Biology subjects

Iyer, K. V.

Publications and source records attributed to Iyer, K. V..

8 recordsLinked to original sources

bioRxiv2026

Aging associated RNA loss impairs the dynamics of RNA and protein condensates

Altered biomolecular condensate dynamics are increasingly implicated in age-associated neurodegenerative disorders, yet the molecular principles governing these changes remain incompletely understood. Here, we demonstrate that aged cells across diverse cellular and organismal models harbor pre-formed, viscous, and persistent stress granules (SGs), which we term alt-SGs. These persistent condensates confer protection to senescent cells under fluctuating stress conditions. Comparative analyses reveal that alt-SGs exhibit elevated RNA-binding protein (RBP)-to-RNA ratios, underscoring a shift in condensate stoichiometry. By quantifying SG composition and dynamics in live cells and in vitro, we establish that RNA concentration is a key determinant of condensate material properties, molecular composition, and dissolution capacity. Importantly, aging cells display diminished absolute RNA concentrations due to reduced RNA metabolic activity. Reactivation of RNA metabolism restores RNA/RBP ratios within SGs and alleviates aging-associated phenotypes. Together, our findings highlight RNA metabolism as a central regulator of condensate stoichiometry and function, linking metabolic decline to altered phase behavior and cellular aging. Key findingsO_LIAging and senescence have Alt-SGs with increased protein/RNA Ratio C_LIO_LIAlt-SGs are persistent after stress removal in aging C_LIO_LIAging is associated with reduced total cellular RNA C_LIO_LIReactivating RNA metabolism rescues SG phenotypes C_LIO_LIAlt-SGs are protective for senescent cell C_LI

cell biology↗

bioRxiv2025

Jlp2 is an RQC complex-independent release factor acting on aberrant peptidyl-tRNA, protecting cells against translation elongation stress

Ribosome stalling generates aberrant nascent peptides that remain tethered to the large ribosomal subunit following ribosome splitting. Such peptidyl tRNA:60S complexes are processed by the Ribosome associated Quality Control (RQC) pathway, where Ltn1 and Rqc1 mediate K48 linked ubiquitination and Rqc2 adds CAT tails to the nascent peptides.Subsequently, Vms1 releases the peptides from tRNA, enabling their proteasomal degradation. However, alternative mechanisms that process these stalled intermediates remain poorly defined. In this study, we identify Jlp2 as a novel factor involved in translation quality control. We find that Jlp2 is a release factor that catalyzes peptide release from tRNA and suppresses excessive CAT tailing when Ltn1-dependent ubiquitination is compromised. We define its ribosome binding properties, substrate scope, and critical residues required for peptide release. Our data support a model in which Jlp2-mediated peptide release constitutes an alternative quality control mechanism to safeguard cells during ribosome stalling and conditions of RQC failure or insufficiency.

molecular biology↗

bioRxiv2024

Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

New1 is a homologue of the essential yeast translation elongation factor eEF3. Lack of New1 has previously been shown to induce queueing of ribosomes upstream of the stop codon on mRNAs encoding specific C-terminal amino acids, primarily lysine and arginine. Here, we used UV crosslinking and analysis of cDNA, long-read nanopore sequencing and proteomics to address the open question of what consequences such queues have for the yeast cell. We show that these queues are ribosomal collisions, which are recognized by the collision sensor and E3 ubiquitin ligase Hel2, marking these collided ribosome complexes for mRNA degradation via canonical no-go decay. Decay is initiated by Cue2-mediated cleavage upstream of the stop codon. Ultimately, this leads to downregulation of encoded proteins, including highly abundant and important metabolic enzymes Pgk1 and Gpm1, as well as translation elongation factors eEF1-alpha and eEF1-beta. Collisions and resulting downstream effects are codon-, rather than amino acid dependent. E.g., for C-terminal lysine and arginine, only specific codons induce collisions upon lack of New1. Our study shows that New1 protects highly abundant and essential genes from degradation by no-go decay thatwould otherwise occur in the absence of translation inhibitors or other direct perturbations of translation.

molecular biology↗

bioRxiv2024

Real-time transcriptomic profiling in distinct experimental conditions

Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis in rapid quality control for long-read RNA-seq. We illustrate its utility through four experimental setups: 1) transcriptome profiling of distinct human cellular populations, 2) identification of experimentally enriched transcripts, 3) transcriptional analysis of cells under heat shock conditions and 4) identification of experimentally manipulated genes (knockout and overexpression) in several yeast strains. We show how to perform multiple layers of quality control as soon as sequencing has started, addressing both the quality of the experimental and sequencing traits. Real-time quality control measures assess sample/condition variability and determine the number of identified genes per sample/condition. Furthermore, real-time differential gene/transcript expression analysis can be conducted at various time points post-sequencing initiation (PSI), revealing dynamic changes in gene/transcript expression between two conditions. Using real-time analysis, which occurs in parallel to the sequencing run, we identified differentially expressed genes/transcripts as early as 1hr PSI. These changes were consistently observed throughout the entire sequencing process. We discuss the new possibilities offered by real-time data analysis, which have the potential to serve as a valuable tool for rapid and cost-effective quality checks in specific experimental settings and can be potentially integrated into clinical applications in the future.

bioinformatics↗

bioRxiv2021

Hedgehog signaling can enhance glycolytic ATP production in the Drosophila wing disc

Energy production and utilization is critically important for animal development and growth. How it is regulated in space and time during tissue growth remains largely unclear. Toward this end, we used a FRET-based adenosine triphosphate (ATP) sensor to dynamically monitor ATP levels across a growing tissue, using the Drosophila wing disc. We discovered that steady-state levels of ATP are spatially uniform across the wing pouch. Pharmacologically inhibiting oxidative phosphorylation, however, reveals spatial heterogeneities in metabolic behavior, whereby signaling centers at compartment boundaries produce more ATP from glycolysis than the rest of the tissue. Genetic perturbations indicate that the conserved Hedgehog (Hh) signaling pathway can enhance ATP production by glycolysis. Collectively, our work reveals a positive feedback loop between Hh signaling and energy metabolism, advancing our understanding of the connection between conserved developmental patterning genes and energy production during animal tissue development.

developmental biology↗

bioRxiv2020

Apico-basal cell compression regulates Lamin A/C levels in Epithelial tissues

Nuclear lamina bridges mechanical forces from the cytoskeleton to the nucleus, to initiate nuclear mechanotransduction. The concentration of nuclear Lamin proteins, particularly Lamin A/C is crucial for the mechanical properties of the nucleus and nuclear mechanotransduction. Recent studies in mesenchymal tissues show that the concentration of Lamin A/C scales with stiffness and concentration of the underlying extracellular matrix (ECM). But in epithelial tissues, that lack a strong cell-ECM interaction, it is still unclear how Lamin A/C is regulated. Here, we show that concentration of Lamin A/C in epithelial tissues scales with apico-basal compression of cells and is independent of ECM concentration. But, ectopically altering the concentration of Lamin A/C does not influence cell shapes in epithelial tissues. Using genetic perturbations in Drosophila epithelial tissues, we reveal that apico-basal cell compression regulates the concentration of Lamin A/C by deforming the nucleus. We observe a similar mechanism of Lamin A/C regulation in mammalian Madin Darby Canine Kidney (MDCK) cells suggesting that this mechanism is evolutionarily conserved. Taken together, our results reveal a unidirectional mechanical coupling between cell mechanics and nuclear mechanics via the regulation of Lamin A/C. We anticipate that mechanism of Lamin A/C regulation that we revealed, could form the basis for understanding nuclear mechanotransduction in epithelial tissues.

cell biology↗

bioRxiv2020

Self-organized patterning of cell morphology via mechanosensitive feedback

Tissue organization is often characterized by specific patterns of cell morphology. How such patterns emerge in developing tissues is a fundamental open question. Here, we investigate the emergence of tissue-scale patterns of cell shape and mechanical tissue stress in the Drosophila wing imaginal disc during larval development. Using quantitative analysis of the cellular dynamics, we reveal a pattern of radially oriented cell rearrangements that is coupled to the buildup of tangential cell elongation. Developing a laser ablation method, we map tissue stresses and extract key parameters of tissue mechanics. We present a continuum theory showing that this pattern of cell morphology and tissue stress can arise via self-organization of a mechanical feedback that couples cell polarity to active cell rearrangements. The predictions of this model are supported by knockdown of MyoVI, a component of mechanosensitive feedback. Our work reveals a mechanism for the emergence of cellular patterns in morphogenesis.

developmental biology↗

bioRxiv2018

Mechanosensitive binding of p120-Catenin at cell junctions regulates E-Cadherin turnover and epithelial viscoelasticity

Studying how epithelia respond to mechanical stresses is key to understanding tissue shape changes during morphogenesis. Here, we study the viscoelastic deformation of the Drosophila pupal wing epithelium in response to mechanical stress that evolves during morphogenesis. We show that wing epithelial tissue viscoelasticity depends on endocytic turnover of E-Cadherin. The fraction of ECadherin undergoing turnover depends on mechanical stress in the epithelium. We identified mechanosensitive binding of the endocytic regulator p120-Catenin (p120) as a mechanism to regulate E-Cadherin turnover. Under high stress, p120 is released into the cytoplasm, destabilizing E-Cadherin complexes and increasing its turnover. In p120 mutants, E-Cadherin turnover is insensitive to mechanical stress. Furthermore, we show that p120 is crucial for the viscoelastic deformation of the wing epithelium. Taken together, our findings reveal that mechanosensitive binding of p120-Catenin tunes epithelial tissue viscoelasticity during morphogenesis.

biophysics↗