Research Article: Major Sensing Proteins in Pathogenic Fungi: The Hybrid Histidine Kinase Family

Date Published: July 28, 2016

Publisher: Public Library of Science

Author(s): Anaïs Hérivaux, Yee-Seul So, Amandine Gastebois, Jean-Paul Latgé, Jean-Philippe Bouchara, Yong-Sun Bahn, Nicolas Papon, Deborah A. Hogan.


Partial Text

The pioneering discovery of histidine kinases (HKs) from Escherichia coli was made in the early 1980s with the identification of the envZ gene [1] (Fig 1A). Further biochemical characterization of the corresponding protein revealed a new type of protein kinase activity, namely HK, to add to the well-known serine/threonine and tyrosine kinases. For a decade, HKs were considered to be restricted to bacteria, but in the 1990s, HKs were identified in plants [2], fungi [3], archaea [4], cyanobacteria [5], and amoebae (Fig 1A) [6]. Soon after, evidence suggested that HKs regulate essential processes in pathogenic bacteria and fungi [7]. Although some HKs appear to be present in humans, typical bacterial or fungal HK-like sensor proteins have not been reported yet in mammals [8], promoting these proteins as ideal targets for future therapeutics [9].

The basic structure of fungal HKs is now well established. They are composed of three main regions (Fig 2A). The first region corresponds to a highly variable N-terminal sequence that determines which stimulus is perceived by the HK. This region is referred to as the “sensor domain.” The central region is the transmitter domain consisting of both histidine kinase A (HisKA) (dimerization/phosphoacceptor) (Fig 2A) and cognate histidine kinase-like ATPase catalytic (HATPase_c) (Fig 2A) subdomains. HisKA domains include an H-box, usually containing a phosphorylatable histidine (see Fig 2A), and an X-box. The HATPase_c subdomain displays four distinct boxes: N-, G1- (sometimes called D-box), F-, and G2-boxes. The third and final region, well conserved in fungal HKs, is the C-terminal receiver domain (RD) (Fig 2A) characterized by the presence of a three amino-acids signature (DDK) including a phosphorylatable aspartate residue (see Fig 2A) [10]. Another important aspect is that fungal HKs are generically defined as hybrid HKs since the transmitter domain is fused to the receiver domain (Fig 1B).

HKs are key signaling proteins involved in the perception and the transduction of a wide range of environmental stimuli in prokaryotes, amoebae, and plants. HKs are also widespread in the fungal kingdom, but their precise roles in the regulation of physiological processes remain fragmentary. The function of several fungal HKs has been studied over the last 15 years using classical reverse genetic approaches, mainly by creating targeted mutants and comparing them with the wild type strain (for a review see [11]). This approach has given insight into the involvement of some fungal HK groups in the response and adaptation to environmental conditions. The most striking associations reported between fungal HKs and physiological processes are summarized below and in Fig 2B.

HKs are widespread in all fungal clades with the exception of Pneumocystidiomycetes (e.g., Pneumocystis jirovecii, the causal agent of pneumocystosis, Fig 2C) and microsporidia (e.g., Enterocytozoon bieneusi, a causal agent of microsporidiasis, Fig 2C). In light of new genomic data, the initial conviction that Ascomycota harbor the largest number of HKs was recently revised. Surprisingly, some previously unexplored early diverging fungal lineages, such as Mucoromycotina (e.g., the fungal pathogen Lichtheimia corymbifera, an agent of human mucormycosis, Fig 2C) and its closely clade Entomophtoromycotina (e.g., Basidiobolus sp. and Conidiobolus sp., agents of human entomophtoromycosis), includes species with about 15–20 predicted HKs [11]. Nevertheless, it is accepted that Ascomycete yeasts (e.g., Candida albicans, Fig 2C) contain fewer HKs than filamentous Ascomycete species (Fig 2C), in which the number of HKs appears particularly variable. Some filamentous Ascomycete families have species that display a large series of HKs, such as Dothideomycetes (e.g., the plant pathogen Zymoseptoria tritici, Fig 2C) or Orbiliomycetes (e.g., the nematode trapping fungus Arthrobotrys oligospora, Fig 2C). However, it is important to note that even within a family, the total number of HKs can drastically differ between species. For example, in Sordariomycetes, Fusarium verticillioides (a pathogen of maize producing deadly mycotoxins) encodes 16 HKs [12], whereas only 9 HK-encoding genes are present in the genome of Beauveria bassiana (a prominent insect pathogen, Fig 2C) [11]. Even more strikingly, in Leotiomycetes, Botrytis cinerea (the cause of the gray mold on many plants) encodes 20 HKs [12], whereas Pseudogymnoascus destructans (the causal agent of the white-nose syndrome in bats, Fig 2C) contains only 6 predicted HKs.

Many functional and evolutionary aspects concerning HKs in the fungal kingdom are still largely uncharted. However, we can assume that the recent expansion of genomic resources along with improved genetic approaches for studying pathogenic fungi (see [22] for a review) will contribute to broadened knowledge about fungal HKs. It is likely that the availability of new genome sequences will aid in identifying unknown HK structures/groups, which will help complete the current classification of this protein family. In the same way, comparative genomics should also expedite comprehensive phylogenetic analyses, enabling us to decipher the evolutionary path that led to the appearance, transfer, duplication, and loss of HK genes in fungi. As recently observed for few species [23,24], the development of novel efficient gene disruption strategies now promotes systematic multiple gene deletions in molds that bear a large number of HKs. In the near future, these powerful genetic approaches will likely help in deciphering (1) the role of each HK in a species, (2) putative genetic interactions, and (3) the basis of their apparent functional redundancy. In addition, although basic HK-mediated signal transduction routes are well characterized, downstream interacting partners and the global architecture of the signaling pathway involving fungal HKs remain critical missing pieces in this field. For instance, fluorescence microscopy technics can provide insight into the subcellular localization of fungal HKs [25]. Notably, with the exception of group VI HKs harboring transmembrane regions, most HKs are not predicted to be localized on the cell surface. Therefore, it will be intriguing to study how an environmental signal is translated into intracellular input signal for intracellular HKs and even a possibility that HKs may collaborate with other sensor proteins. Additionally, it will be highly relevant to determine which of the known HK groups directly communicates with the only currently known downstream candidate, the phosphotransfer shuttle protein Ypd1 (see Fig 1B), and to identify unknown downstream interacting partners. It is puzzling how different signals coming from different HKs are converged into Ypd1 and a few (1 to 2) response regulators, implying that some adaptor or scaffold proteins, hitherto uncharacterized, may play such roles. Overall, we can assume that all the aforementioned strategies and outlooks will accelerate acquisition of new basic knowledge concerning fungal HK properties and general knowledge about signaling pathways involving these proteins. This is of primary importance for the future development of innovative HK-targeted antifungal strategies.




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