Biology subjects

Lal, K.

Publications and source records attributed to Lal, K..

4 recordsLinked to original sources

bioRxiv2026

Genome-wide protein-protein interaction analysis between aquaporins and harpin (HrpZ2) through molecular docking and MD simulations to unravel its role in growth and stress management in tomato.

HrpZ2, a harpin protein produced by Pseudomonas syringae, a gram-negative plant pathogenic bacterium, elicits hypersensitive response and pathogen defense in non-host plants. Harpins from various bacterial sources elicit varying responses in different non-host plants, due to its structural variations, their precise mechanisms of action are not yet completely understood. As per previous reports, harpins from diverse bacterial sources interact with distinctive members of integral membrane proteins, known as aquaporins. For example, harpin (Hpa1Xoo) interacts with OsPIP1;3 in rice, whereas, in Arabidopsis the harpins Hpa1 and HrpZ interacts with AtPIP1;4 and AtPIP1;3 respectively. Here, we conducted the first genome-wide computational screening of protein-protein interactions between HrpZ2 and all 47 members of tomato aquaporins. Molecular docking identified nine interactors across five subfamilies of aquaporins, with HrpZ2 N-terminal residues mediating these interactions. We validated these via molecular dynamics (MD) simulations, principal component analysis, and free energy landscape analysis, assessing the stability (RMSD, RMSF, radius of gyration), dynamics, and affinity (MM-GMSA). PIP complexes, especially PIP2;1 (-460.46 kcal/mol) and PIP1;7 (-303.82 kcal/mol), exhibited superior stability, compactness, and defined energy minima, confirming PIPs as primary sensors of harpins. Non-PIP aquaporins like TIP1;1 and NIP4;1 showed moderate stability, outperforming weaker interactors (SIP2;1, XIP1;5, XIP1;3). These findings provide robust evidence that HrpZ2 preferentially targets PIPs in tomato, while engaging TIPs and NIPs as auxiliary partners. This multifaceted interaction profile of harpins suggests complex plant-pathogen recognition, modulating aquaporin-mediated cellular responses like growth and stress management in plants.

plant biology↗

bioRxiv2026

Molecular basis of tRNA modification by the human m5C methyltransferase NSUN2

RNA 5-methylcytidine (m5C) is a prevalent modification that drives RNA stability and function. In humans, m5C is deposited on distinct RNA substrates by DNMT2/TRDMT1 and the NSUN family, to regulate diverse cellular processes, but how m5C writers recognise their substrates remains unclear. NSUN2 is a major m5C methyltransferase with broad roles in cell physiology and strong links to cancer and neurodevelopmental disorders 1. Here, we reconstitute an active human NSUN2-tRNA complex and capture its post-catalytic, tRNA-bound structure at 3.1 [A] resolution. Using an integrated approach combining biochemistry, cryo-electron microscopy, crosslinking mass spectrometry and molecular dynamics simulations, we show that NSUN2 remodels the tRNA to access the variable-loop target cytidine. Recognition is driven by RNA architecture, with NSUN2 exploiting the L-shaped tRNA scaffold to position the target base in the catalytic centre. We further show that Gly679 at the NSUN2-tRNA interface is important for the stability of the complex, providing a mechanistic basis for how the disease-associated Gly679Arg substitution can impair tRNA binding. Together, these findings establish an RNA-structure-guided mechanism for NSUN2 substrate recognition and methylation and provide general principles for m5C deposition on cellular RNAs and their fundamental role in disease.

molecular biology↗

bioRxiv2025

Molecular identification and functional analysis of HrpZ2, a new member of harpin superfamily from Pseudomonas syringae inducing hypersensitive response in tobacco.

Harpins belong to a group of proteins with distinctive features such as heat stability, glycine richness, and absence of cysteine, and are secreted by many Gram-negative phytopathogens via the type III secretion system. Harpins are known to trigger hypersensitive response followed by induction of systemic acquired resistance in non-host plants. However, the molecular mechanism of harpin-induced hypersensitive response remained largely unexplored, mainly because of lack of structural information. In this study, we report the cloning of a new harpin gene (hrpZ2) from Pseudomonas syringae strain MTCC-11950, belonging to the harpin superfamily. In silico analysis revealed that about 50.29% of the protein consists of alpha-helices, 48.53% are random coils, and only 1.16% are beta-sheets, and nearly half (42%) of the protein consists of intrinsically disordered regions. Based on a prokaryotic predictive model and the presence of a signal peptide on its N-terminus, the subcellular localization of harpin is predicted as extracellular. To date, no experimentally determined crystal structure of any harpin protein is available. Therefore, we built and validated a three-dimentional model (with 99% of residues in allowed/additionally allowed regions and a Z-score of -5.3) of harpin. Phylogenetic analysis and functional domain studies revealed that this new harpin belongs to the harpin superfamily. Infiltration of harpin in tobacco leaves resulted in hypersensitive response, which was associated with oxidative burst, callose deposition, localized cell death, and increased activity of defense-related enzymes such as phenylalanine ammonia-lyase and polyphenol oxidase. Furthermore, infiltration of harpin in non-host plants from different angiosperm families induced hypersensitive response, indicating broad-spectrum agricultural applicability of this new harpin protein. This study elucidates the molecular and functional properties of the new harpin protein and its ability to induce hypersensitive response across a broad range of non-host plants.

plant biology↗

bioRxiv2018

Resumption of spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) through spermatogonial cell therapy

In recent times, stem cell research has gained considerable prominence because of its applications in assisted reproductive technology and the treatment of deadly diseases. In teleost fishes, spermatogonial stem cells have been effectively used to produce progeny of difficult-to-breed fish species and/or commercially valuable species through the surrogacy technique. The present study is the first report of an innovative application of stem cell therapy in teleostean fish species for revitalising the reproductive competence of senescent individuals. Senescent male goldfish, Carassius auratus aged approximately 10 years were procured from an ornamental fish-breeding farm and were reared locally for an additional 2 years. The senescence of the fish was evaluated and confirmed using histological analysis, gonadal index assessment, and germ-cell specific vasa gene expression. Analyses revealed the absence of spermatogonial cells and other germ cells in the testes of the senescent fish (n = 5). Spermatogonial cells from a prepubertal C. auratus male donor were isolated using discontinuous percoll gradients, labelled with the fluorescent dye PKH-26, and transplanted into the gonads of senescent C. auratus males through the urogenital papilla. Six months after the therapy, spermatozoa from males were collected through applying gentle manual pressure on the abdomen and were observed under the microscope. All the senescent therapy-treated C. auratus males produced spermatozoa from the transplanted cells; this was confirmed by retention of PKH-26 in the spermatozoa and diagnostic SSR locus. The senescent males were crossed with gravid C. auratus females through artificial insemination and natural spawning, and viable progeny was produced. These observations suggest that the reproductive competence of senescent individuals of commercially valuable and/or endangered fish species can be revitalised and extended through spermatogonia stem cell therapy to produce functional gametes.

developmental biology↗