
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Helena Friesen
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brenda J. Andrews
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
21
|
Yamakawa Y, Endo Y, Li N, Yoshizawa M, Aoyama M, Watanabe A, Kanamaru K, Kato M, Kobayashi T. Regulation of cellulolytic genes by McmA, the SRF-MADS box protein in Aspergillus nidulans. Biochem Biophys Res Commun 2013; 431:777-82. [DOI: 10.1016/j.bbrc.2013.01.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/09/2013] [Indexed: 11/25/2022]
|
22
|
Lan X, Farnham PJ, Jin VX. Uncovering transcription factor modules using one- and three-dimensional analyses. J Biol Chem 2012; 287:30914-21. [PMID: 22952238 DOI: 10.1074/jbc.r111.309229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Transcriptional regulation is a critical mediator of many normal cellular processes, as well as disease progression. Transcription factors (TFs) often co-localize at cis-regulatory elements on the DNA, form protein complexes, and collaboratively regulate gene expression. Machine learning and Bayesian approaches have been used to identify TF modules in a one-dimensional context. However, recent studies using high throughput technologies have shown that TF interactions should also be considered in three-dimensional nuclear space. Here, we describe methods for identifying TF modules and discuss how moving from a one-dimensional to a three-dimensional paradigm, along with integrated experimental and computational approaches, can lead to a better understanding of TF association networks.
Collapse
Affiliation(s)
- Xun Lan
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | |
Collapse
|
23
|
Masiero S, Colombo L, Grini PE, Schnittger A, Kater MM. The emerging importance of type I MADS box transcription factors for plant reproduction. THE PLANT CELL 2011; 23:865-72. [PMID: 21378131 PMCID: PMC3082269 DOI: 10.1105/tpc.110.081737] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 02/01/2011] [Accepted: 02/14/2011] [Indexed: 05/19/2023]
Abstract
Based on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species.
Collapse
Affiliation(s)
- Simona Masiero
- Dipartimento di Biologia, Universita' degli Studi di Milano, 20133 Milan, Italy
| | | | | | | | | |
Collapse
|
24
|
Zhou X, Liu W, Wang C, Xu Q, Wang Y, Ding S, Xu JR. A MADS-box transcription factor MoMcm1 is required for male fertility, microconidium production and virulence in Magnaporthe oryzae. Mol Microbiol 2011; 80:33-53. [PMID: 21276092 DOI: 10.1111/j.1365-2958.2011.07556.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Appressorium formation is a key step in the infection cycle of Magnaporthe oryzae. Mst12 is a transcription factor essential for appressorium penetration and invasive growth. In this study we used the affinity purification approach to identify proteins that physically associate with Mst12. One of the Mst12-interacting genes identified was MoMCM1, which encodes a MADS-box protein orthologous to yeast Mcm1. MoMcm1 interacted with both Mst12 and Mata-1 in yeast two-hybrid assays. Deletion of MoMCM1 resulted in the loss of male fertility and microconidium production. The Momcm1 mutant was defective in appressorium penetration and formed narrower invasive hyphae, which may be responsible for its reduced virulence. In transformants expressing MoMCM1-eGFP fusion, GFP signals were observed in the nucleus. We also generated the Momcm1 mst12 double mutant, which was defective in penetration and non-pathogenic. On hydrophilic surfaces, germ tubes produced by the double mutant were severely curved, and 20% of them formed appressoria. In contrast, the Momcm1 or mst12 mutant did not form appressoria on hydrophilic surfaces. These results suggest that MoMCM1 and MST12 have overlapping functions to suppress appressorium formation under non-conducive conditions. MoMcm1 may interact with Mst12 and MatA-1 to regulate germ tube identity and male fertility respectively.
Collapse
Affiliation(s)
- Xiaoying Zhou
- Purdue-NWAFU Joint Research Center, Department Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | | | | | | | | | | | | |
Collapse
|
25
|
Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. ACTA ACUST UNITED AC 2010; 26:i334-42. [PMID: 20529925 PMCID: PMC2881360 DOI: 10.1093/bioinformatics/btq175] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Motivation: A global map of transcription factor binding sites (TFBSs) is critical to understanding gene regulation and genome function. DNaseI digestion of chromatin coupled with massively parallel sequencing (digital genomic footprinting) enables the identification of protein-binding footprints with high resolution on a genome-wide scale. However, accurately inferring the locations of these footprints remains a challenging computational problem. Results: We present a dynamic Bayesian network-based approach for the identification and assignment of statistical confidence estimates to protein-binding footprints from digital genomic footprinting data. The method, DBFP, allows footprints to be identified in a probabilistic framework and outperforms our previously described algorithm in terms of precision at a fixed recall. Applied to a digital footprinting data set from Saccharomyces cerevisiae, DBFP identifies 4679 statistically significant footprints within intergenic regions. These footprints are mainly located near transcription start sites and are strongly enriched for known TFBSs. Footprints containing no known motif are preferentially located proximal to other footprints, consistent with cooperative binding of these footprints. DBFP also identifies a set of statistically significant footprints in the yeast coding regions. Many of these footprints coincide with the boundaries of antisense transcripts, and the most significant footprints are enriched for binding sites of the chromatin-associated factors Abf1 and Rap1. Contact:jay.hesselberth@ucdenver.edu; william-noble@u.washington.edu Supplementary information:Supplementary material is available at Bioinformatics online.
Collapse
Affiliation(s)
- Xiaoyu Chen
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | | | | | | | | |
Collapse
|
26
|
Abstract
Darieva and coworkers (Darieva et al., 2010) have shown that the repressor Yox1 and the activator Fkh2-Ndd1 associate with opposite sides of the dimeric Mcm1 transcription factor but nevertheless compete for binding; the outcome determines expression of late mitotic genes in yeast.
Collapse
|
27
|
Guzinska K, Varghese R, Vancura A. Role of Plc1p in regulation of Mcm1p-dependent genes. FEMS Microbiol Lett 2009; 295:245-50. [PMID: 19459978 DOI: 10.1111/j.1574-6968.2009.01602.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
In budding yeasts, phosphoinositide-specific phospholipase C (Plc1p encoded by PLC1 gene) and several inositol polyphosphate kinases represent a nuclear pathway for synthesis of inositol polyphosphates (InsPs), which are involved in several aspects of DNA and RNA metabolism, including transcriptional regulation. Plc1p-produced inositol trisphosphate (InsP(3)) is phosphorylated by Ipk2p/Arg82p to yield InsP(4)/InsP(5). Ipk2p/Arg82p is also a component of ArgR-Mcm1p complex that regulates transcription of genes involved in arginine metabolism. The role of Ipk2p/Arg82p in this complex is to stabilize the essential MADS box protein Mcm1p. Consequently, ipk2Delta cells display reduced levels of Mcm1p and attenuated expression of Mcm1p-dependent genes. Because plc1Delta cells display aberrant expression of several groups of genes, including genes involved in stress response, the objective of this study was to determine whether Plc1p also affects expression of Mcm1p-dependent genes. Here we report that not only ipk2Delta, but also plc1Delta cells display decreased expression of Mcm1p-dependent genes. However, Plc1p is not involved in stabilization of Mcm1p and affects transcription of Mcm1p-dependent genes by a different mechanism, probably involving regulation of chromatin remodeling complexes.
Collapse
Affiliation(s)
- Katarzyna Guzinska
- Department of Biological Sciences, St John's University, Queens, NY 11439, USA
| | | | | |
Collapse
|
28
|
MADS-box transcription factor mig1 is required for infectious growth in Magnaporthe grisea. EUKARYOTIC CELL 2008; 7:791-9. [PMID: 18344407 DOI: 10.1128/ec.00009-08] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Magnaporthe grisea is a model fungus for studying fungus-plant interactions. Two mitogen-activated protein (MAP) kinase genes, PMK1 and MPS1, have been implicated in regulating plant infection processes in M. grisea. However, transcription factors activated by these MAP kinases are not well studied. In this study we functionally characterized the MIG1 gene that encodes a MADS-box transcription factor homologous to Saccharomyces cerevisiae Rlm1. In yeast two-hybrid assays, MIG1 interacts with MPS1, suggesting that MIG1 may function downstream from the MPS1 pathway. The mig1 deletion mutant had a normal growth rate and formed melanized appressoria, but it was nonpathogenic and failed to infect rice leaves through wounds. Appressoria formed by the mig1 mutant developed penetration pegs and primary infectious hyphae, but further differentiation of the secondary infectious hyphae inside live plant cells was blocked. However, the mig1 mutant formed infectious hypha-like structures in heat-killed plant cells or cellophane membranes. In transformants expressing the MIG1-GFP fusion, green fluorescent protein (GFP) signals were not detectable in vegetative hyphae and conidiophores. Mig1-GFP was localized to nuclei in conidia, appressoria, and infectious hyphae. Deletion of the MADS box had no effect on the expression and localization of the MIG1-GFP fusion but eliminated its ability to complement the mig1 mutant. These results suggest that MIG1 may be required for overcoming plant defense responses and the differentiation of secondary infectious hyphae in live plant cells. The MADS-box domain is essential for the function of MIG1 but dispensable for its nuclear localization, which may be associated with the activation of MIG1 by MPS1 during conidiation and plant infection.
Collapse
|
29
|
Battle A, Segal E, Koller D. Probabilistic discovery of overlapping cellular processes and their regulation. J Comput Biol 2008; 12:909-27. [PMID: 16201912 DOI: 10.1089/cmb.2005.12.909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this paper, we explore modeling overlapping biological processes. We discuss a probabilistic model of overlapping biological processes, gene membership in those processes, and an addition to that model that identifies regulatory mechanisms controlling process activation. A key feature of our approach is that we allow genes to participate in multiple processes, thus providing a more biologically plausible model for the process of gene regulation. We present algorithms to learn each model automatically from data, using only genomewide measurements of gene expression as input. We compare our results to those obtained by other approaches and show that significant benefits can be gained by modeling both the organization of genes into overlapping cellular processes and the regulatory programs of these processes. Moreover, our method successfully grouped genes known to function together, recovered many regulatory relationships that are known in the literature, and suggested novel hypotheses regarding the regulatory role of previously uncharacterized proteins.
Collapse
Affiliation(s)
- Alexis Battle
- Computer Science Department, Stanford University, Stanford, CA 94305-9010, USA.
| | | | | |
Collapse
|
30
|
Abstract
Interaction networks, consisting of agents linked by their interactions, are ubiquitous across many disciplines of modern science. Many methods of analysis of interaction networks have been proposed, mainly concentrating on node degree distribution or aiming to discover clusters of agents that are very strongly connected between themselves. These methods are principally based on graph-theory or machine learning. We present a mathematically simple formalism for modelling context-specific information propagation in interaction networks based on random walks. The context is provided by selection of sources and destinations of information and by use of potential functions that direct the flow towards the destinations. We also use the concept of dissipation to model the aging of information as it diffuses from its source. Using examples from yeast protein-protein interaction networks and some of the histone acetyltransferases involved in control of transcription, we demonstrate the utility of the concepts and the mathematical constructs introduced in this paper.
Collapse
Affiliation(s)
- Aleksandar Stojmirović
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | | |
Collapse
|
31
|
Nolting N, Pöggeler S. A MADS box protein interacts with a mating-type protein and is required for fruiting body development in the homothallic ascomycete Sordaria macrospora. EUKARYOTIC CELL 2006; 5:1043-56. [PMID: 16835449 PMCID: PMC1489284 DOI: 10.1128/ec.00086-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 05/01/2006] [Indexed: 11/20/2022]
Abstract
MADS box transcription factors control diverse developmental processes in plants, metazoans, and fungi. To analyze the involvement of MADS box proteins in fruiting body development of filamentous ascomycetes, we isolated the mcm1 gene from the homothallic ascomycete Sordaria macrospora, which encodes a putative homologue of the Saccharomyces cerevisiae MADS box protein Mcm1p. Deletion of the S. macrospora mcm1 gene resulted in reduced biomass, increased hyphal branching, and reduced hyphal compartment length during vegetative growth. Furthermore, the S. macrospora Deltamcm1 strain was unable to produce fruiting bodies or ascospores during sexual development. A yeast two-hybrid analysis in conjugation with in vitro analyses demonstrated that the S. macrospora MCM1 protein can interact with the putative transcription factor SMTA-1, encoded by the S. macrospora mating-type locus. These results suggest that the S. macrospora MCM1 protein is involved in the transcriptional regulation of mating-type-specific genes as well as in fruiting body development.
Collapse
Affiliation(s)
- Nicole Nolting
- Department of General and Molecular Botany, Ruhr University of Bochum, ND6/161, Universitätsstrasse 150, 44780 Bochum, Germany
| | | |
Collapse
|
32
|
Zaromytidou AI, Miralles F, Treisman R. MAL and ternary complex factor use different mechanisms to contact a common surface on the serum response factor DNA-binding domain. Mol Cell Biol 2006; 26:4134-48. [PMID: 16705166 PMCID: PMC1489092 DOI: 10.1128/mcb.01902-05] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor serum response factor (SRF) interacts with its cofactor, MAL/MKL1, a member of the myocardin-related transcription factor (MRTF) family, through its DNA-binding domain. We define a seven-residue sequence within the conserved MAL B1 region essential and sufficient for complex formation. The neighboring Q-box sequence facilitates this interaction. The B1 and Q-box regions also have antagonistic effects on MAL nuclear import, but the residues involved are largely distinct. Both MAL and the ternary complex factor (TCF) family of SRF cofactors interact with a hydrophobic groove and pocket on the SRF DNA-binding domain. Unlike the TCFs, however, interaction of MAL with SRF is impaired by SRF alphaI-helix mutations that reduce DNA bending in the SRF-DNA complex. A clustered SRF alphaI-helix mutation strongly impairs MAL-SRF complex formation but does not affect DNA distortion in the MAL-SRF complex. MAL-SRF complex formation is facilitated by DNA binding. DNase I footprinting indicates that in the SRF-MAL complex MAL directly contacts DNA. These contacts, which flank the DNA sequences protected from DNase I by SRF, are required for effective MAL-SRF complex formation in gel mobility shift assays. We propose a model of MAL-SRF complex formation in which MAL interacts with SRF by the addition of a beta-strand to the SRF DNA-binding domain beta-sheet region, while SRF-induced DNA bending facilitates MAL-DNA contact.
Collapse
Affiliation(s)
- Alexia-Ileana Zaromytidou
- Transcription Laboratory, Lincoln's Inn Fields Laboratories, Cancer Research UK London Research Institute, Room 401, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
| | | | | |
Collapse
|
33
|
Chen M, Hancock LC, Lopes JM. Transcriptional regulation of yeast phospholipid biosynthetic genes. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1771:310-21. [PMID: 16854618 DOI: 10.1016/j.bbalip.2006.05.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 05/30/2006] [Accepted: 05/31/2006] [Indexed: 12/26/2022]
Abstract
The last several years have been witness to significant developments in understanding transcriptional regulation of the yeast phospholipid structural genes. The response of most phospholipid structural genes to inositol is now understood on a mechanistic level. The roles of specific activators and repressors are also well established. The knowledge of specific regulatory factors that bind the promoters of phospholipid structural genes serves as a foundation for understanding the role of chromatin modification complexes. Collectively, these findings present a complex picture for transcriptional regulation of the phospholipid biosynthetic genes. The INO1 gene is an ideal example of the complexity of transcriptional control and continues to serve as a model for studying transcription in general. Furthermore, transcription of the regulatory genes is also subject to complex and essential regulation. In addition, databases resulting from a plethora of genome-wide studies have identified regulatory signals that control one of the essential phospholipid biosynthetic genes, PIS1. These databases also provide significant clues for other regulatory signals that may affect phospholipid biosynthesis. Here, we have tried to present a complete summary of the transcription factors and mechanisms that regulate the phospholipid biosynthetic genes.
Collapse
Affiliation(s)
- Meng Chen
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | | | | |
Collapse
|
34
|
Sun N, Carroll RJ, Zhao H. Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc Natl Acad Sci U S A 2006; 103:7988-93. [PMID: 16702552 PMCID: PMC1472417 DOI: 10.1073/pnas.0600164103] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription regulation is a fundamental biological process, and extensive efforts have been made to dissect its mechanisms through direct biological experiments and regulation modeling based on physical-chemical principles and mathematical formulations. Despite these efforts, transcription regulation is yet not well understood because of its complexity and limitations in biological experiments. Recent advances in high throughput technologies have provided substantial amounts and diverse types of genomic data that reveal valuable information on transcription regulation, including DNA sequence data, protein-DNA binding data, microarray gene expression data, and others. In this article, we propose a Bayesian error analysis model to integrate protein-DNA binding data and gene expression data to reconstruct transcriptional regulatory networks. There are two unique aspects to this proposed model. First, transcription is modeled as a set of biochemical reactions, and a linear system model with clear biological interpretation is developed. Second, measurement errors in both protein-DNA binding data and gene expression data are explicitly considered in a Bayesian hierarchical model framework. Model parameters are inferred through Markov chain Monte Carlo. The usefulness of this approach is demonstrated through its application to infer transcriptional regulatory networks in the yeast cell cycle.
Collapse
Affiliation(s)
- Ning Sun
- *Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520; and
| | - Raymond J. Carroll
- Department of Statistics, Texas A&M University, College Station, TX 77843
| | - Hongyu Zhao
- *Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520; and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
35
|
Abraham DS, Vershon AK. N-terminal arm of Mcm1 is required for transcription of a subset of genes involved in maintenance of the cell wall. EUKARYOTIC CELL 2006; 4:1808-19. [PMID: 16278448 PMCID: PMC1287865 DOI: 10.1128/ec.4.11.1808-1819.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The yeast Mcm1 protein is a member of the MADS box family of transcription factors that interacts with several cofactors to differentially regulate genes involved in cell-type determination, mating, cell cycle control and arginine metabolism. Residues 18 to 96 of the protein, which form the core DNA-binding domain of Mcm1, are sufficient to carry out many Mcm1-dependent functions. However, deletion of residues 2 to 17, which form the nonessential N-terminal (NT) arm, confers a salt-sensitive phenotype, suggesting that the NT arm is required for the activation of salt response genes. We used a strategy that combined information from the mutational analysis of the Mcm1-binding site with microarray expression data under salt stress conditions to identify a new subset of Mcm1-regulated genes. Northern blot analysis showed that the transcript levels of several genes encoding associated with the cell wall, especially YGP1, decrease significantly upon deletion of the Mcm1 NT arm. Deletion of the Mcm1 NT arm results in a calcofluor white-sensitive phenotype, which is often associated with defects in transcription of cell wall genes. In addition, the deletion makes cells sensitive to CaCl2 and alkaline pH. We found that the defect caused by removal of the NT arm is not due to changes in Mcm1 protein level, stability, DNA-binding affinity, or DNA bending. This suggests that residues 2 to 17 of Mcm1 may be involved in recruiting a cofactor to the promoters of these genes to activate transcription.
Collapse
Affiliation(s)
- Deepu S Abraham
- Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers University, 190 Frelinghuysen Rd., Piscataway, NJ 08854-8020, USA
| | | |
Collapse
|
36
|
Buckland PR. The importance and identification of regulatory polymorphisms and their mechanisms of action. Biochim Biophys Acta Mol Basis Dis 2005; 1762:17-28. [PMID: 16297602 DOI: 10.1016/j.bbadis.2005.10.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 10/11/2005] [Accepted: 10/11/2005] [Indexed: 01/16/2023]
Abstract
The search for the genetic variations underlying all human phenotypes is in its infancy but must be one of the long term goals of the scientific community. There is evidence that most, if not all human phenotypes, including illnesses are influenced by the genetic makeup of the individual. There are an estimated 11 million human genetic polymorphisms with a minor allele frequency >1% and possibly many times that number of rare sequence variants. The proportion of these sequence variants which have any functional effect is unknown but it is likely that the majority of those which influence illness lie outside of the amino acid coding regions of genes, and affect the regulation of gene expression--these are called rSNPs. Recent research suggests that about 50% of genes have one or more common rSNPs associated with them and probably most if not all genes have an rSNP within the human population. In the long term, determining which polymorphisms are potentially functional must be done bio-informatically using algorithms based upon experimental data. However, at the current time, the limited data that has been obtained does not allow the creation of such an algorithm. In vitro studies suggest that a large proportion of rSNPs lie within the core and proximal promoter regions of genes but it is not clear how the majority of these influence transcription, as they do not appear to be within any known transcription factor binding sites. However, promoter regions possess a number of sequence-dependent characteristics which make them distinct from the rest of the genome, namely stability, curvature and flexibility. Subtle changes to these features may underlie the mechanisms by which many polymorphisms exert their function.
Collapse
Affiliation(s)
- Paul R Buckland
- Department of Psychological Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| |
Collapse
|
37
|
Gardocki ME, Jani N, Lopes JM. Phosphatidylinositol biosynthesis: biochemistry and regulation. Biochim Biophys Acta Mol Cell Biol Lipids 2005; 1735:89-100. [PMID: 15967713 DOI: 10.1016/j.bbalip.2005.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Revised: 05/14/2005] [Accepted: 05/19/2005] [Indexed: 12/22/2022]
Abstract
Phosphatidylinositol (PI) is a ubiquitous membrane lipid in eukaryotes. It is becoming increasingly obvious that PI and its metabolites play a myriad of very diverse roles in eukaryotic cells. The Saccharomyces cerevisiae PIS1 gene is essential and encodes PI synthase, which is required for the synthesis of PI. Recently, PIS1 expression was found to be regulated in response to carbon source and oxygen availability. It is particularly significant that the promoter elements required for these responses are conserved evolutionarily throughout the Saccharomyces genus. In addition, several genome-wide strategies coupled with more traditional screens suggest that several other factors regulate PIS1 expression. The impact of regulating PIS1 expression on PI synthesis will be discussed along with the possible role(s) that this may have on diseases such as cancer.
Collapse
Affiliation(s)
- Mary E Gardocki
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit MI 48202, USA
| | | | | |
Collapse
|
38
|
Abstract
The intracellular signal transduction pathway by which the yeast Saccharomyces cerevisiae responds to the presence of peptide mating pheromone in its surroundings is one of the best understood signaling pathways in eukaryotes, yet continues to generate new surprises and insights. In this review, we take a brief walk down the pathway, focusing on how the signal is transmitted from the cell-surface receptor-coupled G protein, via a MAP kinase cascade, to the nucleus.
Collapse
Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, 2208 Natural Sciences I, University of California, Irvine, CA 92697-2300, USA.
| |
Collapse
|
39
|
Abstract
The intracellular signal transduction pathway by which the yeast Saccharomyces cerevisiae responds to the presence of peptide mating pheromone in its surroundings is one of the best understood signaling pathways in eukaryotes, yet continues to generate new surprises and insights. In this review, we take a brief walk down the pathway, focusing on how the signal is transmitted from the cell-surface receptor-coupled G protein, via a MAP kinase cascade, to the nucleus.
Collapse
Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, 2208 Natural Sciences I, University of California, Irvine, CA 92697-2300, USA.
| |
Collapse
|
40
|
Carr EA, Mead J, Vershon AK. Alpha1-induced DNA bending is required for transcriptional activation by the Mcm1-alpha1 complex. Nucleic Acids Res 2004; 32:2298-305. [PMID: 15118075 PMCID: PMC419449 DOI: 10.1093/nar/gkh560] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The yeast Mcm1 protein is a founding member of the MADS-box family of transcription factors that is involved in the regulation of diverse sets of genes through interactions with distinct cofactor proteins. Mcm1 interacts with the Matalpha1 protein to activate the expression of the alpha-cell type-specific genes. To understand the requirement of the cofactor alpha1 for Mcm1-alpha1-dependent transcriptional activation we analyzed the recruitment of Mcm1 to the promoters of alpha-specific genes in vivo and found that Mcm1 is able to bind to the promoters of alpha-specific genes in the absence of alpha1. This suggests the function of alpha1 is more complex than simply recruiting Mcm1. Several MADS-box transcription factors, including Mcm1, induce DNA bending and there is evidence the proper bend may be required for transcriptional activation. We analyzed Mcm1-dependent bending of a Mcm1-alpha1 binding site in the presence and absence of alpha1 and found that Mcm1 alone shows a reduced DNA-bend at this site compared with other Mcm1 binding sites. However, the addition of alpha1 markedly increases the DNA-bend and we present evidence this bend is required for full transcriptional activation. These results support a model in which proper DNA-bending by the Mcm1-alpha1 complex is required for transcriptional activation.
Collapse
Affiliation(s)
- Edward A Carr
- Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | | | | |
Collapse
|
41
|
Abstract
Here, we search protein-DNA binding data for prevalent pairs and higher-order tuples of co-occurring transcription factors (TF) in Saccharomyces cerevisiae. While the identification of such modules is dependent on uncertainties of genome-wide data sets, we find several biologically meaningful examples, which allow putative annotation of yet unclassified genes. For the frequently occurring transcriptional module Mcm1-Fkh2-Ndd1, we identified several new target genes involved in cell-cycle control and filament formation. Using large-scale protein interaction data, we demonstrate a significant correlation between co-occurrence of TF binding sites and the vicinity in the protein interaction network. In particular we find that directly interacting transcription factors and those which are members of a protein complex are more likely to occur together as putative DNA-binding modules.
Collapse
Affiliation(s)
- Thomas Manke
- Max-Planck-Institute for Molecular Genetics, Abt Bioinformatik, Ihnestr. 73, 14195 Berlin, Germany
| | | | | |
Collapse
|
42
|
Gardocki ME, Lopes JM. Expression of the yeast PIS1 gene requires multiple regulatory elements including a Rox1p binding site. J Biol Chem 2003; 278:38646-52. [PMID: 12890676 DOI: 10.1074/jbc.m305251200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PIS1 gene is required for de novo synthesis of phosphatidylinositol (PI), an essential phospholipid in Saccharomyces cerevisiae. PIS1 gene expression is unusual because it is uncoupled from the other phospholipid biosynthetic genes, which are regulated in response to inositol and choline. Relatively little is known about regulation of transcription of the PIS1 gene. We reported previously that PIS1 transcription is sensitive to carbon source. To further our understanding of the regulation of PIS1 transcription, we carried out a promoter deletion analysis that identified three regions required for PIS1 gene expression (upstream activating sequence (UAS) elements 1-3). Deletion of either UAS1 or UAS2 resulted in an approximately 45% reduction in expression, whereas removal of UAS3 yielded an 84% decrease in expression. A comparison of promoters among several Saccharomyces species shows that these sequences are highly conserved. Curiously, the UAS3 element region (-149 to -138) includes a Rox1p binding site. Rox1p is a repressor of hypoxic genes under aerobic growth conditions. Consistent with this, we have found that expression of a PIS1-cat reporter was repressed under aerobic conditions, and this repression was dependent on both Rox1p and its binding site. Furthermore, PI levels were elevated under anaerobic conditions. This is the first evidence that PI levels are affected by regulation of PIS1 transcription.
Collapse
|
43
|
Messenguy F, Dubois E. Role of MADS box proteins and their cofactors in combinatorial control of gene expression and cell development. Gene 2003; 316:1-21. [PMID: 14563547 DOI: 10.1016/s0378-1119(03)00747-9] [Citation(s) in RCA: 192] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In all organisms, correct development, growth and function depends on the precise and integrated control of the expression of their genes. Often, gene regulation depends upon the cooperative binding of proteins to DNA and upon protein-protein interactions. Eukaryotes have widely exploited combinatorial strategies to create gene regulatory networks. MADS box proteins constitute the perfect example of cellular coordinators. These proteins belong to a large family of transcription factors present in most eukaryotic organisms and are involved in diverse and important biological functions. MADS box proteins are combinatorial transcription factors in that they often derive their regulatory specificity from other DNA binding or accessory factors. This review is aimed at analyzing how MADS box proteins combine with a variety of cofactors to achieve functional diversity.
Collapse
Affiliation(s)
- Francine Messenguy
- Institut de Recherches Microbiologiques J-M Wiame, Université Libre de Bruxelles, Avenue Emile Gryzon 1, 1070 Brussels, Belgium.
| | | |
Collapse
|
44
|
Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 2003; 4:R43. [PMID: 12844359 PMCID: PMC193630 DOI: 10.1186/gb-2003-4-7-r43] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Revised: 04/28/2003] [Accepted: 05/15/2003] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content of eukaryotic genomes it is necessary to consider the co-occurrence and spatial relationships of individual binding sites. The determination of conserved sequences (often known as phylogenetic footprinting) has identified individual transcription factor binding sites. We extend this concept of functional conservation to higher-order features of transcription control regions. RESULTS We used the genome sequences of four yeast species of the genus Saccharomyces to identify sequences potentially involved in multifactorial control of gene expression. We found 989 potential regulatory 'templates': pairs of hexameric sequences that are jointly conserved in transcription regulatory regions and also exhibit non-random relative spacing. Many of the individual sequences in these templates correspond to known transcription factor binding sites, and the sets of genes containing a particular template in their transcription control regions tend to be differentially expressed in conditions where the corresponding transcription factors are known to be active. The incorporation of word pairs to define sequence features yields more specific predictions of average expression profiles and more informative regression models for genome-wide expression data than considering sequence conservation alone. CONCLUSIONS The incorporation of both joint conservation and spacing constraints of sequence pairs predicts groups of target genes that are specific for common patterns of gene expression. Our work suggests that positional information, especially the relative spacing between transcription factor binding sites, may represent a common organizing principle of transcription control regions.
Collapse
Affiliation(s)
- Derek Y Chiang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Alan M Moses
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
| | - Manolis Kellis
- Whitehead/MIT Center for Genome Research, Department of Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric S Lander
- Whitehead/MIT Center for Genome Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Eisen
- Department of Genome Sciences, Life Sciences Division, Ernest Orlando Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Center for Integrative Genomics and Division of Genetics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
45
|
Current awareness on yeast. Yeast 2002; 19:1277-84. [PMID: 12400546 DOI: 10.1002/yea.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|