Histone Acetylation in Fungal Pathogens of Plants

GNAT family

The members of GNAT family structurally resemble the archetypal HAT Gcn5 and have been relatively well studied. They share the highly conserved catalytic HAT domain with characteristic sequence motifs, of which motif A notably binds acetyl-coA (Lee and Workman, 2007). Some members additionally have an N-terminal PCAF homology domain for substrate selectivity (Xu et al., 1998) and a C-terminal bromodomain for binding acetylated lysine residues. As is the case with most HATs, GCN5 functions as the catalytic component in multi-subunit complexes SAGA, ADA and SLIK, playing important roles in transcriptional activation and various chromatin activities (Grant et al., 1997; Pray-Grant et al., 2002).

GCN5 has been found to be involved in induction of stress-related genes for adaptation to environmental stress in yeasts (Xue-Franzen et al., 2013). In the human pathogen Cryptococcus neoformans, Gcn5 is implicated in the adaptation to the host environment (O'Meara et al., 2010) and in the industrially important saprophyte Trichoderma reesei, induction of cellulase (Xin et al., 2013). The SAGA/ADA complex in Aspergillus nidulans is required for the induction of orsellinic acid during interaction with competing bacteria and also plays a role in the induction of various other secondary metabolite gene clusters under appropriate conditions (Nutzmann et al., 2011). Finally in Neurospora crassa, promoter acetylation by the Gcn5 ortholog NGF-1 is required in the induction of a blue light-inducible gene (Grimaldi et al., 2006).

Overall, these examples of Gcn5 orthologs in ecologically diverse fungi illustrate the process of transcriptional reprogramming at the chromatin level in response to specific environmental cues. Whether such phenomena are truly epigenetic by a definition encompassing an element of heritability, would be debatable and depend on the case. Nonetheless it is possible to expect mechanisms of epigenetic adaptation to host conditions as opposed to genetic adaptation, which will be discussed in the last section of this review.

MYST family

The MYST family, which was named after the initials of the founding members, is the largest family of acetyltransferases with diverse biological functions. In the budding yeast, Esa1 of the NuA4 complex is known to be an essential HAT required for DNA repair and cell cycle progression (Allard et al., 1999; Clarke et al., 1999). Additionally, an Esa1 ortholog in Aspergillus nidulans activates various secondary metabolite gene clusters (Soukup et al., 2012). Sas2 in yeast plays a crucial role in euchromatin/heterochromatin boundary maintenance most notably at telomeres, antagonising the Sir2 HDAC to prevent the spread of heterochromatin (Babiarz et al., 2006; Kimura et al., 2002). Sas3 is a part of the NuA3 complex and although its biological significance is unclear in yeast (Howe et al., 2001), the functions of its orthologs in animals are nevertheless substantial. In animal systems, the role of MYST family HATs in stem cells, development and cancer have been thoroughly documented (Voss and Thomas, 2009). It is of note that MYST family HAT complexes are known to have the broadest range of substrates including non-histone targets. The regulatory role and the ubiquity of protein acetylation had long been suspected to be comparable that of phosphorylation (Kouzarides, 2000). As the greater protein acetylome is being revealed, novel biological implications of HATs (or KATs) are awaiting discovery (Smith and Workman, 2009).

RTT109, a structural homolog of p300/CBP

The p300/CBP family is restricted to animals. Instead in fungi, there exists a fungal specific structural homolog, Rtt109 (Tang et al., 2008). It is responsible for the acetylation of H3K56 (Schneider et al., 2006), a histone residue at the DNA entry and exit point in the core of a nucleosome (Wang et al., 2008) as opposed to the more accessible N-terminal histone tail residues usually targeted by HATs for transcriptional regulation. Rtt109 is known to function in maintaining genome stability and participate in DNA replication (Han et al., 2007) and DNA damage repair (Chen et al., 2008). Therefore it affects cell cycle progression and sensitivity to genotoxic agents (Driscoll et al., 2007).

In the opportunistic animal pathogen Candida albicans, Rtt109 was demonstrated to be required for survival in host macrophages, where the pathogen is subjected to high oxidative stress (Lopes da Rosa et al., 2010). Plant pathogens are similarly exposed to host ROS response (Torres et al., 2006) and sometimes require internal ROS for cellular differentiation related to pathogenesis (Tudzynski et al., 2012). It is therefore possible that Rtt109 may also have implications for such processes in plant pathogenic fungi.

Class I HDACs

Rpd3 from the budding yeast, S. cerevisiae is a founding member of class I HDACs and contains an N-terminal deacetylase domain and a C-terminal tail region (Vidal and Gaber, 1991). In mammalian orthologs including HDAC1, HDAC2 and HDAC3, the C-terminal tail harbors one or two casein kinase-2 (CK2) phosphorylation sites and a sumoylation motif (Sengupta and Seto, 2004; Taunton et al., 1996). In yeast, Rpd3 functions as a catalytic subunit in a multi-protein complex called Sin3. In mammals, HDAC1 and HDAC2 form the catalytic core of the mammalian Sin3, NuRD (Nucleosome Remodeling deacetylase) and CoREST (Co-repressor of Re1-silencing transcription factor) complexes (Yang and Seto, 2008). These complexes are known to interact with sequence-specific transcription factors for transcriptional repression.

Class II HDACs

Hda1, Hos1 and Hos2 (Hda one similar) in the budding yeast contain an N-terminal deacetylase domain and a long C-terminal extension of unknown function (Yang and Seto, 2008). In mammalian orthologs (especially IIa members), only the deacetylase domain is conserved in the extended N-terminal region harboring binding sites for myocyte enhancer factor-2 (MEF2) and 14-3-3 proteins, which play a role in subcellular trafficking of class IIa HDACs (Verdin et al., 2003). Hda1 of S. cerevisiae and its ortholog Clr3 of Schizosacchromyces pombe are found in multi-proteins complexes. However, non-catalytic subunits of these complexes are not conserved in class IIa HDAC complexes of metazoans, indicating that the complexes are specific to fungal species (Yang and Seto, 2008).

Class III HDACs

Class III HDACs are sirtuin family enzymes. This class of proteins is related to the transcriptional repressor Sir2 (Silent information regulator 2) in the budding yeast. Yeast has five sirtuins including Sir2 and four homologs, Hst1-4 (Homolog of Sir two) (Grozinger and Schreiber, 2002). The sirtuin deacetylases contain a conserved catalytic domain that is not related to deacetylase domain of other HDAC classes. Thus, the sirtuins catalyze deacetylation by a different mechanism that requires NAD⁺ as a cofactor. The best-characterized sirtuin protein is the yeast Sir2 that is found in two major complexes: one responsible for silencing telomeric and HM loci and the other for suppressing genetic recombination at the rDNA loci (Gartenberg, 2000). Notably, Sir2 has been linked to aging in yeast by its dependence on NAD⁺ and roles in repression of rDNA recombination. Such role of Sir2 greatly influenced studies of aging in human and related model systems (Guarente, 2013; Park et al., 2013; Smith et al., 2007; Suvarna, 2012).

Epigenetic regulation of pathogen traits

In Fusarium graminearum, the causal agent of Fusarium head blight in wheat and barley, it was shown that FTL1 is required for conidiation and pathogenesis (Ding et al., 2009). FTL1 is homologous to Sif2, which is a component of the Set3 complex in Saccharomyces cerevisiae. Set3 complex contains two histone deacetylases, Hos2 and NAD⁺-dependent Hst1, other than Sif2, Snt1, and YIL112w (Pijnappel et al., 2001). Deletion of HDF1, an ortholog of S. cerevisiae Hos2 in F. graminearum also resulted in significant reduction in virulence as well as defects in deoxynivalenol production, asexual and sexual reproduction (Li et al., 2011). Similarly, in Fusarium fujikuroi, the causal agent of bakanae disease on rice, deletion of two genes encoding HDACs, FfHDA1 (Class II HDAC) and FfHDA2 (Class I HDAC) showed that HDAC activities are crucial for secondary metabolite biosynthesis and virulence on rice. Direct mechanistic link between histone acetylation and expression of gene clusters involved in secondary metabolite biosynthesis of other mycotoxogenic fungi suggests that HDAC-mediated regulatory pathways are evolutionarily conserved and co-opted to invade host plants in pathogenic fungal species (Roze et al., 2007; Shwab et al., 2007).

Recently, Ding et al. reported that in the rice blast fungus, Magnaporthe oryzae, Tig1, which is an ortholog of F. graminearum FTL1, is important for conidiogenesis and growth inside host cells (Ding et al., 2010). The authors also showed that other components of Set3 complex such as Snt1, Hos2, and Set3 are required for full HDAC activity and virulence in the fungus. Interestingly, tig1 mutant was unable to differentiate bulbous invasive hyphae and induced high concentration of reactive oxygen species within plant cells. Hypersensitivity of the mutant to H₂O₂ and osmotin (a plant protein toxic to fungal pathogens) suggests that Set3 complex containing Tig1 participates in activating pathways that enable the fungus to cope with plant defense responses. Although we now have only a handful of studies aimed at understanding epigenetic control of fungal pathogenesis, current data suggest that histone acetylation/deacetylation is a crucial regulatory mechanism during plant infection.

Pathogen-induced epigenetic changes in hosts

The HC-toxin is a host-selective toxin produced by Cochliobolus carbonum. Only the maize plants that carry functional carbonyl reductase (HC-toxin reductase) gene(s) can detoxify HC-toxin (Meeley and Walton, 1991). Therefore, it is a determinant of specificity and virulence in interaction between C. carbonum and the maize plant. HC-toxin is not cytotoxic but cytostatic. Plant cell protoplasts treated with HC-toxin survive longer than do control protoplasts. Such nature of HC-toxin left open the question of how HC-toxin contributes to pathogenesis of C. carbonum on sensitive maize plants, given the necrotrophic lifestyle of the pathogen. Later, it was shown that HC toxin specifically inhibits maize HDACs, leading to proposition of a model where HC-toxin helps the pathogen to establish compatibility with maize via interference of histone acetylation/deacetylation (Brosch et al., 1995).

Depudecin is another HDAC inhibitor produced by a pathogenic fungus, Alternaria brassicicola (Kwon et al., 1998; Matsumoto et al., 1992). Depudecin is chemically unrelated to HC-toxin but, like HC-toxin, it can cause detransformation of oncogene-transformed mammalian cells. Genetic analysis of depudecin biosynthesis genes showed that depudecin is also a virulence factor but its effect is not as dramatic as that of HC-toxin (Wight et al., 2009). Zhou et al. reported that HDAC19 expression is induced in Arabidopsis thaliana challenged with Alternaria brassicicola and correlates with changes in expression of jasmonic acid and ethylene-regulated genes (Zhou et al., 2005). In conjunction with the role of fungal toxins as HDAC inhibitors, it is likely that plant HDACs are conserved regulators of defense-related genes in both monocot and dicot plants and are targeted by pathogens to cause alterations in transcriptional programs of host plants in favor of pathogens.