Biology subjects

Garg, J.

Publications and source records attributed to Garg, J..

5 recordsLinked to original sources

bioRxiv2026

Investigating the function of C-terminal tails of human tubulin isotypes in the motility regulation of cytoplasmic dynein

The intracellular transport system is pivotal for cellular function and integrity, facilitated by cytoskeletal motor proteins such as dynein, which traverse along microtubules (MTs). The heterogeneity of the tubulin isotypes composing MTs introduces functional diversity, potentially affecting cytoskeletal motor proteins interactions with the MT. This in silico study investigated the influence of amino acid sequence variations in the C-terminal tails (CTTs) of six different Homo sapiens tubulin isotypes, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4A, and TUBB5, highly expressed in human brain tumors, and assessed the isotypes effect on the binding of motor protein dynein to MT. Among these isotypes, TUBB2A, TUBB2B, and TUBB2C were found to affect conformational motions of the dyneins microtubule-binding domain (MTBD) and stalk domain. The investigation highlighted the novel role of isotype-specific variations in lateral interactions between tubulin protofilaments (PFs) in determining the proximity of the {beta}-CTT of the adjacent PF to the MTBD, potentially affecting dyneins motility and suggesting how changes in isotype expression directly influence dyneins velocity and processivity and contribute to transport defects associated with neurological disorders and cancers. Isolating specific tubulin isotypes experimentally is challenging due to their high sequence similarity and complex interactions with other microtubule-associated proteins. This makes it challenging to distinguish between different tubulin isotypes and their effects, particularly in tissues where multiple isotypes are co-expressed. Additionally, these isotypes are heavily modified in vivo by post-translational modifications, which further complicate the isolation of a single, unmodified tubulin isotype. As a result, computational approaches have been necessary in this study for exploring these effects in a controlled, isotype-specific manner.

biophysics↗

bioRxiv2023

Rapid measurement and statistical ranking of leaf drought tolerance capacity in cotton

Recent progress in ecological remote sensing calls for a more rapid measurement and a closer assessment of crop drought tolerance traits under field conditions. This study addresses three main questions: (1) If leaf dry matter content (LDMC) is equally effective in indicating cotton drought tolerance as leaf osmotic potential at full turgor ({pi}o); (2) if drought tolerance is inversely related to fiber yield/quality in line with the leaf economics spectrum; and (3) if a reliable statistical model can be developed to rank cotton drought tolerance. The values of{pi} o, along with those of LDMC, of 2736 leaves obtained from cotton variety trials conducted during 2020-2022 in both dryland and irrigated regimes were measured using osmometry. The relationships between{pi} o and LDMC, as well as those between traits and lint yield and fiber quality indices, were investigated using regression analysis. A Bayesian hierarchical linear model was developed to rank cotton drought tolerance based on differences (or adjustments) in{pi} o and LDMC between dryland and irrigated sites. LDMC was not only shown to be an alternate and equally effective drought tolerance trait compared with{pi} o obtained from the widely accepted osmometry method, its use is also estimated to lead to a tenfold increase in measuring speed. A stronger drought tolerance capacity of the tested cotton varieties correlated with a lower lint yield and quality, which is generally consistent with the prediction of the leaf economics spectrum. The drought tolerance rankings using the Bayesian hierarchical model help divide the selected 17 cotton varieties into three groups: (a) more-drought tolerant, (b) less-drought tolerant, and (c) intermediate. The ranking results are interpreted using field-measured data of root distribution and diurnal leaf gas exchange from selected cotton varieties. Our work provides new opportunities for a more rapid measurement and an unambiguous ranking of drought tolerance capacity for crop genotypes under various management regimes.

ecology↗

bioRxiv2022

Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila

Nascent pre-tRNAs are transcribed by RNA polymerase III and immediately bound by La proteins on the UUU-3OH sequence, using a tandem arrangement of the La motif and an adjacent RNA recognition motif-1 (RRM1), resulting in protection from 3-exonucleases and promotion of pre-tRNA folding. The Tetrahymena thermophila protein Mlp1 has been classified as a genuine La protein, despite the predicted absence of the RRM1. We found that Mlp1 functions as a La protein through binding of pre-tRNAs and affecting processing in Tetrahymena thermophila and when expressed in fission yeast. However, unlike in other examined eukaryotes, depletion of Mlp1 results in 3-trailer stabilization. We also observed that 3-trailers in Tetrahymena thermophila are uniquely short relative to other examined eukaryotes, and that 5-leaders have evolved to disfavour pre-tRNA leader/trailer pairing. Our data indicate that this variant Mlp1 architecture is linked to an altered, novel mechanism of tRNA processing in Tetrahymena thermophila.

molecular biology↗

bioRxiv2020

Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila

Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links associated with Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion decreased cellular viability and altered the expression of selected targets. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.

molecular biology↗

bioRxiv2020

A Library Of Induced Pluripotent Stem Cells From Clinically Well-Characterized, Diverse Healthy Human Individuals

A library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a useful resource of normal controls for in vitro human development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of a gender-balanced, racially/ethnically diverse library of hiPSC lines from 40 clinically healthy human individuals who range in age from 22-61. The hiPSCs match the karyotype and short tandem repeat identity of their parental fibroblasts, and have a transcription profile characteristic of pluripotent stem cells. We provide whole genome sequencing data for one hiPSC clone from each individual, genomic ancestry determination, and analysis of Mendelian disease genes and risks. We document similar transcriptomic profiles, single-cell RNA-seq derived cell clusters and physiology of cardiomyocytes differentiated from multiple independent hiPSC lines. This extensive characterization makes this hiPSC library a valuable resource for many studies on human biology.

cell biology↗