Biology subjects

Lubrano, P.

Publications and source records attributed to Lubrano, P..

6 recordsLinked to original sources

bioRxiv2026

Collective protection drives human gut microbiota response to amoxicillin treatment.

The gut microbiota is central to human health, contributing to nutrient processing, metabolite production and protection against pathogens. Yet it is also an unintended target of antibiotic treatments, particularly after oral administration. Antibiotic exposure can therefore disrupt community structure, leading to dysbiosis and promoting the selection of resistant bacteria. Although studies in patients and animal models have shown that these effects vary markedly between individuals, host-related factors have made it difficult to isolate the specific contribution of the microbiota itself. Here, we used a controlled in vitro gut model (MBRA) to examine how 16 human gut microbiotas from the NutriNet-Sante cohort respond to the widely prescribed {beta}-lactam amoxicillin (AMX). By combining dense temporal sampling, 16S amplicon sequencing and mass spectrometry, we observed highly heterogeneous response trajectories, ranging from near-stable communities to strong but reversible disruptions. These differences were not only reflected in the final magnitude of perturbation, but also in the timing, pace and recovery of microbiota change during treatment. Initial community composition partly structured these responses, as Lachnospiraceae/Bacteroidaceae ratio strongly correlated with perturbation. Dynamic quantification of AMX further showed that microbiotas differed in their capacity to deplete the drug over time, thereby altering the duration of exposure above critical concentration thresholds. Supplementation with clavulanic acid that inhibits {beta}-lactamases confirmed that this process was largely mediated by {beta}-lactamase activity. Finally, microbiotas displaying rapid AMX depletion showed reduced selection of resistant Enterobacteriaceae. Together, our results indicate that both initial community composition and the temporal dynamics of antibiotic inactivation jointly determine microbiota resilience and resistance selection.

microbiology↗

bioRxiv2024

Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state

Simultaneous measurements of library barcodes and metabolites can facilitate the screening of metabolically engineered bacterial libraries. Here, we introduce a scalable method for the parallel measurement of protein-based library barcodes and metabolites using flow-injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin, a small 76-amino-acid protein, which we labeled with N-terminal tags of six amino acids to identify bacterial strains. We demonstrate that FI-MS effectively detects intact ubiquitin proteins and identifies the N-terminal barcodes. In the same analysis, we semi-quantify relative concentrations of primary metabolites. As a proof of concept, we engineered six ubiquitin-barcoded CRISPRi strains targeting metabolic enzymes, and analyzed their metabolic profiles and ubiquitin barcodes using FI-MS. Our results show distinct metabolome changes within metabolic pathways targeted by CRISPRi. This method enables fast and simultaneously detection of library barcodes and intracellular metabolites, opening up new possibilities to measure metabolomes of engineered bacteria at scale.

synthetic biology↗

bioRxiv2024

The SPFH complex HflK-HflC regulates aerobic respiration in bacteria

The bacterial HflK-HflC membrane complex is a member of the highly conserved SPFH protein family, which is found throughout all domains of life and includes eukaryotic stomatins, flotillins, and prohibitins. These proteins organize cell membranes and are involved in various processes. However, the exact physiological functions of most bacterial SPFH proteins remain unclear. Here, we report that the HflK-HflC complex in Escherichia coli is required for growth under high aeration. The absence of this complex causes an aerobic growth defect due to a reduced abundance of IspG, a crucial enzyme in the isoprenoid biosynthetic pathway. This reduction leads to lower levels of ubiquinone, reduced respiration, lower ATP levels, and misregulated expression of respiratory genes. The regulation of aerobic respiration by the HflK-HflC complex resembles the mitochondrial respiratory defects caused by prohibitin mutations in mammalian and yeast cells, suggesting a functional commonality between these bacterial and eukaryotic SPFH proteins.

microbiology↗

bioRxiv2023

Purine nucleotide limitation undermines antibiotic action in clinical Escherichia coli

Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics1-4 and promote evolution of antimicrobial resistance (AMR)5,6. However, little is known about which metabolic pathways contribute to AMR, and the underlying mechanisms. Here, we measured antibiotic resistance of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Most of the mutant strains that showed resistance to either of the two tested antibiotics carried mutations in metabolic genes. Resistance mutations against a {beta}-lactam antibiotic (carbenicillin) were associated with purine nucleotide biosynthesis and limited the supply of ATP. We show that ATP limitation confers both resistance and tolerance against {beta}-lactam antibiotics by upregulating the purine nucleoside transporter PunC. These results are clinically relevant, because an E. coli strain isolated from a clinical specimen had a purine nucleotide limitation, which reduced its susceptibility to antibiotics.

microbiology↗

bioRxiv2020

Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics

Multidimensional fitness landscapes provide insights into the molecular basis of laboratory and natural evolution. Yet such efforts are rare and focus only on limited protein families and a single enzyme trait, with little concern about the relationship between protein epistasis and conformational dynamics. Here, we report the first multiparametric fitness landscape for a cytochrome P450 monooxygenase that was engineered for the regio- and stereoselective hydroxylation of a steroid. We developed a computational program to automatically quantify non-additive effects among all possible mutational pathways, finding pervasive cooperative sign and magnitude epistasis on multiple catalytic traits. By using quantum mechanics and molecular dynamics simulations, we show that these effects are modulated by long-range interactions in loops, helices and beta-strands that gate the substrate access channel allowing for optimal catalysis. Our work highlights the importance of conformational dynamics on epistasis in an enzyme involved in secondary metabolism and offers lessons for engineering P450s.

evolutionary biology↗

bioRxiv2018

A thermo-responsive plasmid for biconditional protein expression

Here we develop a temperature sensitive expression vector that allows the selective production of distinct proteins over different temperature ranges with a single plasmid. We use the E. coli cold shock translational control system (the cspA 5Untranslated Transcribed Region - UTR) to drive the expression of a desired protein below a certain temperature threshold, and the lambda phage pL/cI857 transcriptional repressor system to drive the expression of a different protein above a certain temperature threshold. In this developmental work we use the chromogenic reporter proteins amilCP (blue chromoprotein) and monomeric red fluorescent protein (mRFP) to assess the function of the thermo-sensitive regulatory sequences over the desired temperature ranges. Our results show temperature dependent response of the cold shock regulatory sequence. However, our sequence design for the heat shock regulatory sequence did not give the intended result. The integration of these two temperature sensitive elements into a single plasmid awaits the re-design of the heat shock sequence.

synthetic biology↗