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Luo Z, Xiong D, Tian C. The Roles of Gti1/Pac2 Family Proteins in Fungal Growth, Morphogenesis, Stress Response, and Pathogenicity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:488-497. [PMID: 38427716 DOI: 10.1094/mpmi-11-23-0198-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Gti1/Pac2 is a fungal-specific transcription factor family with a stable and conserved N-terminal domain. Generally, there are two members in this family, named Gti1/Wor1/Rpy1/Mit1/Reg1/Ros1/Sge1 and Pac2, which are involved in fungal growth, development, stress response, spore production, pathogenicity, and so on. The Gti1/Pac2 family proteins share some conserved and distinct functions. For example, in Schizosaccharomyces pombe, Gti1 promotes the initiation of gluconate uptake during glucose starvation, while Pac2 controls the onset of sexual development in a pathway independent of the cAMP cascade. In the last two decades, more attention was focused on the Gti1 and its orthologs because of their significant effect on morphological switching and fungal virulence. By contrast, limited work was published on the functions of Pac2, which is required for stress responses and conidiation, but plays a minor role in fungal virulence. In this review, we present an overview of our current understanding of the Gti1/Pac2 proteins that contribute to fungal development and/or pathogenicity and of the regulation mechanisms during infection related development. Understanding the working networks of the conserved Gti1/Pac2 transcription factors in fungal pathogenicity not only advances our knowledge of the highly elaborate infection process but may also lead to the development of novel strategies for the control of plant disease. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zheng Luo
- State Key laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Dianguang Xiong
- State Key laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Chengming Tian
- State Key laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Andreu C, Del Olmo ML. Biotechnological applications of biofilms formed by osmotolerant and halotolerant yeasts. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12589-y. [PMID: 37233754 DOI: 10.1007/s00253-023-12589-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Many microorganisms are capable of developing biofilms under adverse conditions usually related to nutrient limitation. They are complex structures in which cells (in many cases of different species) are embedded in the material that they secrete, the extracellular matrix (ECM), which is composed of proteins, carbohydrates, lipids, and nucleic acids. The ECM has several functions including adhesion, cellular communication, nutrient distribution, and increased community resistance, this being the main drawback when these microorganisms are pathogenic. However, these structures have also proven useful in many biotechnological applications. Until now, the most interest shown in these regards has focused on bacterial biofilms, and the literature describing yeast biofilms is scarce, except for pathological strains. Oceans and other saline reservoirs are full of microorganisms adapted to extreme conditions, and the discovery and knowledge of their properties can be very interesting to explore new uses. Halotolerant and osmotolerant biofilm-forming yeasts have been employed for many years in the food and wine industry, with very few applications in other areas. The experience gained in bioremediation, food production and biocatalysis with bacterial biofilms can be inspiring to find new uses for halotolerant yeast biofilms. In this review, we focus on the biofilms formed by halotolerant and osmotolerant yeasts such as those belonging to Candida, Saccharomyces flor yeasts, Schwannyomyces or Debaryomyces, and their actual or potential biotechnological applications. KEY POINTS: • Biofilm formation by halotolerant and osmotolerant yeasts is reviewed. • Yeasts biofilms have been widely used in food and wine production. • The use of bacterial biofilms in bioremediation can be expanded to halotolerant yeast counterparts.
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Affiliation(s)
- Cecilia Andreu
- Departament de Química Orgànica, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés S/N, 46100, València, Burjassot, Spain
| | - Marcel Lí Del Olmo
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de València, Dr. Moliner 50, 46100, València, Burjassot, Spain.
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Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang RY, Climie D, Usaj M, Hotz M, Stoops EH, Baryshnikova A, Boone C, Botstein D, Andrews BJ, McIsaac RS. A genome-scale yeast library with inducible expression of individual genes. Mol Syst Biol 2021; 17:e10207. [PMID: 34096681 PMCID: PMC8182650 DOI: 10.15252/msb.202110207] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022] Open
Abstract
The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which > 5,600 yeast genes are engineered for transcriptional inducibility with single-gene precision at their native loci and without plasmids. Each strain contains SGA screening markers and a unique barcode, enabling high-throughput genetics. We characterized YETI using growth phenotyping and BAR-seq screens, and we used a YETI allele to identify the regulon of Rof1, showing that it acts to repress transcription. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from eukaryotic and prokaryotic systems shows that native expression is a variable that can bias promoter-perturbing screens, including CRISPRi. We engineered a second expression system, Z3 EB42, that gives lower expression than Z3 EV, a feature enabling conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.
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Affiliation(s)
- Yuko Arita
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- RIKEN Centre for Sustainable Resource ScienceWakoSaitamaJapan
| | - Griffin Kim
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | - Zhijian Li
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Helena Friesen
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Gina Turco
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | | | - Dale Climie
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Matej Usaj
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Manuel Hotz
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | | | | | - Charles Boone
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- RIKEN Centre for Sustainable Resource ScienceWakoSaitamaJapan
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | | | - Brenda J Andrews
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
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Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes 2020; 6:2. [PMID: 31934344 PMCID: PMC6954232 DOI: 10.1038/s41522-019-0113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/16/2019] [Indexed: 01/28/2023] Open
Abstract
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
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Affiliation(s)
- Janne G. Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nora Grahl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven D. Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Mathias Müsken
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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Erdmann J, Thöming JG, Pohl S, Pich A, Lenz C, Häussler S. The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates. Cells 2019; 8:E1129. [PMID: 31547513 PMCID: PMC6829490 DOI: 10.3390/cells8101129] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/13/2022] Open
Abstract
Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.
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Affiliation(s)
- Jelena Erdmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
| | - Andreas Pich
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Christof Lenz
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Göttingen 37075, Germany.
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen 37077, Germany.
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
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Selvarajoo K. Large‐scale‐free network organisation is likely key for biofilm phase transition. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2019.0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kumar Selvarajoo
- Computational and Systems Biology, Biotransformation Innovation Platform (BioTrans), Agency for Science Technology & Research (A*STAR) 61 Biopolis Drive Proteos 13873 Singapore
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Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics 2019; 212:667-690. [PMID: 31053593 DOI: 10.1534/genetics.119.302004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/18/2019] [Indexed: 01/07/2023] Open
Abstract
Signaling pathways can regulate biological responses by the transcriptional regulation of target genes. In yeast, multiple signaling pathways control filamentous growth, a morphogenetic response that occurs in many species including fungal pathogens. Here, we examine the role of signaling pathways that control filamentous growth in regulating adhesion-dependent surface responses, including mat formation and colony patterning. Expression profiling and mutant phenotype analysis showed that the major pathways that regulate filamentous growth [filamentous growth MAPK (fMAPK), RAS, retrograde (RTG), RIM101, RPD3, ELP, SNF1, and PHO85] also regulated mat formation and colony patterning. The chromatin remodeling complex, SAGA, also regulated these responses. We also show that the RAS and RTG pathways coregulated a common set of target genes, and that SAGA regulated target genes known to be controlled by the fMAPK, RAS, and RTG pathways. Analysis of surface growth-specific targets identified genes that respond to low oxygen, high temperature, and desiccation stresses. We also explore the question of why cells make adhesive contacts in colonies. Cell adhesion contacts mediated by the coregulated target and adhesion molecule, Flo11p, deterred entry into colonies by macroscopic predators and impacted colony temperature regulation. The identification of new regulators (e.g., SAGA), and targets of surface growth in yeast may provide insights into fungal pathogenesis in settings where surface growth and adhesion contributes to virulence.
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Piras V, Chiow A, Selvarajoo K. Long‐range order and short‐range disorder in
Saccharomyces cerevisiae
biofilm. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2018.5008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Université Paris‐Sud, Université Paris‐Saclay avenue de la Terrasse 91198 Gif‐sur‐Yvette Cedex France
| | - Adam Chiow
- Department of Pharmaceutical Engineering Singapore Institute of Technology 10 Dover Drive Singapore 138683 Singapore
| | - Kumar Selvarajoo
- Biotransformation Innovation Platform (BioTrans) Agency for Science, Technology & Research A∗STAR 61 Biopolis Drive, Proteos Singapore 138673 Singapore
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Selvarajoo K. Order Parameter in Bacterial Biofilm Adaptive Response. Front Microbiol 2018; 9:1721. [PMID: 30093898 PMCID: PMC6070729 DOI: 10.3389/fmicb.2018.01721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kumar Selvarajoo
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research ASTAR, Singapore, Singapore
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Natural Variation in SER1 and ENA6 Underlie Condition-Specific Growth Defects in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:239-251. [PMID: 29138237 PMCID: PMC5765352 DOI: 10.1534/g3.117.300392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of Saccharomyces cerevisiae. Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to SER1, which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, PSAT1. To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol. Consistent with studies that found widespread effects of different auxotrophies on RNA expression patterns in rich media, we find that the SER1 loss-of-function allele dominates the quantitative trait locus (QTL) landscape under many of these conditions, with a notable exacerbation of the effect in the presence of rapamycin and caffeine. We also identify a major-effect QTL associated with growth on salt that maps to the gene encoding the sodium exporter, ENA6. We demonstrate that the salt phenotype is largely driven by variation in the ENA6 promoter, which harbors a deletion that removes binding sites for the Mig1 and Nrg1 transcriptional repressors. Thus, our results identify natural variation associated with both coding and regulatory regions of the genome that underlie strong growth phenotypes.
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