Biology subjects

Tiwari, T.

Publications and source records attributed to Tiwari, T..

2 recordsLinked to original sources

bioRxiv2026

SPIN: A Scalable Bioinformatics Pipeline for Screening Pathogenicity Related Host-Pathogen Protein INteractions Using AlphaFold3

Traditional experimental approaches have greatly advanced our understanding of protein-protein interactions (PPIs) that govern host susceptibility or resistance. Nonetheless, the molecular characterization of microbial effectors and their cognate host targets remains challenging in many economically important plant pathosystems. AlphaFold3 (AF3) has transformed structural biology by achieving near-experimental accuracy in protein structure and complex prediction. A bioinformatics pipeline SPIN (Screening Pathogenicity-Related Host/Pathogen Protein INteractions) was developed for large-scale prediction of interactions between the host and pathogen-secreted proteins. SPIN integrates three core modules: pathogen and host protein preprocessing using bioinformatics tools (SignalP6.0, OrthoFinder, CD-HIT), AF3-based interaction modeling, supported by automated input generation and output filtering. However, AF3 training bias toward mammalian proteins necessitated careful evaluation in plant systems. Benchmarking against experimentally validated plant PPIs revealed that derivative metrics emphasizing interfacial geometry and residue-level contact (ipSAE and pDockQ) provide superior discrimination compared to native global confidence measures (pTM and ipTM), particularly for proteins with intrinsically disordered regions. A multi-metric confidence scoring framework combining pLDDT, PAE, ipSAE, and pDockQ, improved prediction reliability by enhancing recall and reduced false positives through robust assessment of structural confidence and interface quality. For proof-of-concept, SPIN was applied to examine the molecular landscape underlying two economically important diseases of citrus (Citrus L.) caused by Candidatus Liberibacter asiaticus and Ca. Phytoplasma citri. Both pathogens are phloem-limited and cause distinct symptoms, citrus greening and witches broom, respectively. AF3-predicted interactome data revealed conserved host colonization strategies alongside disease-specific molecular mechanisms, demonstrating the utility of SPIN for dissecting and supporting mechanistic studies in plant-pathogen interactions.

genomics↗

bioRxiv2025

Synthetic Biology Driven Melanin Deposition for Wood Coating

Pigments are widely utilized in industries such as textiles, cosmetics, food, and packaging. However, conventional synthetic pigment production relies on petroleum-based feedstocks, consumes significant energy, and involves toxic chemicals raising environmental and safety concerns. Natural pigments offer a sustainable and biodegradable alternative, yet their large-scale application is hindered by limited availability, batch variability, and geographical dependence. To overcome this, microbial biosynthesis has attracted attention as a controllable and scalable route for pigment production independent of environmental fluctuations. Nevertheless, most existing approaches retain multistep workflows - pigment synthesis, extraction, purification, and application. This compromises process efficiency and reproducibility. Herein, we present a whole-cell biocatalytic approach for melanin synthesis and deposition, wherein recombinant E. coli expressing tyrosinase is employed to convert L-tyrosine into melanin through copper-dependent oxidative polymerization. By harnessing intact microbial cells as self-contained biocatalytic units, this system bypasses the need for enzyme extraction and purification. Prior to applying the culture media containing melanin on material surfaces such as cotton and wood, the process conditions were optimized to enhance melanin yield. Subsequently, the material surfaces incubated in the melanin culture medium were characterized for their surface morphology and chemical modifications through scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The color fastness properties of the material were also evaluated in the presence of water and detergents and subsequently improved through post-treatment processes. In addition, the melanin-coated cotton demonstrated enhanced photothermal performance compared to uncoated controls. All these taken together, this work establishes a simplified and potentially scalable route toward sustainable pigment production and direct application through enzyme-driven in situ biocatalysis on various material surfaces.

bioengineering↗