Biology subjects

PANDEY, A. K.

Publications and source records attributed to PANDEY, A. K..

5 recordsLinked to original sources

bioRxiv2025

Unveiling the PET plastics degradation potential of the thermostable EstS1 esterase through integrated biochemical, structural, and morphological analyses

Enzymatic polyethylene terephthalate (PET) plastic degradation is a promising approach to combat the exploding plastic pollution. EstS1, a pH-tolerant, thermostable esterase, has been previously recognized for its degradation potential against phthalate diester plasticizers. The present study elucidates the exceptional potential of this enzyme to degrade crystalline PET plastic and its primary intermediate, bis(2-hydroxyethyl)terephthalate (BHET), into terephthalate. Kinetic analyses revealed that EstS1 degrades 75% of BHET in 1h, liberating mono(2-hydroxyethyl) terephthalate (MHET) and terephthalate as end products. The co-crystal structure of wild-type EstS1 with BHET exhibited the electron density of BHET, MHET, and ethylene glycol, including MHET bound at the active site, in a canonical tetrahedral intermediate conformation. The complex structure of BHET with the Ser154Ala mutant of EstS1 further accommodated two BHET molecules, one interacting directly with the catalytic triad and the oxyanion hole. MD simulation analysis revealed highly stable interactions of BHET at the active site of EstS1. Moreover, SEM imaging displayed significant degradation of the crystalline PET plastic film by EstS1 esterase over a period of 15 days, both under controlled and soil-based fluctuating environmental conditions, highlighting its versatility to varying environmental conditions. XPS analysis discovered the increase in -C-O-, -C-N-, -N-H-, and -N=O- bonds at the surface of EstS1-treated PET film, indicating effective degradation. Consequently, this comprehensive kinetic, structural, and morphology-based analysis of the PET-degrading potential of EstS1 esterase encourages further enzyme engineering studies to exploit the dual potential of EstS1 esterase to degrade both plastic and plasticizers.

biophysics↗

bioRxiv2025

Dissecting ARL15 Function in Rheumatoid Arthritis: Insights from Ex Vivo and In Vitro Synovial Fibroblast Models

ARL15, coding for a small GTPase was identified as a non-HLA susceptibility gene in rheumatoid arthritis (RA) through a GWAS in a North Indian cohort. Serum adiponectin and ARL15 levels were higher in RA patients with the associated genotype. The present study aimed to delineate the functional role of ARL15 in RA pathobiology using gene knockdown (KD) combined with transcriptomic profiling in both ex-vivo RA synovial fibroblasts (RASF) and in vitro MH7A cell lines. In RASF, ARL15 KD led to the downregulation of COMP-an extracellular matrix stabilizer linked to severe RA-alongside upregulation of adiponectin and IFN response genes such as IFI6 and USP18. Furthermore, upregulation of NPTX1 and MX1, previously associated with disease modulation and treatment response was observed. Downregulation of CTGF, CD248, and PTX3 suggested involvement of ARL15 in inflammation and RA-associated cardiovascular risk. In contrast, ARL15 KD in MH7A cells displayed distinct gene signatures with upregulated cytokines (IL1A, IL8, CXCLs) and downregulated inflammatory regulators (DOCK2, TLR4, TGFB2), reflecting an inflammatory bias distinct from the patient-derived RASF. This divergence highlights the limitations of immortalized cell models in capturing patient heterogeneity and disease complexity. However, the dual-system approach underscores the multifaceted role of ARL15 in regulating connective tissue architecture, inflammation, and immune response. These key findings position ARL15 as a promising therapeutic target, warranting further investigation in RA animal models and genomic medicine. Taken together, this work provides a compelling rationale to pursue ARL15 targeted interventions in RA management.

immunology↗

bioRxiv2025

Integrative spatial transcriptomic analysis pinpoints the role of TaMCO3 encoding ferroxidase in wheat root tip iron mobilization

Roots play an critical role in the sensing and absorption of essential minerals from the rhizosphere. Iron (Fe) deficiency, for example, triggers a well-known series of physiological and molecular responses within roots that facilitate uptake, which differs between monocots and dicots. In monocots, little is known about molecular responses that occur within specific root development zones in response to iron deprivation, and how these differences results in overall nutrient uptake. Here, we conducted a transcriptome analysis of wheat root tips under Fe deficiency (-Fe) and performed a comparative transcriptome analysis with the previous datasets generated from the whole root. Gene ontology analysis of differentially expressed genes highlighted the significance of oxidoreductase activity and metal/ion transport in the root tip, which are critical for Fe mobilisation. Interestingly, wheat, an allohexaploid species consisting of three different genomes (A, B, and D) displayed varying gene expression levels arising from the three genomes that contributed to similar molecular functions. Detailed analysis of oxidoreductase function at the root tip revealed multiple multi-copper oxidase (MCO) proteins, such as Fe-responsive TaMCO3, that likely contribute to the overall ferroxidase activity. Detailed characterisation of TaMCO3 shows that it complements the yeast FET3 mutant and rescues the -Fe sensitivity phenotype of Arabidopsis atmco3 mutants by enhancing vascular Fe loading. Transgenic wheat lines overexpressing TaMCO3 exhibited increased root Fe accumulation and improved tolerance to -Fe by augmenting the expression of Fe-mobilizing genes. Our findings highlight the role of spatially resolved gene expression in -Fe responses, suggesting strategies to reprogram cells for improved nutrient stress tolerance.

plant biology↗

bioRxiv2023

An efficient hairy root system for genome editing of a β-ODAP pathway gene in Lathyrus sativus

Grass pea (Lathyrus sativus) is an ideal legume crop for resource-poor farmers, having resistance to various biotic and abiotic stresses. The seeds of this plant are rich in protein and are the only known dietary source of L-homoarginine. Moreover, it thrives with minimal inputs making it a promising crop in grain legume breeding programs with immense potential for food security. Despite these advantages, the global area under its cultivation has decreased because of the presence of an antinutrient compound, {beta}-N-oxalyl-L-,{beta}-diamino propionic acid ({beta}-ODAP), which results in neurolathyrism both in humans and animals. Multiple efforts in the past have resulted in the development of improved varieties with low ODAP. Still, due to variations in response to the environment, stable low-ODAP lines have not been developed for large-scale cultivation. In this paper, we report in planta characterization of Oxalyl-CoA Synthetase (OCS) involved in the oxalylating step leading to {beta}-ODAP production. We established a hairy root transformation system for Lathyrus and demonstrated the genome editing of LsOCS. Further, we show that oxalate accumulates in these hairy roots due to loss-of-function of the OCS gene. This is the first report of functional analysis of a Lathyrus gene in Lathyrus. The hairy root genome editing system we developed can be used as a quick system for functional studies of Lathyrus genes.

plant biology↗

bioRxiv2022

Transcriptome and biochemical analysis pinpoint multi-layered molecular processes associated with iron deficiency tolerance in hexaploid wheat

Iron (Fe) is an essential nutrient for plants that is indispensable for many physiological activities. Although few genotypes were identified with contrasting tolerance to Fe deficiency, the molecular insight into the distinct biochemical and transcriptional responses determining the trait is poorly known. This study aimed to identify the molecular and biochemical basis for the contrasting Fe deficiency tolerance in wheat genotype showing tolerance to Fe deficiency (cv. Kanchan-KAN) compared to susceptible (cv. PBW343-PBW) cultivar. Under Fe deficiency, the KAN show delayed chlorosis, high SPAD values and low malondialdehyde activity compared to PBW. The shoot transcriptomics studies show that a large set of genes for photosynthetic pathways were highly induced in PBW, suggesting its sensitivity to Fe deficiency. Although, under Fe deficiency, both the cultivars show distinct molecular re-arrangements, including high expression of genes involved in Fe uptake (including membrane transporters) and mobilization, the gene expression level was higher in KAN. Furthermore, the KAN cultivar also shows high ubiquitination activity in the shoot tissue suggesting a high turnover of proteins in the tolerant cultivar. These observations were also co-related with the high root phytosiderophores biosynthesis and its release that contributes to the enhanced Fe translocation index in KAN. Overall, our work provides the key link to understanding the mechanistic insight for the Fe deficiency tolerance in hexaploid wheat. This will enable wheat breeders to select genotypes for better Fe use efficiency for agriculture.

plant biology↗