Biology subjects

Ferrell, M.

Publications and source records attributed to Ferrell, M..

3 recordsLinked to original sources

bioRxiv2025

A horizontally acquired cyclic di-GMP phosphodiesterase regulated by zinc and quorum sensing

The second messenger cyclic di-GMP (cdG) in V. cholerae is indispensable for the regulation of biofilm formation, motility, and a variety of other important bacterial behaviors in the majority of bacteria. The human pathogen Vibrio cholerae has a diverse repertoire of diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that control the intracellular cdG concentration depending on local environmental cues and its physiological state. Determining the transcriptional regulation of these enzymes and the respective environmental signals that control their activity is important to understand how and when V. cholerae switches between motile and sessile lifestyles in different environments. In some strains of the current V. cholerae 7th pandemic El Tor biotype, the horizontally acquired Vibrio Seventh Pandemic 2 (VSP-2) island encodes an uncharacterized PDE at the gene locus vc0515 which we named zpdA (Zinc-inhibited Phosphodiesterase-A). We show here that zpdA transcription is repressed by Zur when Zn2+ is abundant, as well as by the quorum sensing regulator HapR when cells grow to high density. Furthermore, we find that the PDE activity of the purified ZpdA protein is inhibited by Zn2+ but is dependent on alternative divalent cations such as Mn2+, which we find is elevated in V. cholerae cells grown under zinc limiting conditions. We conclude that ZpdA is an active metal-dependent PDE that is regulated by Zn2+ availability at both the level of transcription and post-translation leading to elevated cdG levels when Zn2+ is abundant. Our results demonstrate the important role of metal availability in modulating cdG signaling in bacteria. ImportanceV. cholerae colonizes estuarine environments and human host where it transitions between motile to sessile states which are controlled by cdG levels. cdG levels change in response to a variety of signals and are controlled by the activity of DGCs and PDEs, enzymes that make and degrade cdG. In this work, we show that Zn2+ and the cell density regulator HapR repress ZpdA, the PDE present in the VSP-2 island, at the level of transcription, and that Zn2+unexpectedly alters the PDE activity of ZpdA protein itself. Our study highlights the role of metal availability as an important signaling cue that controls V. cholerae biology.

microbiology↗

bioRxiv2024

Gut microbial metabolite imidazole propionate impairs endothelial cell function and promotes the development of atherosclerosis

BackgroundThe microbially generated amino acid-derived metabolite imidazole propionate (ImP) contributes to the pathogenesis of type 2 diabetes. However, the effect of ImP on endothelial cell physiology and its role in atherosclerotic coronary artery disease (CAD) is unknown. Using both human and animal model studies, we investigated the potential contributory role of ImP in the development of atherosclerosis. MethodsPlasma levels of ImP were measured in patients undergoing elective cardiac angiography (n = 831) by means of ultra high-performance liquid chromatography coupled to tandem mass spectrometry. Odds ratios (ORs) and corresponding 95% confidence intervals for CAD were calculated based on the ImP quartiles using both univariable and multivariable logistic regression models. Atheroprone apolipoprotein E-/- (Apoe-/-) mice fed a high-fat diet were additionally treated with ImP (800 {micro}g) or vehicle and aortic atherosclerotic lesion area was evaluated after 12 weeks. In a mouse model of carotid artery injury, the effect of ImP on vascular regeneration was examined. Using human aortic endothelial cells (HAECs) the effect of ImP on functional properties of endothelial cells were assessed. Next-generation sequencing, western blot analysis, siRNA-based gene knockdown and tamoxifen-inducible Cre-loxP experiments were performed to investigate ImP-mediated molecular mechanisms. ResultsPlasma ImP levels in subjects undergoing cardiac evaluation were associated with increased risk for prevalent CAD. In atheroprone Apoe-/- mice ImP increased atherosclerotic lesion size. We found that ImP dose-dependently impaired migratory and angiogenic properties of human endothelial cells, and promoted an increased inflammatory response. Long-term exposure to ImP impaired the repair potential of the endothelium after an arterial insult. Mechanistically, ImP attenuated insulin receptor signaling by suppressing PI3K/AKT pathway leading to the sustained activation of the forkhead box protein O1 (FOXO1) transcription factor. Genetic inactivation of endothelial FOXO1 signaling in ImP-treated mice enhanced the angiogenic activity and preserved the vascular repair capacity of endothelial cells after carotid injury. ConclusionsOur findings reveal a hitherto unknown role of the microbially produced histidine-derived metabolite ImP in endothelial dysfunction and atherosclerosis, suggesting that ImP metabolism is a potential therapeutic target in atherosclerotic cardiovascular disease.

systems biology↗

bioRxiv2017

SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification

High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

bioinformatics↗