Biology subjects

Catania, S.

Publications and source records attributed to Catania, S..

6 recordsLinked to original sources

bioRxiv2026

Variable ectopic heterochromatin islands provide an alternative route to antifungal heteroresistance in Cryptococcus neoformans

The fungal pathogen Cryptococcus neoformans is estimated to cause approximately 180,000 deaths annually, primarily among immunocompromised HIV patients in resource-limited countries in central and southern Africa. Economic constraints regularly restrict treatment to fluconazole monotherapy. Unstably resistant cells arise in any otherwise fluconazole-sensitive C. neoformans population, with such heteroresistance often involving chromosome 1 disomy. Here we uncover a form of heteroresistance that occurs by a mechanism distinct from aneuploidy. Transient islands of histone H3 lysine 9 methylation-dependent heterochromatin occur at several locations across the genomes of clinical isolates from African patients. Some islands dissipate in the absence of fluconazole selection but are restored upon re-exposure. Deletion of specific heterochromatin island-located genes increased fluconazole resistance in an otherwise wild-type background, suggesting that heterochromatin-mediated alterations in gene expression elicit unstable resistance. Thus, in addition to aneuploidy, transient heterochromatin islands also appear to contribute to C. neoformans fluconazole heteroresistance. Heterochromatin islands have recently been shown to confer unstable antifungal resistance in the ascomycete fungus Schizosaccharomyces pombe (fission yeast) and fungal species of the Mucor circinelloides complex. Thus, similar unstable resistant epimutations may be widespread in pathogenic fungi, however, their instability and inaccessibility to detection by direct sequencing poses challenges for monitoring this form of heteroresistance in clinical settings.

microbiology↗

bioRxiv2026

The Cryptococcus neoformans titanide is a pathogenic morphotype that arises from typical yeast cells in response to host-relevant conditions

Fungal morphogenesis is a major driver of disease outcome. For the opportunistic fungal pathogen Cryptococcus neoformans, extreme morphological heterogeneity within the lung environment drives dissemination, immune evasion, and drug resistance. One such morphotype is the small, oval, titanide (2-3 {micro}m). This poorly understood cell type is prevalent in lung histology and under in vitro conditions that mimic the host environment to generate cellular heterogeneity. Titanides appear after 24 hours post-induction and by 72 hours are the dominant morphotype. Despite their prevalence and the significance of cryptococcal morphogenesis for virulence, their origin remains unclear and their biology unstudied. Using TEM and fluorescence microscopy we demonstrate that titanides display distinct morphological features; they possess thin cell walls and capsules with reduced Pathogen Associated Molecular Pattern exposure and altered distribution. These features distinguish titanides from previously described C. neoformans small cells such as in vivo seed cells (4-6 {micro}m, high cell-wall mannan content) and micro cells (round, <1 m, with thick cell walls). Using microfluidics, we answer key questions pertaining to their origin and cell fate and further our understanding of C. neoformans typical cell and titanide morphological plasticity in host-relevant conditions. Interestingly, despite their thin cell walls, we show that titanides display an increased resistance to cell wall/membrane stressors and are an effective infectious propagule in a murine model. Together, these findings establish a definition and essential characterisation of the titanide morphotype and provide new insight into a key player in C. neoformans pathogenesis.

microbiology↗

bioRxiv2021

Structural basis of ATP-dependent high-fidelity epigenome maintenance

Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance-type cytosine methyltransferase identified in the fungal or protist kingdoms. DNMT5 requires ATP and displays exquisite hemimethyl-DNA specificity. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out the DNA duplex. ATP binding then triggers a striking structural reconfiguration of the methyltransferase catalytic pocket that enables cofactor binding, completion of base-flipping, and catalysis. Unmethylated DNA binding fails to open cofactor pocket and subsequent ATP binding triggers its ejection to ensure fidelity. This chaperone-like, enzyme-remodeling role of the SNF2 domain illuminates how energy can be used to enable faithful epigenetic memory. HighlightsO_LIStructures of DNMT5 reveal mechanism of ATP-dependent DNA methylation C_LIO_LIHemimethylated CpG recognition triggers partial base flipping of the target cytosine C_LIO_LIHemimethylated DNA induces rigid body rotation to activate the SNF2 ATPase domain C_LIO_LIMTase catalytic pocket is remodeled by the SNF2 ATPase to achieve specificity C_LI

molecular biology↗

bioRxiv2020

ATP hydrolysis by the SNF2 domain of the ultraspecific maintenance methylase Dnmt5 drives recognition and modification of hemimethylated DNA

C. neoformans Dnmt5 is an ultraspecific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step that is essential for DNA methylation. Such coupling occurs independently of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating the Dnmt5 ATP binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a flipped-out conformation of the target cytosine bypass the SNF2 domains requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to base-flipping by the DNMT domain. These findings establish a new role for a SNF2 ATPase domain: controlling substrate recognition and catalysis by an adjoined enzymatic domain. This coupling may contribute to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.

molecular biology↗

bioRxiv2017

Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle

Active centromeres are defined by the presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location CENP-A chromatin and kinetochores are maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A itself promote deposition of new CENP-A following replication. Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences. Intrinsic properties of centromeric DNA may favour the assembly of CENP-A rather than H3 nucleosomes. Here we investigate histone dynamics on centromeric DNA. We show that during S-phase histone H3 is deposited as a placeholder at fission yeast centromeres and is subsequently evicted in G2 when we detect deposition of the majority of new CENP-ACnp1. We also find that centromeric DNA has an innate property of driving high rates of turnover of H3 containing nucleosomes resulting in low nucleosome occupancy. When placed at an ectopic chromosomal location in the absence of any CENP-ACnp1 assembly, centromeric DNA retains its ability to impose S-phase deposition and G2 eviction of H3, suggesting that features within this DNA program H3 dynamics. As RNAPII occupancy on this centromere DNA coincides with H3 eviction in G2, we propose a model in which RNAPII-coupled chromatin remodelling promotes replacement of H3 with CENP-ACnp1 nucleosomes.

cell biology↗

bioRxiv2017

Epigenetic maintenance of DNA methylation after evolutionary loss of the de novo methyltransferase

Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles, yet has been lost many times in diverse eukaryotic lineages. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase, Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 MYA. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 MY through a process analogous to Darwinian evolution of the genome.

molecular biology↗