Biology subjects

Madhani, H.

Publications and source records attributed to Madhani, H..

7 recordsLinked to original sources

bioRxiv2024

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured--with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

microbiology↗

bioRxiv2023

Dynamics of evolution in Irano-Anatolian and Caucasus biodiversity hotspots: Evolutionary radiation and its drivers in Gypsophila (Caryophyllaceae)

O_LIDiversification rates vary through time, with bursts of rapid diversification underscoring species richness across the Tree of Life. Yet the abiotic and biotic factors that correlate with periods of rapid diversification are not well known. C_LIO_LIWe explored the diversification dynamics of Gypsophila (Caryophylleae: Caryophyllaceae), a large and diverse genus with a high degree of endemism in the Irano-Anatolian and Caucasus biodiversity hotspots. We tested the hypothesis of young and recent diversification of biodiversity in these two hotspots and investigated the biotic and abiotic, and paleoenvironmental cofactors of diversification within the Caryophylleae tribe, with a special focus on Gypsophila. C_LIO_LIOur analysis identified multiple shifts in the diversification rate within Caryophylleae, including a newly identified shift in Gypsophila, which began approximately 3 million years ago and was triggered by both paleoenvironmental factors and morphological novelties. These novelties were enabled by explosive diversification of woodiness and perenniality and were facilitated through the high adaptability of Gypsophila to gypsum soil and the harsh environments of alpine habitats. C_LIO_LIThese findings reveal the highly dynamic evolutionary history of both the Caryophylleae clade and Gypsophila, consistent with the extensive historical fluctuations in the geology and climate of the Irano-Anatolian and Caucasus biodiversity hotspots. This study significantly improves our understanding of the dynamics of evolution in the Irano-Anatolian and Caucasus biodiversity hotspots and highlights the impact of environmental changes and morphological innovations on diversification rates. C_LI

plant biology↗

bioRxiv2021

Mechanism of innate immune reprogramming by a fungal meningitis pathogen

How deadly fungal pathogens overcome mammalian innate immunity is largely unknown. Cryptococcus neoformans, the most common cause of fungal meningitis, induces a pathogenic type 2 response characterized by pulmonary eosinophilia and alternatively activated macrophages. Using forward genetics, we identified a fungal secreted protein, Cpl1, necessary and sufficient to enhance alternative activation of primary macrophages in vitro. Cpl1-enhanced polarization requires Toll-like receptor 4, a known mediator of allergen-induced type 2 responses. Cpl1 is essential for virulence, drives polarization of interstitial macrophages in vivo, and requires type 2 cytokine signaling for its impact on infectivity. C. neoformans selectively associates with polarized interstitial macrophages during infection, supporting a direct hostpathogen interaction. This work identifies a secreted effector produced by a human fungal pathogen that reprograms innate immunity to enable tissue infection. One sentence summaryIdentification of a secreted fungal effector that promotes virulence by enhancing type 2 inflammation

immunology↗

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↗

bioRxiv2018

Chromatin rewiring mediates programmed evolvability via aneuploidy

Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis1, and yet specific aneuploidies can be adaptive during environmental stress2,3. Here, we identify a chromatin-based system for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire resistance to antifungal drugs4,5 and for ploidy reduction after mating6. We discovered that the ancestor of C. albicans and two related pathogens evolved a variant of histone H2A that lacks the conserved phosphorylation site for Bub1 kinase7, a key regulator of chromosome segregation1. Expression of this variant controls the rates of aneuploidy and antibiotic resistance in this species. Moreover, CENP-A/Cse4, the histone H3 that specifies centromeres, is depleted from tetraploid mating products and virtually eliminated from cells exposed to aneuploidy-promoting cues. Thus, changes in chromatin regulation can confer the capacity for rapid evolution in eukaryotes.

genetics↗

bioRxiv2018

Real time genetic compensation operationally defines the dynamic demands of feedback control

Biological signaling networks use feedback control to dynamically adjust their operation in real time. Traditional static genetic methods such as gene knockouts or rescue experiments often can identify the existence of feedback interactions, yet are unable to determine what feedback dynamics are required. Here, we implement a new strategy, closed loop optogenetic compensation (CLOC), to address this problem. Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver--on the fly--an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion. Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators. CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.

systems biology↗

bioRxiv2017

Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

Packaging of pericentromeric DNA into heterochromatin is crucial for genome stability, development and health, yet its endogenous triggers remain poorly understood1. A defining feature of pericentromeric heterochromatin is histone H3 lysine 9 methylation (H3K9me)2-4. In S. pombe, transcripts derived from the pericentromeric dg and dh repeat during S phase5-7 promote heterochromatin formation through two pathways: an RNAi-dependent mechanism involving recruitment of the Clr4 H3K9 methyltransferase complex (CLR-C) via the RITS complex8-13, and RNAi-independent mechanism involving an RNAPII-associated RNA-binding protein Seb1, the repressor complex SHREC, and RNA processing activities14-19. We show here that Seb1 promotes long-lived RNAPII pausing. Pause sites associated with sequence-specific Seb1 RNA binding events are significantly enriched in pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Remarkably, globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking functional RITS, demonstrating that RNAPII pausing can be sufficient to trigger de novo heterochromatin independently of RNAi. These results uncover Seb1-mediated polymerase stalling as a new signal for nucleating heterochromatin assembly in repetitive DNA.

molecular biology↗