Biology subjects

Ganguly, A.

Publications and source records attributed to Ganguly, A..

27 records · Page 2Linked to original sources

bioRxiv2020

Structural characterization of Myxococcus xanthus MglC, a component of polarity control system, and its interactions with MglB

Myxococcus xanthus displays two types of motilities i.e. Social (S) and Adventurous (A). The pole-to-pole reversals of these motility regulator proteins is the key to this process. Here, we determined ~1.85 [A] resolution crystal structure of MglC, which revealed that despite sharing <9% sequence identity, both MglB and MglC adopt Regulatory Light Chain 7 (RLC7) family fold. Interestingly, MglC is structurally unique compared to the other known RLC7 family proteins having ~30{degrees}-40{degrees} shift in the orientation of functionally important 2 helix. Using isothermal titration calorimetry and gel filtration chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using combination of small angle X-ray scattering and molecular docking studies, we show that MglBC complex is formed by MglC homodimer sandwiched between two homodimers of MglB. In BriefKapoor et al. report the crystal structure of Myxococcus xanthus MglC, a Roadblock Light Chain 7 (RLC7) family protein, involved in polarity reversal. The structure reveals a distinct orientation of 2 helix compared to other RLC7 proteins. They also demonstrate that MglC binds a GTPase activating protein, MglB, with submicromolar range dissociation constant. HighlightsO_LIMglC adopts RLC7 fold and has distinct structural features. C_LIO_LIMglC interacts MglB to form a stable complex having submicromolar range dissociation constant. C_LIO_LIMglC homodimer is sandwiched between two MglB homodimers to form a 2:4 stoichiometric complex. C_LI

biophysics↗

bioRxiv2020

Bibliome Variant Database: Automated Identification and Annotation of Genetic Variants in Primary Literature

The Bibliome Variant Database (BVdb) is a freely available reference database containing over 1 million human genetic variants mapped to the human genome that have been mined from primary literature. The BVdb is designed to facilitate variant interpretation in clinical and research contexts by reducing or eliminating the time required to search for literature describing a given variant. Users can search the database using gene symbols, HGVS variant nomenclature, genomic positions, or rsIDs. Each variant page lists references in the database that describe the variant, as well as the exact gene symbol and variant text description identified in each reference. AVAILABILITY AND IMPLEMENTATIONThe BVdb is freely available at http://bibliome.ai

bioinformatics↗

bioRxiv2020

Slow Axonal Transport and Presynaptic Targeting of Clathrin Packets

Clathrin has established roles in endocytosis, with clathrin-cages enclosing membrane infoldings, followed by rapid disassembly and reuse of monomers. However, in neurons, clathrin synthesized in cell-bodies is conveyed into axons and synapses via slow axonal transport; as shown by classic pulse-chase radiolabeling. What is the cargo-structure, and mechanisms underlying transport and presynaptic-targeting of clathrin? What is the precise organization at synapses? Combining live-imaging, mass-spectrometry (MS), Apex-labeled EM-tomography and super-resolution, we found that unlike dendrites where clathrin transiently assembles/disassembles as expected, axons contain stable transport-packets that move intermittently with an anterograde bias; with actin/myosin-VI as putative tethers. Transport-packets are unrelated to endocytosis, and the overall kinetics generate a slow biased flow of axonal clathrin. Synapses have integer-numbers of clathrin-packets circumferentially abutting the synaptic-vesicle cluster, advocating a model where delivery of clathrin-packets by slow axonal transport generates a radial organization of clathrin at synapses. Our experiments reveal novel trafficking mechanisms, and an unexpected nanoscale organization of synaptic clathrin.

neuroscience↗

bioRxiv2019

Atypical Protein Kinase C iota (PKC{lambda}/{iota}) Ensures Mammalian Development by Establishing the Maternal-Fetal Exchange Interface

In utero mammalian development relies on the establishment of the maternal-fetal exchange interface, which ensures transportation of nutrients and gases between the mother and the fetus. This exchange interface is established via development of multinucleated syncytiotrophoblast cells (SynTs) during placentation. In mouse, SynTs develop via differentiation of the trophoblast progenitor cells (TSPCs) of the placenta primordium and in human, SynTs are developed via differentiation of villous cytotrophoblast (CTB) progenitors. Despite the critical need in pregnancy progression, conserved signaling mechanisms that ensure SynT development are poorly understood. Herein, we show that Atypical Protein Kinase C iota (PKC{lambda}/I) plays an essential role in establishing the SynT differentiation program in trophoblast progenitors. Loss of PKC{lambda}/I in the mouse TSPCs abrogates SynT development leading to embryonic death at ~E9.0. We also show that PKC{lambda}/I-mediated priming of trophoblast progenitors for SynT differentiation is a conserved event during human placentation. PKC{lambda}/I is selectively expressed in the first-trimester CTBs of a developing human placenta. Furthermore, loss of PKC{lambda}/I in CTB-derived human trophoblast stem cells (Human TSCs) impairs their SynT differentiation potential both in vitro and after transplantation in immunocompromised mice. Our mechanistic analyses indicate that PKC{lambda}/I signaling maintains expression of GCM1, GATA2, and PPAR{gamma}, which are key transcription factors to instigate SynT differentiation programs in both mouse and human trophoblast progenitors. Our study uncovers a conserved molecular mechanism, in which PKC{lambda}/I signaling regulates establishment of the maternal-fetal exchange surface by promoting trophoblast progenitor to SynT transition during placentation.

developmental biology↗

bioRxiv2019

Trophoblast paracrine signaling regulates placental hematoendothelial niche

The placenta acts as a major organ for hematopoiesis. It is believed that placental hematopoietic stem and progenitor cells (HSPCs) migrate to the fetal liver to ensure optimum hematopoiesis in the developing embryo. The labyrinth vasculature in a mid-gestation mouse placenta provides a niche for the definitive hematopoietic stem cell (HSC) generation and expansion. It has been proposed that these processes are regulated by a host of paracrine factors secreted by trophoblast giant cells (TGCs) at the maternal-fetal interface. However, the molecular mechanism by which the TGCs regulate the hematoendothelial niche in a developing placenta is yet to be defined. Using a TGC-specific Gata2 and Gata3 double knockout mouse model, we show that the loss of GATA2 and GATA3 at the TGC layer leads to fetal growth retardation and embryonic death due to disruptions in the delicate hematopoietic-angiogenic balance in the developing placenta. Using single-cell RNA-Seq analyses, we also show that the loss of GATA factors in the TGCs results in the loss of HSC population within the placental labyrinth and is associated with defective placental angiogenesis. Interestingly, we also found that this TGC-specific GATA factor-loss leads to impaired differentiation and distribution of trophoblast progenitor cells. Our study helps to define the GATA-dependent non-autonomous signaling mechanisms of the primary parietal trophoblast giant cells by which it regulates the delicate hematopoietic-angiogenic balance in the developing placenta.

developmental biology↗

bioRxiv2019

FRA1 modulates cortical microtubule localization of CMU proteins

Construction of the cell wall demands harmonized deposition of cellulose and matrix polysaccharides. Cortical microtubules orient the deposition of cellulose by guiding the trajectory of plasma membrane-embedded cellulose synthase complexes. Vesicles containing matrix polysaccharides are thought to be transported by the FRA1 kinesin to facilitate their secretion along cortical microtubules. The cortical microtubule cytoskeleton thus provides a platform to coordinate the delivery of cellulose and matrix polysaccharides, but the underlying molecular mechanisms remain unknown. Here, we show that the tail region of the FRA1 kinesin physically interacts with CMU proteins which are important for the microtubule-dependent guidance of cellulose synthase complexes. Interaction with CMUs did not affect microtubule binding or motility of the FRA1 kinesin but had an opposing effect on the cortical microtubule localization of CMU1 and CMU2 proteins, thus regulating the lateral stability of cortical microtubules. Phosphorylation of the FRA1 tail region by CKL6 inhibited binding to CMUs and consequently reversed the extent of cortical microtubule decoration by CMU1 and CMU2. Genetic experiments demonstrated the significance of this interaction to the growth and reproduction of Arabidopsis thaliana plants. We propose that modulation of CMUs microtubule localization by FRA1 provides a mechanism to control the coordinated deposition of cellulose and matrix polysaccharides.

plant biology↗

bioRxiv2019

Model-based control of individual finger movements for prosthetic hand function

Prosthetic devices for hand difference have advanced considerably in recent years, to the point where the mechanical dexterity of a state-of-the-art prosthetic hand approaches that of the natural hand. Control options for users, however, have not kept pace, meaning that the new devices are not used to their full potential. Promising developments in control technology reported in the literature have met with limited commercial and clinical success. We have previously described a biomechanical model of the hand that could be used for prosthesis control. In this study, we report on three key elements of the biomechanical simulations relevant to prosthesis control: we show the performance of the model in replicating recorded hand kinematics and find average correlations of 0.89 between modelled and recorded motions; we show that the computational performance of the simulations is fast enough to achieve real-time control with a robotic hand in the loop; and we describe the use of the model for controlling object gripping. Despite some limitations in accessing sufficient driving signals, the model performance shows promise as a controller for prosthetic hands when driven with recorded EMG signals. We identify areas for future work to address these limitations.

bioengineering↗

bioRxiv2017

Processive movement of actin by biased polymerization: a new paradigm of axonal transport

Classic pulse-chase studies have shown that actin is conveyed in slow axonal transport, but the mechanistic basis for this movement is unknown. Recently, we reported that axonal actin was surprisingly dynamic, with focal assembly/dis-assembly events (\"hotspots\") and elongating polymers along the axon-shaft (\"trails\"). Using a combination of live imaging, super-resolution microscopy, and modeling, here we explore how these axonal actin dynamics can lead to processive transport. We found abundant actin nucleation, along with a slow, anterogradely-biased flow of actin in axon-shafts. Starting with first principles of monomer/filament assembly - and incorporating imaging data - we generated a quantitative model simulating axonal hotspots and trails. Our simulations predict that the axonal actin dynamics indeed lead to an anterogradely-biased flow of the population, at rates consistent with slow transport. Collectively, the data point to a surprising scenario where local assembly and biased polymerization generate the slow axonal transport of actin. This mechanism is distinct from polymer-sliding, and seems well suited to convey highly dynamic cytoskeletal cargoes.\n\nAcknowledgementsThis work was supported by an NIH grant to SR (R01NS075233). The authors thank Stephanie Gupton (UNC) for the Mena/Vasp constructs.

neuroscience↗

bioRxiv2017

Function of the Arabidopsis kinesin-4, FRA1, requires abundant processive motility

Processivity is important for kinesins that mediate intracellular transport. Structure-function analyses of N-terminal kinesins have identified several non-motor regions that affect processivity in vitro. However, whether these structural elements affect kinesin processivity and function in vivo is not known. Here, we used an Arabidopsis kinesin-4, called Fragile Fiber1 (FRA1), which is thought to mediate vesicle transport to test whether mutations that alter processivity in vitro behave similarly in vivo and whether processivity is important for FRAs function. We generated several FRA1 mutants that differed in their run lengths in vitro and then transformed them into the fra1-5 mutant for complementation and in vivo motility analyses. Our data show that the behavior of processivity mutants in vivo can differ dramatically from in vitro properties, underscoring the need to extend structure-function analyses of kinesins in vivo. In addition, we found that high density of processive motility is necessary for FRA1s physiological function.\n\nSummaryThis study shows that the motility of kinesin mutants can differ significantly between in vitro and in vivo conditions and that abundant processive motility is important for FRA1 kinesins function.

cell biology↗