Biology subjects

Shah, D. D.

Publications and source records attributed to Shah, D. D..

6 recordsLinked to original sources

bioRxiv2025

A Sulfotransferase from a Gut Microbe Acts on Diverse Phenolic Sulfate Compounds, Including Acetaminophen Sulfate

Sulfonation is one of the two main phase II detoxification pathways in eukaryotes that transforms non-polar compounds into hydrophilic metabolites. Sulfotransferases catalyze these reactions by transferring a sulfo group from a donor to an acceptor molecule. Human cytosolic sulfotransferases use only 3-phosphoadenosine 5-phosphosulfate (PAPS) as a donor to sulfonate a variety of chemicals. Less understood are microbial aryl-sulfate sulfotransferases (ASSTs), which catalyze sulfo transfer reactions, without utilizing PAPS as a donor. Currently, the identity of physiological sulfo donor substrates remains unknown and sulfo acceptor substrates are underexplored. With this study, we aim to understand the potential contribution of a gut microbial enzyme to sulfonation chemistry by uncovering substrate preferences. Here, we show that a sulfotransferase (BvASST) from the prevalent gut microbe Bacteroides vulgatus (now Phocaeicola vulgatus) is a versatile catalyst that utilizes a wide range of phenolic molecules as substrates that are commonly encountered by the host. With this action, it has the ability to modulate concentrations of donor phenolic sulfates like acetaminophen sulfate, dopamine sulfate, p-coumaric acid sulfate, indoxyl sulfate, and p-cresol sulfate in vitro. Moreover, we report a large adaptability in the acceptor preferences with the evidence of sulfonation for many biologically relevant phenolic molecules including p-coumaric acid, p-cresol, dopamine, acetaminophen, tyramine, and 4-ethylphenol. These results suggest that such gut microbial enzymes may impact the detoxification of a variety of phenolic molecules in the host, which were previously thought to be solely detoxified via human sulfotransferases. However, further in vivo studies are necessary to understand potential contributions of ASSTs in host detoxification processes.

biochemistry↗

bioRxiv2025

Competitions for tyrosine breakdown: In synthetic microbial communities and between a gut microbial pathway and a human pathway

Tyrosine, a versatile amino acid that undergoes diverse transformations to produce both beneficial and detrimental metabolites. The modulation of these metabolites results from direct competition among different metabolic pathways responsible for the breakdown of tyrosine whether it be the competition between distinct microbes or the rivalry between a microbe and its host. The fight between microbes for the available tyrosine might drive potential changes to the communities present in various environments. In contrast, if the similar contest for tyrosine is presented between a gut microbial pathway and a human pathway, it can hold potential to affect the human health. In this work, we present various metabolic outcomes of tyrosine within synthetic microbial communities which are prominently driven by specific enzyme activities of tyrosine breakdown pathways. Additionally, we developed a metabolic diversion of the human tyrosine breakdown pathway facilitated by a gut microbial enzyme. This approach holds promise as a novel strategy to develop potential therapeutic interventions in future for addressing metabolic disorders like tyrosinemias (I, II, III), hawkinsinuria, and alkaptonuria, associated with the human tyrosine breakdown pathway.

synthetic biology↗

bioRxiv2024

Diversity and prevalence of amino acid decarboxylase enzymes in the human gut microbiome -- a bioinformatics investigation

Biogenic amines play numerous biological functions that include neuromodulation, maintenance of the gut health and motility, gastric acid secretion, regulation of immune response, cell growth, and gene expression. Therefore, it is crucial to comprehend the potential modulation of these molecules by the human gut microbiota. A primary pathway for the generation of these molecules involves the decarboxylation of amino acids, a process facilitated by enzymes known as amino acid decarboxylases (AADCs). Here, we conducted a bioinformatic analysis to understand diversity and prevalence of AADCs from the most prevalent members of the human gut microbiome. This study aims to understand how human gut microbes generate metabolites that influence health and disease, through specific enzyme activities, with a focus on recognizing the potential role of gut microbiota in neuromodulation, gastrointestinal dysfunctions, immune response regulation, and other critical biological functions. Our results indicate that AADCs are most abundant in the prominent gut microbial genera, namely Bacteroides, Parabacteroides, Alistipes, and Enterococcus. Furthermore, among AADCs, arginine decarboxylases are the most common, present in approximately 60% of the frequently found members of the human gut microbiome, followed by aspartate 1-decarboxylases and glutamate decarboxylases. We also found that Enterococcus faecalis harbors the most variety of amino acid decarboxylases, potentially playing an important role in driving decarboxylation chemistry in the human gut. In addition, our sequence analyses of various AADCs demonstrated that a tetrad of amino acids in the PLP binding motif can provide functional identification for AADCs. We hypothesize that the diversity in AADCs and the microbes that harbor them has the potential to alter host metabolic outputs. This could provide a mechanism to use specific changes in microbial genera or species to understand possible metabolite modulations that might influence biological functions. Such studies could lay the groundwork for developing future disease markers or therapeutic interventions.

biochemistry↗

bioRxiv2024

Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase

Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbe Bacteroides fragilis forms multiple neuromodulatory molecules such as {gamma}-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and {beta}-alanine. We evolved BfGAD and doubled its taurine productivity. Additionally, we increased its specificity towards the substrate L-glutamate. Here, we provide a chemical strategy via which the BfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.

biochemistry↗

bioRxiv2024

Bioinformatic analysis of sulfotransferases from an unexplored gut microbe, Sutterella wadsworthensis 3_1_45B: Possible roles towards detoxification via sulfation by the members of the human gut microbiome

Sulfation, primarily facilitated by sulfotransferases, plays a crucial role in the detoxification pathways of both endogenous substances and xenobiotics, enhancing their water solubility and promoting metabolism and elimination. Traditionally, this bioconversion has been attributed to a family of human cytosolic sulfotransferases (hSULTs) known for their high sequence similarity and dependence on 3-phosphoadenosine 5-phosphosulfate (PAPS) as a sulfate donor. However, recent studies have revealed the presence of PAPS-dependent sulfotransferases within gut commensals, indicating that the gut microbiome may harbor a diverse array of sulfotransferase enzymes and may contribute to detoxification processes via sulfation. In this study, we investigated the prevalence of sulfotransferases in the members of the human gut microbiome. Interestingly, we stumbled upon a different class of sulfotransferases, known as aryl-sulfate sulfotransferases (ASSTs). ASSTs have been characterized from a few different prokaryotes including E. coli. ASSTs do not utilize PAPS which is the default sulfate donor for the human sulfotransferases. Our bioinformatics analyses revealed that the gut microbial genus Sutterella possesses a significant number of asst genes, possibly encoding multiple ASST enzymes. Fluctuations in the microbes of the genus Sutterella have been associated with various health conditions. For this reason, we characterized 17 different ASSTs from Sutterella wadsworthensis 3_1_45B with bioinformatics. Our findings reveal that SwASSTs share similarities with E. coli ASST but also exhibit significant structural variations and sequence diversity. These differences might drive potential functional diversification and likely reflect an evolutionary divergence from their PAPS-dependent counterparts.

biochemistry↗

bioRxiv2023

The prevalence of motility within the human oral microbiota

The human oral and nasal microbiota contains approximately 770 cultivable bacterial species. More than 2000 genome sequences of these bacteria can be found in the expanded Human Oral Microbiome Database (eHOMD). We developed HOMDscrape, a freely available Python software tool to programmatically retrieve and process amino acid sequences and sequence identifiers from BLAST results acquired from the eHOMD website. Using the data obtained through HOMDscrape, the phylogeny of proteins involved in bacterial flagellar motility, Type 4 pilus driven twitching motility, and Type 9 Secretion system (T9SS) driven gliding motility was constructed. A comprehensive phylogenetic analysis was conducted for all components of the rotary T9SS, a machinery responsible for secreting various enzymes, virulence factors, and enabling bacterial gliding motility. Results revealed that the T9SS outer membrane {beta}-barrel protein SprA of human oral microbes underwent horizontal evolution. Overall, we catalog motile microbes that inhabit the human oral microbiota and document their evolutionary connections. These results will serve as a guide for further studies exploring the impact of motility on shaping of the human oral microbiota.

microbiology↗