Biology subjects

Saravanan, S.

Publications and source records attributed to Saravanan, S..

3 recordsLinked to original sources

bioRxiv2021

The evolution of regulatory elements in the emerging promoter variant strains of HIV-1

In a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naive subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1/LEF-1, RBEIII, AP-1, and NF-{kappa}B, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy. Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions - transcriptional activation and transcriptional silencing. The various phases of viral latency -establishment, maintenance, and reversal -collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a functional cure more challenging in HIV-1C.

microbiology↗

bioRxiv2021

Moving patronin foci and growing microtubule plus ends direct the spatiotemporal dynamics of Rho signaling and myosin during apical constriction

The contraction of the amnioserosa by apical constriction provides the major force for Drosophila dorsal closure. The nucleation, movement and dispersal of apicomedial actomyosin complexes generate pulsed constrictions during early dorsal closure whereas persistent apicomedial and circumapical actomyosin complexes drive the unpulsed constrictions that follow. What governs the spatiotemporal assembly of these distinct complexes, endows them with their pulsatile dynamics, and directs their motility remains unresolved. Here we identify an essential role for microtubule growth in regulating the timely contraction of the amnioserosa. We show that a symmetric cage of apical microtubules forms around the coalescing apicomedial myosin complex. An asymmetric tail of microtubules then trails the moving myosin complex and disperses as the myosin complex dissolves. Perturbing microtubule growth reduced the coalescence and movement of apicomedial myosin complexes and redistributed myosin and its activator, Rho kinase to the circumapical pool and altered the cell constriction and tissue contraction dynamics of the amnioserosa. We show that RhoGEF2, the activator of the Rho1 GTPase, is transiently associated with microtubule plus end binding protein EB1 and the apicomedial actomyosin complex. Our results suggest that microtubule growth from moving patronin platforms modulates actomyosin contractility through the spatiotemporal regulation of Rho1 activity. We propose that microtubule reorganisation enables a self-organising, mechanosensitive feedback loop that buffers the tissue against mechanical stresses by modulating actomyosin contractility.

cell biology↗

bioRxiv2020

High-throughput identification of nuclear envelope protein interactions in Schizosaccharomyces pombe using an arrayed membrane yeast-two hybrid library

The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins in the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two hybrid sys-tem. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nu-clear membrane: Cut11/Ndc1, Lem2, and Ima1/Samp1/NET5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11 mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.

cell biology↗