Browsing by Author "Srabani Kar"

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Algal genomics tools: technological updates and progress
(Elsevier, 2023) Niwas Kumar; Srabani Kar; Amit Srivastava; Chiranjib Banerjee; Pratyoosh Shukla
Microalgae are renewable and sustainable green biofactories that generate a huge repertoire of bioprospective products and bioenergy materials. In past decades huge advancements have been made to study the microalgal genome, transcriptome, and proteome, which have led to the generation of enormous data sets of the genome-wide transcriptome, proteome, and their interactions like protein–protein interactions in different microalgae. Such tremendous advancements are due to the development of various types of transformation, genetic manipulation strategies, and technological improvements in other fields like data analysis and machine learning, which have been applied to different microalgae. Owing to such technological advancements complemented by colossal price reduction in genome sequencing technologies, many algal genomes are sequenced now or are being sequenced. This chapter discusses the importance and recent advancements which have been made in studying the genomics of microalgae and highlights the shortcomings and benefits of different functional genomic approaches. © 2023 Elsevier Inc. All rights reserved.
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.
Protein Engineering in Cyanobacterial Biotechnology: Tools and Recent Updates
(Bentham Science Publishers, 2024) Swati Tyagi; Srabani Kar; Amit Srivastava; Pratyoosh Shukla
Cyanobacteria have emerged as a microbial cell factory to produce a variety of bioprod-ucts, including peptides and proteins. Cyanobacteria stand out among other organisms due to their photoautotrophic metabolism and ability to produce a wide range of metabolites. As photoau-totrophic hosts can produce industrial compounds and proteins by using minimal resources such as sunlight, atmospheric carbon dioxide, and fewer nutrients, cyanobacteria are cost-effective industrial hosts. Therefore, the use of protein engineering tools for rational protein design, and the de-sired modification of enzyme activity has become a desirable undertaking in cyanobacterial biolo-gy. Protein engineering can improve their biological functions as well as the stability of their intracellular proteins. This review aims to highlight the success of protein engineering in the direction of cyanobacterial biotechnology and outlines the emerging technologies, current challenges, and prospects of protein engineering in cyanobacterial biotechnology. © 2024 Bentham Science Publishers.
Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria
(Elsevier Ltd, 2022) Niwas Kumar; Srabani Kar; Pratyoosh Shukla
Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality. © 2022 Elsevier Ltd