Biology subjects

Bhalla, H.

Publications and source records attributed to Bhalla, H..

4 recordsLinked to original sources

bioRxiv2026

Mapping the structural coverage of Arabidopsis thaliana plant developmental proteins: Insights from Experimental and AlphaFold Approaches

BackgroundPlant development is a multifaceted process governed by intricate protein regulatory networks. High-throughput sequencing methods have vastly expanded plant transcriptomic and proteomic datasets, yet there is a large discrepancy between structural information for plant developmental proteins and the UniProt sequence entries. Advances in X-ray crystallography, NMR spectroscopy, and Cryo-EM have enabled the determination of protein complex structures and their dynamics. AI-driven tools like AlphaFold have revolutionized analysis of protein structural intricacies. However, available three-dimensional structural models predominantly prioritize the human proteome and other mammals over plants. Assessing structural coverage of plant developmental proteins is thus essential to identify research gaps, guide structure-function studies, and advance agriculture. ResultsHere, we focus on mapping the structural coverage of developmental proteins in Arabidopsis thaliana. We observed a substantial disparity in the Protein Data Bank (PDB) representation of Arabidopsis thaliana proteins compared to those of Homo sapiens. Our analysis identified 16,389 reviewed UniProt entries, of which only 1,038 have experimentally determined structures. Functional mapping using PlantGSEA revealed 3,485 proteins associated with plant developmental processes; of which only 337 (9.67%) have experimentally determined structures. In contrast, analysis of the AlphaFold database showed that 69.85% of the 39,278 Arabidopsis thaliana UniProt protein entries have predicted structures. Notably, all 3,485 plant developmental proteins (100%) from Arabidopsis thaliana are covered by AlphaFold models. The substantially higher structural coverage provided by AlphaFold for Arabidopsis thaliana, relative to Homo sapiens, highlights the strength of computational approaches in addressing the challenges of structural studies of difficult-to-crystallize proteins. Furthermore, 79.15% of reviewed A. thaliana protein models exhibit high confidence (pLDDT > 70), indicating reliable structural predictions. Although the experimental structural coverage of Arabidopsis thaliana developmental proteins remains limited, AlphaFold has markedly expanded the accessible structural landscape. ConclusionThis study investigated the structural coverage of Arabidopsis thaliana plant developmental proteins, underscoring the critical need for structural studies using both experimental and AlphaFold approaches. It provides research directions for bridging the knowledge gap in understanding molecular mechanisms of plant development.

bioinformatics↗

bioRxiv2026

Characterization of Self-Incompatibility Genes in Brassica rapa var. Toria and Yellow sarson

Self-incompatibility (SI), a reproductive mechanism that prevents self-pollen from fertilizing the ovule, is widespread in flowering plants, including the Brassicaceae family, where it promotes outcrossing, genetic diversity, and hybrid vigor. Although prevalent in Brassica rapa, an economically vital crop, it remains poorly characterized in widely grown varieties, such as toria and yellow sarson, with prior studies primarily focused on Brassica napus. Given its potential for hybrid breeding and crop improvement in rapeseed (B. rapa), we characterized key SI-regulatory genes, analyzing their phylogenetic relationships, structure-function dynamics, and expression patterns. Our results indicate sequence, structural, and functional homology as well as conservation with previously known candidates. This study identifies SRK, FER, and ARC1 as essential, while MLPK plays a minor role in SI for the varieties under study. Furthermore, we identified that SRK, FER, and MLPK activate ROS during the SI response, while ARC1 does not. Our findings establish a foundation for harnessing this natural system to integrate agriculturally important traits and sustain them across generations via outcrossing.

plant biology↗

bioRxiv2024

Structural Insights into Competitive Binding Dynamics between RALF23/33 and PCP-B in Brassicaceae Pollination

Ensuring successful fertilization, viable offspring production, genetic isolation, and maintaining species integrity is pivotal for the survival of flowering plants. Members of Brassicaceae employ a "gatekeeping mechanism" involving interaction between stigmatic membrane-bound Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) receptor, FERONIA, GPI anchored protein LLG2 (LORELEI-LIKE GLYCOPHOSPHATIDYLINOSITOL-ANCHORED PROTEIN 2) and autocrine secreted RALF23/33 (Rapid alkalinization factor) peptide. This binding establishes a barrier for pollen hydration by inducing ROS (Reactive Oxygen Species). Conversely, in the presence of compatible pollen, paracrine-secreted cysteine-rich peptides such as PCP-B{gamma} compete with RALF23/33 for binding to the FERONIA-LLG2 complex, thus reducing ROS levels, ensuring successful pollen hydration and germination. Despite its crucial role, the structural basis of this competitive binding dynamics remains elusive owing to the lack of structural data and the inherent flexibility of these peptides. Using structural modeling, molecular docking, and simulations, this study reveals that PCP-B{gamma} binds to the same negatively charged pocket in the FERONIA-LLG2 complex as RALF23, displacing and interrupting the heterodimerized structure, thus reducing ROS levels to promote pollination. Our study unveils the experimental data-based predicted models, competitive binding dynamics, and mechanism behind this "gatekeeping mechanism," shedding light on the molecular mechanism underlying this pollen hydration barrier in Brassicaceae.

plant biology↗

bioRxiv2024

Structural insights into the recognition of RALF peptides by FERONIA receptor kinase during Brassicaceae Pollination

Ensuring species integrity and successful reproduction is pivotal for the survival of angiosperms. Members of Brassicaceae family employ a "lock and key" mechanism involving stigmatic (sRALFs) and pollen RALFs (pRALFs) binding to FERONIA, a Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) receptor, to establish a prezygotic hybridization barrier. In the absence of compatible pRALFs, sRALFs bind to FERONIA, inducing a lock state for pollen tube penetration. Conversely, compatible pRALFs act as a key, facilitating successful fertilization. Competing pRALFs reduce the sRALFs binding to FERONIA in a dose-dependent manner, enabling pollen tube penetration. Despite its crucial role in Brassicaceae hybridization, the structural basis of this binding remains elusive owing to the highly flexible nature of RALF peptides. Using advanced structural modeling techniques and flexible peptide molecular docking, this study reveals that pRALFs and sRALFs bind to negatively charged pockets in FERONIA with varying binding affinities. Our study unveils the structural basis of this binding, shedding light on the molecular mechanism underlying hybridization barriers in Brassicaceae.

plant biology↗