Biology subjects

Khan, S. M.

Publications and source records attributed to Khan, S. M..

3 recordsLinked to original sources

bioRxiv2018

A novel interaction between Gβγ and RNA polymerase II regulates cardiac fibrosis.

G{beta}{gamma} subunits are involved in many different signalling processes in various compartments of the cell, including the nucleus. To gain insight into the functions of nuclear G{beta}{gamma}, we investigated the functional role of G{beta}{gamma} signalling in regulation of GPCR-mediated gene expression in primary rat neonatal cardiac fibroblasts. Following activation of the angiotensin II type I receptor in these cells, G{beta}{gamma} dimers interact with RNA polymerase II (RNAPII). Our findings suggest that G{beta}1 recruitment to RNAPII negatively regulates the fibrotic transcriptional response, which can be overcome by strong fibrotic stimuli. The interaction between G{beta}{gamma} subunits and RNAPII expands the role for G{beta}{gamma} signalling in cardiac fibrosis. The G{beta}{gamma}-RNAPII interaction was regulated by signaling pathways in HEK 293 cells that diverged from those operating in cardiac fibroblasts. Thus, the interaction may be a conserved feature of transcriptional regulation although such regulation may be cell-specific.

biochemistry↗

bioRxiv2018

Mechanics of CaMKII-actin networks

Calcium calmodulin dependent kinase (CaMKII) has an important role in dendritic spine remodelling upon synaptic stimulation. Using fluorescence video microscopy and image analysis, we investigated the architectural dynamics of rhodamine-phalloidin stabilized F-actin networks cross-linked by CaMKII. We used automated image analysis to identify F-actin bundles and cross-over junctions and developed a dimensionless metric to characterize network architecture. Similar networks were formed by three different CaMKII species with ten-fold length difference in the linker region between the kinase domain and holoenzyme hub; implying linker length is not a primary determinant of F-actin binding. Electron micrographs showed that, at physiological molar ratios, single CaMKII holoenzymes cross-linked multiple F-actin filaments in random networks, whereas at higher CaMKII / F-actin ratios filaments bundled. Light microscopy established that random networks resisted macromolecular crowding, with polyethylene glycol mimicking cytoplasmic osmolarity, and blocked ATP-powered compaction by myosin-2 mini-filaments. Importantly, the networks disassembled following addition of calcium calmodulin and were then rapidly spaced into compacted foci by myosin motors or, more slowly, aggregated by crowding. Single molecule TIRF microscopy showed CaMKII dissociation from surface-immobilized G-actin exhibited a mono-exponential dwell-time distribution, whereas CaMKII bound to F-actin networks had a long-lived fraction, trapped at cross-over junctions. Release of CaMKII from F-actin, triggered by calcium calmodulin did not require ATP (hence phosphorylation) and was too rapid to measure with video-rate imaging. The residual bound-fraction was reduced substantially upon addition of an NMDA receptor peptide analogue. These results provide mechanistic insights to CaMKII-actin interactions at the collective network and single molecule level. Our findings argue that CaMKII-actin networks in dendritic spines are stable enough to protect the basal network architecture against physical stress but once CaMKII is disengaged by calcium calmodulin and sequestered by receptors at the synapse; F-actin compaction by myosin motors stabilizes the expanded spine compatible with the recorded times.

biophysics↗

bioRxiv2017

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

Plasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated \"gold standards\" of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes.\n\nTo illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia.

microbiology↗