Biology subjects

AminiTabrizi, R.

Publications and source records attributed to AminiTabrizi, R..

4 recordsLinked to original sources

bioRxiv2025

Transcriptional and metabolic stasis define desiccation-induced dormancy in a soil bacterium until water vapor initiates resuscitation.

Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soil Arthrobacter. While drying reduced cultivability relative to hydrated controls, water vapor rehydration fully restored it. Ribosomal RNA proportions remained constant throughout all treatments, and mRNA profiles showed stable composition during desiccation--changing only during transitions into and out of desiccation-induced dormancy. Six transcriptional modules displayed distinct expression patterns in desiccated-rehydrated samples relative to hydrated controls, including desiccation-rehydration responsive and rehydration-specific profiles. Targeted intracellular metabolomics revealed similarly static profiles during desiccation, with a cluster of ribonucleosides and nucleobases increasing in response to desiccation and returning to baseline levels upon rehydration with water vapor. These findings demonstrate that both mRNA and metabolite profiles remain essentially frozen in desiccated Arthrobacter, with dynamic changes occurring only during state transitions. These results have important implications in environments with frequent drying cycles where stable mRNA in dormant cells combined with intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity. Our results suggest that RNA-based activity assessments in periodically dry environments require careful consideration of dormancy-associated molecular preservation. SIGNIFICANCE STATEMENTMetabolic activity quickly ceases in drying bacteria as they enter desiccation-induced dormancy. We show mRNA and metabolite profiles were variable during drying and rewetting but did not change while desiccated. Additionally, water vapor stimulated the shift from the static to active state when exiting desiccation-induced dormancy. These shifts coincided with increased cultivability, indicating water vapor resuscitated dry cells. Because RNAs are transient, labile molecules that are turned over rapidly in growing bacteria, the presence of RNA in the environment is used as a marker for microbial activity. Our research shows this assumption may not hold for desiccated cells, indicating reliance on RNA as a marker of activity in environments that experience drying may obscure estimates of in situ microbial activity.

microbiology↗

bioRxiv2025

Creatine synthesis is a tumor suppressor pathway hypostatic to one-carbon metabolism

Methylene tetrahydrofolate reductase 2 (MTHFD2), the rate-limiting enzyme of mitochondrial one-carbon metabolism, is one of the most highly expressed metabolic enzymes across diverse cancers and lymphoproliferative disorders. However, its exact roles in oncogenic metabolism remain poorly defined. We show that MTHFD2 is a key regulator of mitochondrial energetics in Epstein-Barr virus-transformed B lymphoblastoid cell lines (LCLs), an in vitro model of post-transplant lymphoproliferative disorder (PTLD). We also delineate a role for MTHFD2 in fueling de novo creatine synthesis; MTHFD2 mediates the production of glycine, a necessary substrate for creatine synthesis, through serine catabolism. Aminomethyltransferase (AMT) suppression short-circuits the glycine cleavage system (GCS) to augment LCL mitochondrial glycine levels. Creatine synthesis is hypostatic to mitochondrial one-carbon metabolism; inhibition of creatine synthesis improves LCL fitness only when MTHFD2 is lost. Our findings emplace MTHFD2 at the nexus of amino acid and energy metabolism pathways in LCLs, with potential clinical ramifications for PTLD. Highlights* Complete activation of creatine synthesis in an in vitro cellular model of PTLD * Creatine synthesis is a major sink for mitochondrial 1C-derived glycine * Reverse GCS activity due to AMT deficiency in lymphoblastoid cells * Epistasis between mitochondrial 1C metabolism and creatine synthesis eTOC BlurbLeung et al. demonstrate that MTHFD2 is crucial for creatine synthesis in lymphoproliferative disorders. MTHFD2 supports forward 1C flux through SHMT and drives reverse GCS activity to augment mitochondrial glycine, a substrate for creatine synthesis. Tumor-suppressive effects of creatine synthesis are unmasked with MTHFD2 loss, exhibiting metabolic epistasis.

molecular biology↗

bioRxiv2024

Suppression of T cell function by phosphoethanolamine, a metabolite enriched in tumor interstitial fluid

Nutrient stress represents a significant barrier for antitumor immunity, and tumor interstitial fluid (TIF) often contains metabolites that hinder immune function. However, it is difficult to isolate the effects of tumor nutrient stress from other suppressive factors. Thus, we employed a chemically-defined cell culture medium based on the metabolomic profile of TIF: Tumor Interstitial Fluid Medium (TIFM). Culture of CD8+ T cells in TIFM limited cell expansion and impaired CD8+ T cell effector functions upon restimulation, suggesting tumor nutrient stress alone is sufficient to drive T cell dysfunction. We identified phosphoethanolamine (pEtn), a phospholipid intermediate, as a driver of T cell dysfunction. pEtn dampened TCR signaling by depleting T cells of diacylglycerol required for TCR signal transduction. Reduction of pEtn accumulation in tumors improved intratumoral T cell function and tumor control, suggesting pEtn accumulation plays a dominant role in TME immunosuppression.

immunology↗

bioRxiv2022

MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data

BackgroundMicrobiomes are now recognized as main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e. metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. ResultsHere, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line based pipeline for the analysis, visualization, and presentation of metabolomics data by direct injection FTICR-MS after molecular formula assignment has been performed. When compared to all other available FTICR software, MetaboDirect is superior with respect to its compute time as it only requires a single line of code that launches a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences that provide a comprehensive experimental assessment of metabolite connectives within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of the microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. ConclusionApplication of MetaboDirect to FTICR-MS-based metabolomics datasets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the FTICR-MS research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. Source code and Users guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/) respectively.

bioinformatics↗