Biology subjects

Sampathkumar, A.

Publications and source records attributed to Sampathkumar, A..

12 recordsLinked to original sources

bioRxiv2025

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores within statistical error of the winners of the recent CASP16 competition. Unexpectedly, the top Kaggle strategy involved a pipeline for discovering 3D templates, without the use of deep learning. We integrated this template-modeling pipeline and other Kaggle strategies to develop a single model RNAPro that retrospectively outperformed individual Kaggle models on the same test set. These results suggest a growing importance of template-based modeling in RNA structure prediction.

biophysics↗

bioRxiv2023

Replication protein-A, RPA, plays a pivotal role in the maintenance of recombination checkpoint in yeast meiosis

DNA double-strand breaks (DSBs) activate DNA damage responses (DDR) in both mitotic and meiotic cells. A single-stranded DNA (ssDNA) binding protein, Replication protein-A (RPA) binds to the ssDNA formed at DSBs to activate ATR/Mec1 kinase for the response. Meiotic DSBs induce homologous recombination monitored by a meiotic DDR called the recombination checkpoint that blocks the pachytene exit in meiotic prophase I. In this study, we showed the essential role of RPA in the maintenance of the recombination checkpoint during S. cerevisiae meiosis. The depletion of an RPA subunit, Rfa1, in a recombination-defective dmc1 mutant, fully alleviates the pachytene arrest with the persistent unrepaired DSBs. RPA depletion decreases the activity of a meiosis-specific CHK2 homolog, Mek1 kinase, which in turn activates the Ndt80 transcriptional regulator for pachytene exit. These support the idea that RPA is a sensor of ssDNAs for the activation of meiotic DDR. Rfa1 depletion also accelerates the prophase I delay in the zip1 mutant defective in both chromosome synapsis and the recombination, suggesting that the accumulation of ssDNAs rather than defective synapsis triggers prophase I delay in the zip1 mutant.

genetics↗

bioRxiv2023

Cell wall pectic β-1,4-galactan contributes to increased plant freezing tolerance induced by cold acclimation

Subzero temperatures are often lethal to plants. Many temperate plants have a mechanism called cold acclimation that allows them to sense a drop in temperature and prepare for freezing stress through accumulation of soluble sugars and cryoprotective proteins. Plant cells are surrounded by a cell wall and as ice formation primarily occurs in the extracellular matrix (the apoplast), cell wall properties are important for plant freezing tolerance. Although previous studies have shown that the amounts of constituent sugars of the cell wall, in particular those present in pectic polysaccharides, are altered by cold acclimation, the significance of this change during cold acclimation has not been clarified. We found that {beta}-1,4-galactan, which forms neutral side chains of pectin, accumulates in the cell walls of Arabidopsis and various freezing tolerant vegetables during cold acclimation. The gals1 gals2 gals3 triple mutant, which has reduced {beta}-1,4-galactan in the cell wall, exhibited reduced freezing tolerance compared with wild-type Arabidopsis during initial stages of cold acclimation. Expression of genes involved in the galactan biosynthesis pathway such as GALACTAN SYNTHASES and UDP-glucose 4-epimerases were induced during cold acclimation in Arabidopsis explaining galactan accumulation. Cold acclimation resulted in a decrease in extensibility and an increase in rigidity of the cell wall in the wild type, whereas these changes were not observed in the gals1 gals2 gals3 triple mutant. These results indicate that the accumulation of pectic {beta}-1,4-galactan contributes to acquired freezing tolerance by cold acclimation via changes in cell wall mechanical properties.

plant biology↗

bioRxiv2023

Microtubule-mediated cell shape regulation contributes to efficient cell packing in Arabidopsis thaliana cotyledons

Recent advances have started to uncover the mechanisms involved in organ and cell shape regulation. However, organizational principles of epidermal cells in different tissues remain poorly understood. Here, we show that polygonal representations of cotyledon pavement cells (PCs) in Arabidopsis thaliana exhibit increasing irregularity in side lengths and internal vertex angles during early stages of development. While the shape of PCs in cotyledons is more complex than that of cells in the shoot apical meristem (SAM), the polygonal representations of these cells share similar irregularity of side length. Comparison of the surface cell area with the area of the regular polygons, having optimally spaced tri-cellular junctions, reveals suboptimal junction placement for coverage in cotyledons and SAM. We also found that cotyledons show increased packing density compared to the SAM, indicating that PCs forgo coverage of larger areas to potentially increase tissue stability. The identified shape irregularity and cell packing is associated with microtubule cytoskeleton. Our study provides a framework to analyze reasons and consequences of irregularity of polygonal shapes for biological as well as artificial shapes in larger organizational context. SummaryWe provide a polygonal cell representation in a tissue context and use it to draw conclusions about cell packing in epidermis of A. thaliana cotyledon.

developmental biology↗

bioRxiv2022

DEFECTIVE KERNEL1 (DEK1) regulates cellulose synthesis and affects primary cell wall mechanics

The cell wall is one of the defining features of plants, controlling cell shape, regulating growth dynamics and hydraulic conductivity, as well as mediating plants interactions with both the external and internal environments. Here we report that a putative mechanosensitive Cys-protease DEFECTIVE KERNEL1 (DEK1) interacts with cell wall integrity (CWI) pathways and regulation of cellulose synthesis. Our results indicate that DEK1 is an important regulator of cellulose synthesis in epidermal tissue of Arabidopsis thaliana cotyledons during early post-embryonic development. DEK1 is involved in regulation of cellulose synthase complexes (CSCs) by modifying their biosynthetic properties, possibly through interactions with various cellulose synthase regulatory proteins. Mechanical properties of the primary cell wall are altered in DEK1 modulated lines supporting a role in maintenance of CWI. DEK1 affects stiffness of the cell wall and thickness of the cellulose microfibrils bundles in epidermal cell walls of cotyledons.

plant biology↗

bioRxiv2022

A novel role of 3,5-cAMP in the regulation of actin cytoskeleton in Arabidopsis.

The role of cyclic adenosine monophosphate (3,5-cAMP) in plants is not well understood, and here, we report a novel role of 3,5-cAMP in regulating the actin cytoskeleton. The 3,5-cAMP treatment affects the thermal stability of 51 proteins, including a vegetative actin isoform, ACTIN2. Consistent with the above results, the increase in 3,5-cAMP levels, obtained either by feeding or by chemical modulation of 3,5-cAMP metabolism, is sufficient to partially rescue the short hypocotyl phenotype of the actin2 actin7 mutant, severely compromised in actin level. No such complementation was measured for a positional isomer of 3,5-cAMP, 2,3-cAMP, attesting to the specificity of 3,5-cAMP treatment. Moreover, supplementation of 3,5-cAMP partly counters the activity of an actin-depolymerizing drug latrunculin B. In vitro characterization of the 3,5-cAMP - actin interaction argues against the direct binding. Instead, based on the proteomics characterization of the act2act7 mutant supplemented with 3,5-cAMP, we hypothesize that 3,5-cAMP affects cytoskeleton dynamic by modulation of calcium signaling, and actin binding proteins.

plant biology↗

bioRxiv2021

Topological properties accurately predict cell division events and organization of Arabidopsis thaliana's shoot apical meristem

Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at a tissue level. We show that a classifier based on the SAM network properties is predictive of cell division events, with validation accuracy of 82%, on par with that based on cell size alone. Further, we demonstrate that the combination of topological and biological properties, including: cell size, perimeter, distance, and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule mediated cell-to-cell growth coordination in influencing tissue-level topology. Altogether, the results from our network-based analysis demonstrates a feedback mechanism between tissue topology and cell division in A. thalianas SAMs. Summary statementwe use a network representation of live cell imaging data from SAMs in Arabidopsis thaliana to predict cell division events and their consequences at a tissue level.

systems biology↗

bioRxiv2021

2',3'-cAMP treatment mimics abiotic stress response

The role of the RNA degradation product 2,3-cyclic adenosine monophosphate (2,3-cAMP) is poorly understood. Recent studies have identified 2,3-cAMP in plant material and determined its role in stress signaling. The level of 2,3-cAMP increases upon wounding, dark, and heat, and 2,3-cAMP by binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insight into 2,3-cAMP function, we used a multi-omics approach combining transcriptomics, metabolomics, and proteomics to dissect Arabidopsis response to 2,3-cAMP treatment. We demonstrated that 2,3-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway from human cells might also exist in plants. Transcriptomic analysis revealed only minor overlap between 2,3-cAMP-and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2,3-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses including protein and RNA degradation products, glucosinolates, chaperones and SG components. Finally, we demonstrated that 2,3-cAMP treatment influences the movement of processing bodies, supporting the role of 2,3-cAMP in the formation and motility of membraneless organelles.

plant biology↗

bioRxiv2020

Pod indehiscence in common bean is associated to the fine regulation of PvMYB26 and a non-functional abscission layer

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris, the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5-kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated to the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that this is the result of selection at orthologous loci. One-sentence summaryA non-functional abscission layer determines the loss of pod shattering; mapping data, and parallel gene expression and histological analysis support PvMYB26 as the candidate gene for pod indehiscence.

genetics↗

bioRxiv2020

Long-term single-cell imaging and simulations of microtubules reveal driving forces for wall pattering during proto-xylem development

Plants are the tallest organisms on Earth; a feature sustained by solute-transporting xylem vessels in the plant vasculature. The xylem vessels are supported by strong cell walls that are assembled in intricate patterns. Cortical microtubules direct wall deposition and need to rapidly re-organize during xylem cell development. We established long-term live-cell imaging of single Arabidopsis cells undergoing proto-xylem trans-differentiation, resulting in spiral wall patterns, to investigate the microtubule re-organization. The initial disperse microtubule array rapidly readjusted into well-defined microtubule bands, which required local de-stabilization of individual microtubules in band-interspersing gap regions. Using extensive microtubule simulations, we could recapitulate the process in silico and found that local recruitment of microtubule-bound nucleation is critical for pattern formation, which we confirmed in vivo. Our simulations further indicated that the initial microtubule alignment impact microtubule band patterning. We confirmed this prediction using katanin mutants, which have microtubule organization defects, and uncovered active KATANIN recruitment to the forming microtubule bands. Our combination of quantitative microscopy and modelling outlines a framework towards a comprehensive understanding of microtubule re-organization during wall pattern formation.

plant biology↗

bioRxiv2019

A microtubule-mediated mechanical feedback controls leaf blade development in three dimensions

Many plant species have thin leaf blades, which is an important adaptation that optimizes the exchanges with the environment. Here, we provide evidence that their three-dimensional geometry is governed by microtubule alignment along mechanical stress patterns in internal walls. Depending on the primary shape of the primordium, this process has the potential to amplify an initial degree of flatness, or promote the formation of nearly axisymmetric, mostly elongating organs, such as stems and roots. This mechanism may explain leaf evolution from branches, which is alternative to Zimmermanns influential, but widely questioned, telome theory.\n\nOne Sentence SummaryMechanical feedback controls leaf development in three dimensions

developmental biology↗

bioRxiv2017

AtRsgA from Arabidopsis thaliana controls maturation of the small subunit of the chloroplast ribosome

SummaryPlastid ribosomes are very similar in structure and function to ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favourable at biological conditions, it requires activity of many assembly factors. Here, we have characterized a homolog of bacterial rsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA-sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were upregulated, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signalling pathways. To conclude, this study reveals a new chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.\n\nSignificance statementAtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants and smaller, but more numerous chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and - targeted proteins were less abundant, while the corresponding transcripts were upregulated in the mutant. We analyse the transcriptional responses of several retrograde signalling pathways to suggest a mechanism underlying this compensatory response.

molecular biology↗