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Mina S, Hérivaux A, Yaakoub H, Courdavault V, Wéry M, Papon N. Structure and distribution of sensor histidine kinases in the fungal kingdom. Curr Genet 2024; 70:17. [PMID: 39276214 DOI: 10.1007/s00294-024-01301-w] [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: 05/24/2024] [Revised: 07/02/2024] [Accepted: 08/17/2024] [Indexed: 09/16/2024]
Abstract
Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.
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Affiliation(s)
- Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
| | - Anaïs Hérivaux
- Univ Angers, Univ Brest, IRF, SFR ICAT, Angers, F-49000, France
| | - Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, Angers, F-49000, France
- Nantes-Université, INRAE, UMR 1280, PhAN, Nantes, 44000, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Méline Wéry
- Univ Angers, SFR ICAT, Angers, F-49000, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, Angers, F-49000, France.
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2
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Herman K, Bleichrodt R. Go with the flow: mechanisms driving water transport during vegetative growth and fruiting. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Predicted Functional and Structural Diversity of Receiver Domains in Fungal Two-Component Regulatory Systems. mSphere 2021; 6:e0072221. [PMID: 34612676 PMCID: PMC8510515 DOI: 10.1128/msphere.00722-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fungal two-component regulatory systems incorporate receiver domains into hybrid histidine kinases (HHKs) and response regulators. We constructed a nonredundant database of 670 fungal receiver domain sequences from 51 species sampled from nine fungal phyla. A much greater proportion (21%) of predicted fungal response regulators did not belong to known groups than previously appreciated. Receiver domains in Rim15 response regulators from Ascomycota and other phyla are very different from one another, as are the duplicate receiver domains in group XII HHKs. Fungal receiver domains from five known types of response regulators and 20 known types of HHKs exhibit distinct patterns of amino acids at conserved and variable positions known to be structurally and functionally important in bacterial receiver domains. We inferred structure/activity relationships from the patterns and propose multiple experimentally testable hypotheses about the mechanisms of signal transduction mediated by fungal receiver domains.
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Bourret RB, Kennedy EN, Foster CA, Sepúlveda VE, Goldman WE. A Radical Reimagining of Fungal Two-Component Regulatory Systems. Trends Microbiol 2021; 29:883-893. [PMID: 33853736 DOI: 10.1016/j.tim.2021.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
Bacterial two-component regulatory systems (TCSs) mediate signal transduction by transferring phosphoryl groups between sensor kinase and response regulator proteins, sometimes using intermediary histidine-phosphotransferase (Hpt) domains to form multistep phosphorelays. Because (i) almost all known fungal sensor kinases exhibit a domain architecture characteristic of bacterial TCS phosphorelays, (ii) all known fungal Hpts are stand-alone proteins suited to shuttle between cytoplasm and nucleus, and (iii) the best-characterized fungal TCS is a canonical phosphorelay, it is widely assumed that most or all fungal TCSs function via phosphorelays. However, fungi generally encode more sensor kinases than Hpts or response regulators, leading to a disparity between putative phosphorelay inputs and outputs. The simplest resolution of this paradox is to hypothesize that most fungal sensor kinases do not participate in phosphorelays. Reimagining how fungal TCSs might function leads to multiple testable predictions.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
| | - Emily N Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Clay A Foster
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Victoria E Sepúlveda
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - William E Goldman
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
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Progressive loss of hybrid histidine kinase genes during the evolution of budding yeasts (Saccharomycotina). Curr Genet 2017; 64:841-851. [DOI: 10.1007/s00294-017-0797-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 11/26/2022]
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Navarro-Arias MJ, Dementhon K, Defosse TA, Foureau E, Courdavault V, Clastre M, Le Gal S, Nevez G, Le Govic Y, Bouchara JP, Giglioli-Guivarc'h N, Noël T, Mora-Montes HM, Papon N. Group X hybrid histidine kinase Chk1 is dispensable for stress adaptation, host–pathogen interactions and virulence in the opportunistic yeast Candida guilliermondii. Res Microbiol 2017; 168:644-654. [DOI: 10.1016/j.resmic.2017.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/03/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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Kilani J, Fillinger S. Phenylpyrroles: 30 Years, Two Molecules and (Nearly) No Resistance. Front Microbiol 2016; 7:2014. [PMID: 28018333 PMCID: PMC5159414 DOI: 10.3389/fmicb.2016.02014] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/01/2016] [Indexed: 12/30/2022] Open
Abstract
Phenylpyrroles are chemical analogs of the natural antifungal compound pyrrolnitrin. Fenpiclonil, but mainly fludioxonil are registered against multiple fungal crop diseases since over 25 years for seed or foliar treatment. They have severe physiological impacts on the pathogen, including membrane hyperpolarization, changes in carbon metabolism and the accumulation of metabolites leading to hyphal swelling and burst. The selection and characterization of mutants resistant to phenylpyrroles have revealed that these fungicides activate the fungal osmotic signal transduction pathway through their perception by a typical fungal hybrid histidine kinase (HHK). The HHK is prone to point mutations that confer fungicide resistance and affect its sensor domain, composed of tandem repeats of HAMP motifs. Fludioxonil resistant mutants have been selected in many fungal species under laboratory conditions. Generally they present severe impacts on fitness parameters. Since only few cases of field resistance specific to phenylpyrroles have been reported one may suspect that the fitness penalty of phenylpyrrole resistance is the reason for the lack of field resistance.
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Affiliation(s)
- Jaafar Kilani
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris SaclayThiverval-Grignon, France
- Université Paris-Sud, Université Paris-SaclayOrsay, France
| | - Sabine Fillinger
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris SaclayThiverval-Grignon, France
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Lavín JL, Ramírez L, Pisabarro AG, Oguiza JA. Genomewide analysis of phytochrome proteins in the phylum Basidiomycota. J Basic Microbiol 2015; 55:1141-7. [PMID: 25847700 DOI: 10.1002/jobm.201500078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/20/2015] [Indexed: 11/07/2022]
Abstract
Phytochromes are photoreceptor proteins involved in the detection of the red and far-red regions of the visible light spectrum. Fungal phytochromes are hybrid histidine kinases with a conserved domain architecture composed of an N-terminal photosensory module and a C-terminal regulatory output module that includes the histidine kinase and response regulator receiver domains. In this study, we have analyzed the distribution, domain architecture, and phylogenetic analysis of phytochrome proteins in 47 published genome sequences among the phylum Basidiomycota. Genome analysis revealed that almost every genome of basidiomycetes contained at least one gene encoding a phytochrome protein. Domain architecture of fungal phytochromes was completely conserved in the identified phytochromes of basidiomycetes, and phylogenetic analysis clustered these proteins into clades related with the phylogenetic classification of this fungal phylum.
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Affiliation(s)
- José L Lavín
- Genome Analysis Platform, Functional Genomics Unit, CIC bioGUNE & CIBERehd, Bizkaia Technology Park, Derio, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Spain
| | - José A Oguiza
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Spain
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Defosse TA, Sharma A, Mondal AK, Dugé de Bernonville T, Latgé JP, Calderone R, Giglioli-Guivarc'h N, Courdavault V, Clastre M, Papon N. Hybrid histidine kinases in pathogenic fungi. Mol Microbiol 2015; 95:914-24. [DOI: 10.1111/mmi.12911] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Tatiana A. Defosse
- Biomolécules et Biotechnologies Végétales; EA 2106; Université François-Rabelais de Tours; Tours France
| | | | - Alok K. Mondal
- Institute of Microbial Technology; Chandigarh India
- School of Life Sciences; Jawaharlal Nehru University; New Delhi India
| | | | | | - Richard Calderone
- Georgetown University Medical Center; Department of Microbiology & Immunology; Washington DC USA
| | | | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales; EA 2106; Université François-Rabelais de Tours; Tours France
| | - Marc Clastre
- Biomolécules et Biotechnologies Végétales; EA 2106; Université François-Rabelais de Tours; Tours France
| | - Nicolas Papon
- Biomolécules et Biotechnologies Végétales; EA 2106; Université François-Rabelais de Tours; Tours France
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10
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Dual-histidine kinases in basidiomycete fungi. C R Biol 2014; 337:111-6. [PMID: 24581805 DOI: 10.1016/j.crvi.2013.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 12/15/2013] [Accepted: 12/17/2013] [Indexed: 11/20/2022]
Abstract
Dual-histidine kinases (HKs) are complex hybrid HKs containing in a single polypeptide two HK transmitter modules (T) and two-response regulator received domains (R) that are combined in a TRTR geometry. In fungi, this protein family is limited to some particular species of the phylum Basidiomycota and absent in the other phyla. This study extends the investigation of dual-HKs to 80 fully sequenced genomes of basidiomycetes, analyzing their distribution, domain architecture and phylogenetic relationships. Moreover, similarly to dual-HKs of basidiomycetes, several species of bacteria were found that contain hybrid HKs with a TRTR domain architecture encoded in a single gene.
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11
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Lavín JL, García-Yoldi A, Ramírez L, Pisabarro AG, Oguiza JA. Two-component signal transduction in Agaricus bisporus: a comparative genomic analysis with other basidiomycetes through the web-based tool BASID2CS. Fungal Genet Biol 2012; 55:77-84. [PMID: 23123423 DOI: 10.1016/j.fgb.2012.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 09/28/2012] [Accepted: 09/29/2012] [Indexed: 11/16/2022]
Abstract
Two-component systems (TCSs) are signal transduction mechanisms present in many eukaryotes, including fungi that play essential roles in the regulation of several cellular functions and responses. In this study, we carry out a genomic analysis of the TCS proteins in two varieties of the white button mushroom Agaricus bisporus. The genomes of both A. bisporus varieties contain eight genes coding for TCS proteins, which include four hybrid Histidine Kinases (HKs), a single histidine-containing phosphotransfer (HPt) protein and three Response Regulators (RRs). Comparison of the TCS proteins among A. bisporus and the sequenced basidiomycetes showed a conserved core complement of five TCS proteins including the Tco1/Nik1 hybrid HK, HPt protein and Ssk1, Skn7 and Rim15-like RRs. In addition, Dual-HKs, unusual hybrid HKs with 2 HK and 2 RR domains, are absent in A. bisporus and are limited to various species of basidiomycetes. Differential expression analysis showed no significant up- or down-regulation of the Agaricus TCS genes in the conditions/tissue analyzed with the exception of the Skn7-like RR gene (Agabi_varbisH97_2|198669) that is significantly up-regulated on compost compared to cultured mycelia. Furthermore, the pipeline web server BASID2CS (http://bioinformatics.unavarra.es:1000/B2CS/BASID2CS.htm) has been specifically designed for the identification, classification and functional annotation of putative TCS proteins from any predicted proteome of basidiomycetes using a combination of several bioinformatic approaches.
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Affiliation(s)
- José L Lavín
- Genetics and Microbiology Research Group, Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain
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12
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Li D, Agrellos OA, Calderone R. Histidine kinases keep fungi safe and vigorous. Curr Opin Microbiol 2010; 13:424-30. [PMID: 20542727 DOI: 10.1016/j.mib.2010.04.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/23/2010] [Accepted: 04/27/2010] [Indexed: 01/10/2023]
Abstract
Signal transduction in human pathogenic fungi, like in other microorganisms, regulates a number of adaptive transcriptional responses to a variety of environmental cues. Among signal relay proteins, sensor, histidine kinase proteins (HK) are auto-phosphorylated upon perception of an environmental cue, and initiate a phosphorelay that results in transcriptional regulation of genes associated with specific stress signals or multiple stress cues. Human pathogenic fungi utilize HK proteins to adapt to stress, grow, sporulate, undergo morphogenesis, mate, sense anti-fungal drugs, and cause disease. While much is known about HK and RR proteins functionally, the MAPK pathways and downstream transcription factors and gene targets are largely unstudied in human pathogenic fungi. However, as HK proteins are broadly conserved and not apparently in humans, we suggest that they offer exploitation as new targets in anti-fungal drug discovery.
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Affiliation(s)
- Dongmei Li
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
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