Biology subjects

Tohidifar, P.

Publications and source records attributed to Tohidifar, P..

4 recordsLinked to original sources

bioRxiv2026

Metabolic engineering of Yarrowia lipolytica for higher fatty alcohol production

Fatty alcohols are versatile chemicals with growing demand across a broad range of industries, yet conventional production methods pose environmental challenges. Microbial biosynthesis offers a promising alternative, if hosts can be engineered to achieve high product titers. The industrially relevant oleaginous yeast Yarrowia lipolytica is well suited to this challenge because of its natural capacity for lipid metabolism. Here, we engineered Y. lipolytica W29 for fatty alcohol production by disrupting pathways involved in lipogenesis and fatty alcohol oxidation, identifying fatty alcohol oxidation as a major constraint on product accumulation. Initial engineering yielded fatty alcohol titers of 2.5 g/L from 40 g/L glucose. Subsequent optimization of media supplements and nutrient concentrations, combined with deletion of the citrate transporter CEX1 and addition of 1% Tergitol to the extractive culture medium, increased titers to 10.9 g/L in shake flasks with 80 g/L glucose and a carbon-to-nitrogen ratio of 60. Scaling the process to fed-batch bioreactor cultivation further increased titers to 19.4 g/L. These results demonstrate that combining metabolic engineering with medium and process optimization enables high-titer fatty alcohol production in Y. lipolytica.

synthetic biology↗

bioRxiv2021

Characterization of opposing responses to phenol by Bacillus subtilis chemoreceptors

Bacillus subtilis employs ten chemoreceptors to move in response to chemicals in its environment. While the sensing mechanisms have been determined for many attractants, little is known about the sensing mechanisms for repellents. In this work, we investigated phenol chemotaxis in B. subtilis. Phenol is an attractant at low, micromolar concentrations, and a repellent at high, millimolar concentrations. McpA was found to be the principal chemoreceptor governing the repellent response to phenol and other related aromatic compounds. In addition, the chemoreceptors McpC and HemAT were found to the govern the attractant response to phenol and related compounds. Using receptor chimeras, McpA was found to sense phenol using its signaling domain rather than its sensing domain. These observations were substantiated in vitro, where direct binding of phenol to the signaling domain of McpA was observed using saturation-transfer difference nuclear magnetic resonance. These results further advance our understanding of B. subtilis chemotaxis and demonstrate that the signaling domain of B. subtilis chemoreceptors can directly sense chemoeffectors. IMPORTANCEBacterial chemotaxis is commonly thought to employ a sensing mechanism involving the extracellular sensing domain of chemoreceptors. Some ligands, however, appear to be sensed by the signaling domain. Phenolic compounds, commonly found in soil and root exudates, provide environmental cues for soil microbes like Bacillus subtilis. We show that phenol is sensed both as an attractant and a repellent. While mechanism for sensing phenol as an attractant is still unknown, we found that phenol is sensed as a repellent by the signaling domain of the chemoreceptor McpA. This study furthers our understanding of the unconventional sensing mechanisms employed by the B. subtilis chemotaxis pathway.

microbiology↗

bioRxiv2020

The unconventional cytoplasmic sensing mechanism for ethanol chemotaxis in Bacillus subtilis

Motile bacteria sense chemical gradients using chemoreceptors, which consist of distinct sensing and signaling domains. The general model is that the sensing domain binds the chemical and the signaling domain induces the tactic response. Here, we investigated the unconventional sensing mechanism for ethanol taxis in Bacillus subtilis. Ethanol and other short-chain alcohols are attractants for B. subtilis. Two chemoreceptors, McpB and HemAT, sense these alcohols. In the case of McpB, the signaling domain directly binds ethanol. We were further able to identify a single amino-acid residue Ala431 on the cytoplasmic signaling domain of McpB, that when mutated to a serine, reduces taxis to ethanol. Molecular dynamics simulations suggest ethanol binds McpB near residue Ala431 and mutation of this residue to serine increases coiled-coil packing within the signaling domain, thereby reducing the ability of ethanol to bind between the helices of the signaling domain. In the case of HemAT, the myoglobin-like sensing domain binds ethanol, likely between the helices encapsulating the heme group. Aside from being sensed by an unconventional mechanism, ethanol also differs from many other chemoattractants because it is not metabolized by B. subtilis and is toxic. We propose that B. subtilis uses ethanol and other short-chain alcohols to locate prey, namely alcohol-producing microorganisms. ImportanceEthanol is a chemoattractant for Bacillus subtilis even though it is not metabolized and inhibits growth. B. subtilis likely uses ethanol to find ethanol-fermenting microorganisms for prey. Two chemoreceptors sense ethanol: HemAT and McpB. HemATs myoglobin-like sensing domain directly binds ethanol, but the heme group is not involved. McpB is a transmembrane receptor consisting of an extracellular sensing domain and a cytoplasmic signaling domain. While most attractants bind the extracellular sensing domain, we found that ethanol directly binds between inter-monomer helices of the cytoplasmic signaling domain of McpB, using a mechanism akin to those identified in many mammalian ethanol-binding proteins. Our results indicate that the sensory repertoire of chemoreceptors extends beyond the sensing domain and can directly involve the signaling domain.

microbiology↗

bioRxiv2019

Four chemoreceptors govern bidirectional pH taxis in Bacillus subtilis

We investigated pH taxis in Bacillus subtilis. This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We found that four chemoreceptors are involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid and base-sensing chemoreceptors, we identified four critical amino-acid residues - Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB - involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria.\n\nIMPORTANCEMany bacteria can sense the pH in their environment and then use this information to direct their movement towards more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis. This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid and base sensing chemoreceptors. By analyzing the response of these chimeric receptors, we were able to identify four critical amino-acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.

microbiology↗