Browsing by Author "Rajeev Kumar Azad"

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Comprehensive multifaceted gene network analysis towards understanding multi-metal and oxidative stress responses in Synechocystis PCC 6803
(Elsevier Ltd, 2025) Srabani Kar; Eetika Chot; Ahmad Bereimipour; Rajeev Kumar Azad; Pratyoosh Shukla
Cyanobacteria, owing to their simple nutrient requirements, rapid growth, and well-sequenced genomes, are recognized as powerful systems for advancing research and for the bioremediation of environmental pollutants, including heavy metals and antibiotic residues. Among them, the widely studied Synechocystis sp. PCC 6803 serves as a well-established molecular chassis for diverse biotechnological applications. In this study, we explored the Synechocystis PCC 6803 transcriptomic data to decipher the multi-metal and oxidative stress-related gene co-expression networks and hub genes using the Weighted Gene Co-expression Network Analysis (WGCNA) tool. Our study revealed that cofactor biosynthesis, transcriptional regulatory proteins, efflux pumps, and the degradation of L-tryptophan and L-arginine constitute crucial responses of PCC 6803 specifically to H2O2 stress. Notably, the ABC-transporter functions prominently under Zn and Fe stress, where an ATP-independent periplasmic transporter was uniquely associated with Cd stress. In addition, the glutathione-mediated antioxidant defense was uniquely linked to Fe stress, carotenoid to both H2O2 and Zn stresses, and phosphorelay signalling to Fe and H2O2 stresses. Further, the DNA topoisomerase I and low-affinity CO2 uptake proteins were identified as common hub proteins in both WGCNA and PPI analyses, critically responsive to H2O2 and Zn stresses, respectively. Our studies revealed shared and unique mechanisms orchestrated by Synechocystis PCC 6803 against different metals and oxidative stress, providing valuable insights into stress-tolerant strain engineering for various bioremediation applications. © 2025 Elsevier Ltd.
Improved GA-ANN based optimized bio-deinking strategy for laccase produced from Trametes versicolor GGRK18, and its gene co-expression network analysis
(Elsevier Ltd, 2025) Guddu Kumar Gupta; Tallon Coxe; Eetika Chot; Rajeev Kumar Kapoor; Deepak Chhabra; Nishi K. Bhardwaj; Rajeev Kumar Azad; Pratyoosh Shukla
Recycling of waste paper through chemical deinking process led the generation of toxic agents and caused severe issues. Therefore, an alternative deinking process of recycled waste paper is necessity to sustain the eco-friendly environment. This study reports the production of laccase from Trametes versicolor GGRK18 using a genetic algorithm-artificial neural network (GA-ANN) tool, resulting in increased 21.5-fold i.e., 42.06 ± 1.1–906.17 ± 46.76 U/mL laccase activity. The biochemical studies revealed that laccase showed optimum activity at 60 ℃ and pH 4.0, retaining more than 90 % residual activity . Interestingly, the metal ion K+ influenced the laccase activity by 4830.91 ± 129.3 U/mL, and obtained laccase showed an apparent K m value of 0.5 µM and V max of 1666.67 µmol/mL/min. Furthermore, the deinking efficiency was improved by 48 % and 29.3 % for photocopier and newspaper, while the brightness increased by 34.6 % and 10.4 %, respectively, compared to the control values. The tearing index was significantly improved with 18.2 % and burst factor efficiently decreased by 21.1 % of deinked pulp. Furthermore, our study employs Weighted Correlation Network Analysis (WGCNA)-an R package designed to elucidate gene interactions– using next-generation sequencing data. The resulting network revealed over 70000 interactions among approximately 8917 unique genes, which clustered into 11 distinct modules of co-expressed genes; importantly, laccase genes exhibited co-expression patterns associated with various metabolic processes and oxidative stress pathways. In addition, this study also gives a combinatory strategy for waste paper recycling using laccase-mediated paper deinking and its mechanistic understanding of co-expressed genes in T. versicolor. © 2025 Elsevier Ltd.