Projects in our lab
Current projects in the lab focus on exploring interactions that exists within biological systems.
We use microbial metabolism and vitamin biosynthesis and utilization pathways to probe enzyme-substrate, enzyme-enzyme and microbe-microbe interactions.
Have a look at some of our projects below!
How is vitamin B12's lower ligand synthesized and attached?
The anaerobic biosynthesis of Vitamin B12 involves the bza operon, which contains three methyltransferases BzaC, BzaD, and BzaE, each with unique domains and unprecedented functions. We have established that BzaC plays the role of a SAM:hydroxybenzimidazole-riboside methyltransferase*, and are currently exploring BzaD and BzaE for their mechanisms and cofactor requirements as well as the role of the Domain of Unknown Function DUF2284 embedded within the bza operon.
Cross-feeding of vitamins and their biosynthesis intermediates in microbial co-cultures
We have successfully demonstrated that synthetic co-cultures of vitamin B1 biosynthesis mutants can be used to investigate the exchange of the vitamin and its intermediates. We also look at the changing co-culture dynamics, in terms of the microbes and the concentrations of the intermediates involved.
Ecosystems in the environment are composed of microbial consortia, many of which are auxotrophic for the synthesis of essential biomolecules i.e. they are unable to synthesize them. Vitamins B1, B6, B7 and B12 and their biosynthesis intermediates are critical metabolites that microbes do not synthesize and instead obtain them from other members of their communities.
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The modular nature of the vitamin B1 (thiamin) and vitamin B6 biosynthesis allows for such auxotrophies to be commonly observed in nature. So far, the exchange of the key intermediates in this pathway has not been systematically studied
Investigating the molecular basis of nucleobase specificity in nucleotide-utilizing enzymes
Nucleotide-utilizing reactions in biological chemistry are typically specific for a particular nucleotide triphosphate inspite of the molecules ATP, CTP, GTP, and UTP being identical to one another apart from their nucleobase. For example, ATP- or GTP-dependent kinases are specific for the A or G part of the molecule, even though the reaction that occurs is a phosphate transfer. Another curious example - ATP is a commonly found as a co-substrate for the biosynthesis of cofactors FAD, NAD, SAM, and Coenzyme A, and the adenine is part of the final cofactor.
The role of adenine in this case is not catalytically apparent, and thus we imagine, could be replaced with G, C, or U to produce the corresponding 'unnatural cofactors'. We have investigated the molecular basis of adenine specificity in FAD, and are currently investigating the specificity aspect of the nucleobase in enzyme catalysis and biological chemistry (1,2,3).
Deveoping a simple, low-cost vitamin detection bioassay
Promoting vitamin literacy among the general public is hindered by the lack of effective communication regarding their biosynthesis and reliable methods for assessing the concentrations of these essential micronutrients in our daily diets. While the significance of vitamins is widely recognized, accessible and reliable quantitative information is still lacking. This project, funded by the Higher Education Financing Agency (HEFA), aims to provide a set of standardized and easy-to-conduct
biological tests (bioassays) for determining the range of vitamin (B1, B3, B6, B7, and B12) concentrations in food.
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Illustration credit: Rajiv Eipe
Investigating the structure-sequence relationship in rhodanese domain proteins to probe their role in sulfur transfer and other bacterial metabolism
Sulfur metabolism in bacteria is unique since sulfur-containing metabolites not only constitute essential cofactors (e.g., thiamin, SAM, biotin etc.) to support enzymatic reactions in the cell but play essential roles in redox homeostasis, and cell signaling providing defence against antibiotic stress conditions. The key metabolites responsible for such functions, are reactive oxidised sulfur-bound sulfur species like oxidised thioredoxin, GSH, Cysteine and gas transmitter H2S.
Recent reports provide evidence that establishes a direct link between such reactive sulfur metabolites with antibiotic resistance and oxidative stress relief in pathogenic bacteria. Sulfurtransferases are a group of enzymes responsible for producing these reactive sulfur metabolites from their less reactive reduced forms. 3-mercapto pyruvate sulfurtransferase (3-MST) and Thiosulfate sulfurtransferase (TST) are the two major sulfurtransferases involved in the biogenesis of many reactive sulfur metabolites. We have investigated methods to alter the amount of H2S and persulfides in cells by exploiting 3-MST. We are currently investigating the structure sequence relationship between different homologs of 3-MST and their differences with the TSTs, majorly focusing on understanding the molecular basis for substrate specificity, the role of the inactive domain in 3-MST, and their combined physiological effects in bacteria under oxidative and antibiotic stress conditions in both aerobic and anaerobic conditions.
Contact us for more information on what’s going on in the lab.