Biology subjects

Santhanam, B.

Publications and source records attributed to Santhanam, B..

5 recordsLinked to original sources

bioRxiv2022

A molecular mechanism for membrane chaperoning by a late embryogenesis abundant protein

Environmental stress can result in substantial damage to proteins, membranes, and genetic material, impacting organismal survival1-3. Stress tolerance can be conferred by intrinsically disordered proteins (IDPs)4 that lack stable tertiary structure. IDPs from the large family of late embryogenesis abundant (LEA) proteins confer a fitness advantage when heterologously expressed5,6. Such protection suggests a general molecular function leading to stress tolerance, although the mechanisms remain unclear. Here, we report that a tardigrade LEA protein that confers stress tolerance in yeast acts as a molecular chaperone for the mitochondrial membrane. This protein, named HeLEA1, localizes to the mitochondrial matrix, and harbors conserved LEA sequence motifs that undergo dynamic disorder-to-helical transition upon binding to negatively charged membranes. Yeast expressing HeLEA1 show increased mitochondrial membrane fluidity, increased membrane potential, and enhanced tolerance to hyperosmotic stress under non-fermentative growth without significantly altering mitochondrial lipid composition or triggering a generic stress response. We demonstrate that membrane binding ameliorates excess surface tension, possibly by stabilizing lipid packing defects. Evolutionary analysis suggests that HeLEA1 homologs localize to different membrane-bound organelles and share similar sequence and biophysical features. We suggest that membrane chaperoning by LEA proteins represents a general biophysical solution that can operate across the domains of life.

biophysics↗

bioRxiv2021

A Multi-Omics and Bioenergetics Longitudinal Aging Dataset in Primary Human Fibroblasts with Mitochondrial Perturbations

Aging is a process of progressive change. In order to develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omic longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Fibroblasts were sourced from both healthy donors (n=6) and individuals with lifespan-shortening mitochondrial disease (n=3). The dataset includes cytological, bioenergetic, DNA methylation, gene expression, secreted proteins, mitochondrial DNA copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the "hallmarks of aging", with the descriptive characterization of aging such as epigenetic age clocks. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells, and cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/

cell biology↗

bioRxiv2021

Limited specificity of molecular interactions incurs an environment-dependent fitness cost in bacteria

Reliable operation of cellular programs depends crucially on the specificity of biomolecular interactions. In gene regulatory networks, the appropriate expression of genes is determined through the specific binding of transcription factors (TFs) to their cognate DNA sequences. However, the large genomic background likely contains many DNA sequences showing similarity to TF target motifs, potentially allowing for substantial non-cognate TF binding with low specificity. Whether and how non-cognate TF binding impacts cellular function and fitness remains unclear. We show that increased expression of different transcriptional regulators in Escherichia coli and Salmonella enterica can significantly inhibit population growth across multiple environments. This effect depends upon (i) TF binding to a large number of DNA sequences with low specificity, (ii) TF cooperativity, and (iii) the ratio of TF to DNA. DNA binding due to the limited specificity of promiscuous or non-native TFs can thus severely impact fitness, giving rise to a fundamental biophysical constraint on gene regulatory design and evolution.

molecular biology↗

bioRxiv2020

Cryo-EM reveals the complex architecture of dynactin's shoulder and pointed end

Dynactin is a 1.1 MDa complex that activates the molecular motor, dynein, for ultra-processive transport along microtubules. In order to do this it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder positions the four identical p50 subunits in different conformations to bind dynactins filament and securely houses the p150 subunit. The pointed end map allows us to build the first structure of p62, and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.

molecular biology↗

bioRxiv2020

A multivalent fuzzy interface drives reversible COPII coat assembly.

Protein secretion is initiated at the endoplasmic reticulum by the COPII coat, which self-assembles to form vesicles. Here, we examine the mechanisms by which the outer scaffolding layer of the coat drives local assembly of a structure rigid enough to enforce membrane curvature, yet able to readily disassemble at the Golgi. An intrinsically disordered region in the outer coat protein, Sec31, drives binding with an inner coat layer via multiple distinct interfaces. Interactions are individually dispensable but combinatorially reinforce each other, suggesting coat oligomerization is driven by the cumulative effects of multivalent interactions. Such a multimodal assembly platform could be readily reversed at the Golgi via perturbation of each individual interface. These design principles provide an explanation for how cells build a powerful yet transient scaffold to direct vesicle traffic.

cell biology↗