Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes

Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorised into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: (i) characterisation of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; (ii) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups and (iii) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step towards deciphering the evolution of TCS signaling in living organisms

Histidine kinases : structure and distribution in eukaryotes and functional characterization in Scedosporium apiospermum encountered in cystic fibrosis.

Les histidine kinases (HKs) représentent une vaste famille de protéines impliquées dans la perception des signaux environnementaux chez les bactéries, les champignons et les plantes. Ces protéines joueraient notamment un rôle majeur dans l’adaptation aux stresses, mais aussi dans la virulence de nombreux micro-organismes procaryotes et eucaryotes. Si les HKs sont à présent bien connues chez les bactéries et les plantes, tant sur un plan structural que fonctionnel, les connaissances concernant ces protéines chez les autres clades de l’arbre du vivant demeurent plus que fragmentaires. C’est ainsi que le premier objectif de ce travail a consisté en l’exploration in silico de la structure et de la distribution des HKs chez les organismes eucaryotes dans le cadre de plusieurs études bioinformatiques : i) chez les champignons inférieurs, ii)chez les levures bourgeonnantes et enfin iii) à travers l’ensemble des super-groupes eucaryotes. Les HKs n’étant pas retrouvées chez les mammifères, elles suscitent depuis quelques années une attention particulière de la communauté scientifique en tant que nouvelles cibles pour le développement d’antimicrobiens. C’est précisément dans ce contexte que la partie expérimentale de ce projet a été initiée au sein du GEIHP. Cette équipe porte en effet ses efforts sur le filamenteux multi-résistant Scedosporium apiospermum qui se situe au second rang parmi les moisissures capables de coloniser chroniquement les poumons des patients atteints de mucoviscidose. Ainsi, dans l’optique d’identifier de nouvelles cibles thérapeutiques du champignon, la seconde partie de ce projet s’est focalisée sur la caractérisation fonctionnelle des HKs chez Scedosporium apiospermum. En parallèle, cette étude nous a également amenés à développer de nouveaux outils moléculaires adaptés à S.apiospermum en vue de futures études d’imageries de fluorescence et de bioluminescence.Histidine kinases (HKs) represent a broad family of proteins involved in the perception of environmental signals in bacteria, fungi and plants.These proteins play a major role in stress adaptation, but also in the virulence of many prokaryotic and eukaryotic microorganisms. Although HKs are now well known in bacteria and plants, both structurally and functionally, knowledge about these proteins in other clades of the living tree remains more than fragmentary. Thus the first objective of this work was the in silico exploration of the structure and distribution of HKs in eukaryotic organisms through several bioinformatics studies : i) in the lower fungi, ii)in budding yeasts, and finally iii) across all eukaryotic supergroups. Since HKs are not found in mammals, they have been attracting attention in recent years from the scientific community as new targets for the development of antimicrobials. It is precisely in this context that the experimental part of this project was initiated in the GHEIHP. This team is focusing on the multi-resistant filamentous Scedosporiumapiospermum, which ranks second among the molds capable of chronycally conolizing the lungs of cysticfibrosis patients. Thus, in order to identify new therapeutic targets of the fungus, the second part of this project focused on the functional characterization of HKs in S. apiospermum. In parallel, this study also led us to develop new molecular tools adapted to S. apiospermum for future studies of fluorescence or bioluminescence imaging

Histidine kinases : structure and distribution in eukaryotes and functional characterization in Scedosporium apiospermum encountered in cystic fibrosis.

Les histidine kinases (HKs) représentent une vaste famille de protéines impliquées dans la perception des signaux environnementaux chez les bactéries, les champignons et les plantes. Ces protéines joueraient notamment un rôle majeur dans l’adaptation aux stresses, mais aussi dans la virulence de nombreux micro-organismes procaryotes et eucaryotes. Si les HKs sont à présent bien connues chez les bactéries et les plantes, tant sur un plan structural que fonctionnel, les connaissances concernant ces protéines chez les autres clades de l’arbre du vivant demeurent plus que fragmentaires. C’est ainsi que le premier objectif de ce travail a consisté en l’exploration in silico de la structure et de la distribution des HKs chez les organismes eucaryotes dans le cadre de plusieurs études bioinformatiques : i) chez les champignons inférieurs, ii)chez les levures bourgeonnantes et enfin iii) à travers l’ensemble des super-groupes eucaryotes. Les HKs n’étant pas retrouvées chez les mammifères, elles suscitent depuis quelques années une attention particulière de la communauté scientifique en tant que nouvelles cibles pour le développement d’antimicrobiens. C’est précisément dans ce contexte que la partie expérimentale de ce projet a été initiée au sein du GEIHP. Cette équipe porte en effet ses efforts sur le filamenteux multi-résistant Scedosporium apiospermum qui se situe au second rang parmi les moisissures capables de coloniser chroniquement les poumons des patients atteints de mucoviscidose. Ainsi, dans l’optique d’identifier de nouvelles cibles thérapeutiques du champignon, la seconde partie de ce projet s’est focalisée sur la caractérisation fonctionnelle des HKs chez Scedosporium apiospermum. En parallèle, cette étude nous a également amenés à développer de nouveaux outils moléculaires adaptés à S.apiospermum en vue de futures études d’imageries de fluorescence et de bioluminescence.Histidine kinases (HKs) represent a broad family of proteins involved in the perception of environmental signals in bacteria, fungi and plants.These proteins play a major role in stress adaptation, but also in the virulence of many prokaryotic and eukaryotic microorganisms. Although HKs are now well known in bacteria and plants, both structurally and functionally, knowledge about these proteins in other clades of the living tree remains more than fragmentary. Thus the first objective of this work was the in silico exploration of the structure and distribution of HKs in eukaryotic organisms through several bioinformatics studies : i) in the lower fungi, ii)in budding yeasts, and finally iii) across all eukaryotic supergroups. Since HKs are not found in mammals, they have been attracting attention in recent years from the scientific community as new targets for the development of antimicrobials. It is precisely in this context that the experimental part of this project was initiated in the GHEIHP. This team is focusing on the multi-resistant filamentous Scedosporiumapiospermum, which ranks second among the molds capable of chronycally conolizing the lungs of cysticfibrosis patients. Thus, in order to identify new therapeutic targets of the fungus, the second part of this project focused on the functional characterization of HKs in S. apiospermum. In parallel, this study also led us to develop new molecular tools adapted to S. apiospermum for future studies of fluorescence or bioluminescence imaging

Les récepteurs histidine kinases : structure et distribution chez les eucaryotes et caractérisation fonctionnelle chez l’espèce Scedosporium apiospermum rencontrée au cours de la mucoviscidose.

Histidine kinases (HKs) represent a broad family of proteins involved in the perception of environmental signals in bacteria, fungi and plants.These proteins play a major role in stress adaptation, but also in the virulence of many prokaryotic and eukaryotic microorganisms. Although HKs are now well known in bacteria and plants, both structurally and functionally, knowledge about these proteins in other clades of the living tree remains more than fragmentary. Thus the first objective of this work was the in silico exploration of the structure and distribution of HKs in eukaryotic organisms through several bioinformatics studies : i) in the lower fungi, ii)in budding yeasts, and finally iii) across all eukaryotic supergroups. Since HKs are not found in mammals, they have been attracting attention in recent years from the scientific community as new targets for the development of antimicrobials. It is precisely in this context that the experimental part of this project was initiated in the GHEIHP. This team is focusing on the multi-resistant filamentous Scedosporiumapiospermum, which ranks second among the molds capable of chronycally conolizing the lungs of cysticfibrosis patients. Thus, in order to identify new therapeutic targets of the fungus, the second part of this project focused on the functional characterization of HKs in S. apiospermum. In parallel, this study also led us to develop new molecular tools adapted to S. apiospermum for future studies of fluorescence or bioluminescence imaging.Les histidine kinases (HKs) représentent une vaste famille de protéines impliquées dans la perception des signaux environnementaux chez les bactéries, les champignons et les plantes. Ces protéines joueraient notamment un rôle majeur dans l’adaptation aux stresses, mais aussi dans la virulence de nombreux micro-organismes procaryotes et eucaryotes. Si les HKs sont à présent bien connues chez les bactéries et les plantes, tant sur un plan structural que fonctionnel, les connaissances concernant ces protéines chez les autres clades de l’arbre du vivant demeurent plus que fragmentaires. C’est ainsi que le premier objectif de ce travail a consisté en l’exploration in silico de la structure et de la distribution des HKs chez les organismes eucaryotes dans le cadre de plusieurs études bioinformatiques : i) chez les champignons inférieurs, ii)chez les levures bourgeonnantes et enfin iii) à travers l’ensemble des super-groupes eucaryotes. Les HKs n’étant pas retrouvées chez les mammifères, elles suscitent depuis quelques années une attention particulière de la communauté scientifique en tant que nouvelles cibles pour le développement d’antimicrobiens. C’est précisément dans ce contexte que la partie expérimentale de ce projet a été initiée au sein du GEIHP. Cette équipe porte en effet ses efforts sur le filamenteux multi-résistant Scedosporium apiospermum qui se situe au second rang parmi les moisissures capables de coloniser chroniquement les poumons des patients atteints de mucoviscidose. Ainsi, dans l’optique d’identifier de nouvelles cibles thérapeutiques du champignon, la seconde partie de ce projet s’est focalisée sur la caractérisation fonctionnelle des HKs chez Scedosporium apiospermum. En parallèle, cette étude nous a également amenés à développer de nouveaux outils moléculaires adaptés à S.apiospermum en vue de futures études d’imageries de fluorescence et de bioluminescence

SAKrificing an Essential Stress-Sensing Pathway Improves Aspergillus fumigatus Germination

International audienceFungal infections represent a major problem in human health. This is particularly the case of infections caused by the filamentous fungus Aspergillus fumigatus , affecting millions of people worldwide

Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients

Abstract Rationale Recent studies have revealed that the lung microbiota of critically ill patients is altered and predicts clinical outcomes. The incidence of invasive fungal infections, namely, invasive pulmonary aspergillosis (IPA), in immunocompromised patients is increasing, but the clinical significance of variations in lung bacterial communities is unknown. Objectives To define the contribution of the lung microbiota to the development and course of IPA. Methods and measurements We performed an observational cohort study to characterise the lung microbiota in 104 immunocompromised patients using bacterial 16S ribosomal RNA gene sequencing on bronchoalveolar lavage samples sampled on clinical suspicion of infection. Associations between lung dysbiosis in IPA and pulmonary immunity were evaluated by quantifying alveolar cytokines and chemokines and immune cells. The contribution of microbial signatures to patient outcome was assessed by estimating overall survival. Main results Patients diagnosed with IPA displayed a decreased alpha diversity, driven by a markedly increased abundance of the Staphylococcus, Escherichia, Paraclostridium and Finegoldia genera and a decreased proportion of the Prevotella and Veillonella genera. The overall composition of the lung microbiome was influenced by the neutrophil counts and associated with differential levels of alveolar cytokines. Importantly, the degree of bacterial diversity at the onset of IPA predicted the survival of infected patients. Conclusions Our results reveal the lung microbiota as an understudied source of clinical variation in patients at risk of IPA and highlight its potential as a diagnostic and therapeutic target in the context of respiratory fungal diseases.This work was supported by the Fundação para a Ciência e a Tecnologia (FCT) (PTDC/SAU-SER/29635/2017 to CC and PTDC/MED-GEN/28778/2017 to AC). Additional support was provided by FCT (UIDB/50026/2020 and UIDP/50026/2020); the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) (NORTE-01-0145-FEDER-000013 and NORTE-01-0145-FEDER-000023); the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement number 847507 (to AC); and the “la Caixa” Foundation (ID 100010434) and FCT under the agreement LCF/PR/HR17/52190003 (to AC). Individual support was provided by FCT (SFRH/BD/136814/2018 to SMG, CEECIND/03628/2017 to AC and CEECIND/04058/2018 to CC). The TG group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by the ERDF, the CERCA Programme/Generalitat de Catalunya, the Catalan Research Agency (AGAUR) SGR423, the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement ERC-2016-724173 and an INB Grant (PT17/0009/0023—ISCIII-SGEFI/ERDF).Peer ReviewedPostprint (author's final draft

Milestones in the discovery of histidine kinases (HKs) and currently accepted canonical signaling pathways involving HKs in prokaryotes, plants, amoebae, and fungi.

<p>(A) Historical timeline depicting the evolution of knowledge concerning HKs. In the order of appearance from left to right: the EnvZ osmosensor in <i>Escherichia coli</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref001" target="_blank">1</a>], the phytohormone ethylene receptor ETR1 in <i>Arabidopsis thaliana</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref002" target="_blank">2</a>], the Sln1 osmosensor in <i>Saccharomyces cerevisiae</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref003" target="_blank">3</a>], the RcaE cyanobacteriochrome [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref005" target="_blank">5</a>], the discadenine receptor DhkA in <i>Dictyostelium discoideum</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref006" target="_blank">6</a>], the quorum sensing-associated Chk1 in <i>Candida albicans</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref026" target="_blank">26</a>], the virulence factor Fos-1 in <i>Aspergillus fumigatus</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref027" target="_blank">27</a>], the dimorphism-related Drk1 in <i>Blastomyces dermatitidis</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref028" target="_blank">28</a>], the Bos-1 osmosensor in <i>Botrytis cinerea</i> [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref029" target="_blank">29</a>], the <i>Cryptococcus neoformans</i> Tco1 and Tco2 (a first functionally characterized dual HK) [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref030" target="_blank">30</a>], and the <i>Metarhizium robertsii</i> Mhk1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref031" target="_blank">31</a>]. (B) Canonical schemes depicting signaling pathways involving HKs in prokaryotes, amoebae, plants, and fungi. In prokaryotes, most signaling pathways involving HKs simply consist of two components. The perception of a stimulus by the sensor domain (grey box) induces the autophosphorylation of a conserved histidine (H, pink box) by the catalytic domain (N G₁ F G₂, yellow box) in the HK. The phosphate is then transferred to a conserved aspartate residue (D) located on a cytosolic response regulator (RR) and the activated RR governs the expression of response genes. In plant cells, most (but not all) HKs constitute the initial sensing proteins of a four-step phosphorelay signaling pathway involving phosphorylation events of two downstream elements, i.e., histidine phosphotransfer shuttle proteins (Hpt) and RRs. Note that a first phosphorylatable receiver domain (DDK) is fused to the catalytic domain (N G₁ F G₂) in the HK. As observed for the archetypal two-component system in prokaryotes, the activated RR governs the expression of response genes. In amoebae, similarly to plants, a four-step phosphorelay signaling pathway is observed, but this latter controls a downstream cyclic AMP pathway. Finally, in fungi, knowledge is very fragmented, but initial studies in <i>Saccharomyces cerevisiae</i> have demonstrated that HKs also constitute the initial sensing proteins of a four-step phosphorelay signaling pathway that governs a cascade of mitogen-activated protein (MAP) kinases.</p

Structure, classification, function, and distribution of fungal HKs at a glance.

<p>(A) Basic structure of fungal HKs. They are composed of three main regions: a highly variable N-terminal sequence that determines which stimulus is perceived by the HK (“sensor” domain), a central transmitter domain consisting of both histidine kinase A (HisKA) and cognate histidine kinase-like ATPase catalytic subdomains (HATPase_c), and a C-terminal receiver domain showing a three amino-acids signature (DDK). Fungal HKs are currently categorized in 16 groups according to the sequence analysis of two regions: the H-box signature (alignment of group III HKs from major pathogenic fungi are provided in the right panel) containing the phosphorylatable histidine (red background) and the combination of domains found in the N-terminus. Domains that compose the N-terminal sensor region of major HK groups, whose functions have been at least partially characterized, are provided on the left panel. Abbreviations: HAMP, Histidine kinases-Adenylate cyclases-Methyl accepting proteins and Phosphatases; TH, Transmembrane Helix; PAS, Period circadian protein-Aryl hydrocarbon receptor nuclear translocator protein-Single-minded protein; GAF, cGMP-specific phosphodiesterases-Adenylyl cyclases-FhlA; PHY, Phytochrome; S/Tkrd, Serine/Threonine kinase related domain. (B) Some notable functions currently assigned to the prominent groups III, VI, VIII, X, and dual HKs (for more details see [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005683#ppat.1005683.ref011" target="_blank">11</a>]). (C) Quantitative and qualitative distribution of HKs in fungal clades. The total number of HKs and the occurrence of major HK groups are provided for a panel of representative well-known pathogenic and non-pathogenic (n-p) fungi. A grey box signifies that the corresponding HK groups are not observed in the species. A colored box signifies that a unique member of the corresponding HK group is found in the species and the number of members is only indicated when many members are observed. Abbreviations: A, Ascomycota; B; Basidiomycota; Pe, Pezizomycotina; Sa, Saccharomycotina; Ta, Taphrinomycotina; Us, Ustilaginomycotina, Pu, Pucciniomycotina; Ag, Agaricomycotina; Mu, Mucoromycotina; Mi, Microsporidia.</p