Biology subjects

Aron, A. T.

Publications and source records attributed to Aron, A. T..

14 recordsLinked to original sources

bioRxiv2026

A pyoverdine-type metallophore is required for lanthanide-dependent growth in Pseudomonas putida

Lanthanides (Ln) are recently discovered cofactors for alcohol metabolism in a growing number of bacteria, including the soil-dwelling bacterium Pseudomonas putida, yet the mechanisms for Ln uptake are poorly defined. Here, we discovered that the non-ribosomal peptide synthase biosynthetic gene cluster, pvdLIJD, was essential to Ln-dependent growth in P. putida. Pyoverdine G4R and its precursor ferribactin were identified as pvdLIJD gene products with La-responsive abundances, and both chelated La as well as iron. Deletion of the putative pyoverdine outer membrane transport system encoded by fpvA and exbBD:tonB were strongly linked to Ln-dependent growth in a concentration-dependent manner. Global transcriptomes were remodeled in response to La, but weak evidence of transcriptional pvdLIJD regulation and no evidence of discernment between La provided as chloride versus oxide were observed. Overall, this work establishes pyoverdines as metallophores involved in La uptake, re-framing them from strictly iron-scavenging siderophores to dual-purpose metallophores with Ln-binding activity.

microbiology↗

bioRxiv2026

A frameshift mutation drives divergent biosynthesis of metallophores in Methylobacterium extorquens

Iron is widely considered the first metallocofactor, evolving as iron-sulfur clusters in early life. While iron-chelating siderophores have been widely characterized across microbial life, the lanthanide-chelating metallophore, methylolanthanin, has only recently been described in Methylobacterium extorquens AM1. Methylolanthanin shares structural similarities to the siderophore rhodopetrobactin but contains 4-hydroxybenzoate chelating moieties in place of canonical 3,4-dihydroxybenzoates. Here we compare M. extorquens AM1, which produces methylolanthanin, and the closely related M. extorquens PA1, which produces rhodopetrobactin. We present a pathway for the biosynthesis of both metallophores and describe the unusual synthesis of methylolanthanins 4-HB moieties from tyrosine. We uncover a frameshift mutation in the predicted 3-dehydroshikimate dehydratase, mllF, that prevents production of rhodopetrobactin in AM1 through truncation of the catalytically essential N-terminus. We find that deletion of the uncharacterized gene mllG reveals a cryptic branch of the pathway, leading to production of both methylolanthanin and rhodopetrobactin. Finally, we discover that rhodopetrobactin production in this mutant is enabled through the activity of a 3-dehydroshikimate dehydratase in a separate biosynthetic gene cluster. These insights highlight an evolutionary mechanism for metallophore diversification through pseudogenization and regulation of distinct biosynthetic gene clusters with shared aromatic intermediates.

microbiology↗

bioRxiv2026

Metal homeostasis is remodeled in response to different quiescence triggers

Cells can enter a reversible non-proliferative state called quiescence either spontaneously or in response to nutrient deprivations. Metal ions are essential nutrients and play wide-ranging regulatory and signaling roles in biological processes. We previously showed that zinc is an essential nutrient for the mammalian cell cycle as zinc deprivation drives cells into quiescence, and this quiescent state is associated with changes in iron, copper, and manganese, suggesting broad remodeling of metal homeostasis. Here we examine whether metal remodeling is a general feature of quiescence by inducing quiescence via different triggers (zinc deficiency, serum starvation, and growth factor withdrawal) in MCF10A cells. Fluorescence microscopy and elemental analysis reveal significant trigger-dependent changes in the labile and total metal pools of quiescent cells. To gain insight into these differences, we carried out RNA sequencing and differential expression analysis, focusing on metal associated, metal regulatory, and metal homeostasis genes. While core quiescence pathways are shared across triggers, quiescence states remain molecularly distinct. A significant percent of 2458 metal homeostasis annotated genes are differentially expressed including 55% in starvation-induced quiescence, 50% in zinc deficiency-induced quiescence and 21% in growth factor withdrawal-induced quiescence. Our results also showed unique alteration of genes involved in major metal dependent processes including antioxidant activity, oxidative phosphorylation, heme metabolism, and chromatin accessibility in different quiescence states. Overall, this work demonstrates that metal homeostasis is systematically rewired during cellular quiescence with associated effects on genes that regulate critical biological processes. Significance StatementCells constantly evaluate their nutrient and energy status and integrate these signals into proliferation-quiescence decisions. Quiescence prevents cells from passing damage to daughter cells. Metals are essential micronutrients for biological processes. While limitation of zinc can drive cells into quiescence and alter other metals, how metals are remodeled and whether this is a common feature of quiescence was unknown. Here we examined three quiescence triggers by modifying growth media and serum, the primary source of metals. We report significant changes in labile and total Cu, Fe, Zn and Mn pools, and metal associated genes in response to distinct quiescence triggers. These changes converge on mitochondrial function, cellular antioxidant activity, and heme biosynthesis in a trigger specific manner.

cell biology↗

bioRxiv2026

Cooperative siderophore use stabilizes a protective leaf microbiome

Plant-associated microbial communities provide crucial protection against pathogens. Specialized metabolites play key roles in plant-microbe and microbe-microbe interactions and, ultimately, in plant health; however, the molecular mechanisms underlying their plant-protecting properties remain largely unknown. Nutrient deficiency (e.g., iron) on leaf surfaces creates intense competition among microbes, driving both antagonism and cooperation. Using a gnotobiotic Arabidopsis thaliana model and a synthetic leaf microbial community, we show that community stability and plant protection depend on cooperative siderophore exchange between the basidiomycete yeast Rhodotorula kratochvilovae and commensal Pseudomonas species. Removal of Pseudomonas caused a strong shift in the community metabolome and accumulation of the yeast siderophore rhodotorulic acid (RA). RA selectively promoted the growth of commensal Pseudomonas via TonB-dependent transporters, which are absent in pathogenic Pseudomonas strains. Inactivation of these transporter genes abolished RA uptake, destabilized the synthetic community, and eliminated protection against Pseudomonas syringae infection. RA and Rhodotorula also induced host iron-deficiency and jasmonate-related defense metabolites, linking microbial cooperation to plant stress responses. These findings reveal that microbial siderophore exchange acts as a key mechanism that maintains stability in the phyllosphere microbiome. Rather than solely promoting competition, iron-binding compounds can serve as cooperative currencies that align microbial fitness with host protection.

microbiology↗

bioRxiv2024

ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization

Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the re-identification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder that leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes these information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.

bioinformatics↗

bioRxiv2023

High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones

Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time. In this study, we integrated spatiotemporal and multi-omic sample collection in an intensive sampling effort of phytoplankton ecology in Monterey Bay, California during the spring of 2021. Sampling methods coupled: (1) manual shipboard CTD sampling, (2) autonomous sampling using a Long-Range Autonomous Underwater Vehicle (LRAUV) equipped with an Environmental Sampling Processor (ESP), and (3) high-resolution physical measurements by an autonomous vertical profiler (Wirewalker). Sampling occurred as upwelling waned alongside declining domoic acid (DA) and low abundances of toxigenic Pseudo-nitzschia. Conditions needed to spark a widespread and toxic Pseudo-nitzschia bloom were absent, yet low-level DA was driven by similar mechanisms to those causing elevated DA. Three DA biosynthetic intermediate molecules were reported in the environment for the first time. Both shipboard and ESP sampling approaches identified DA biosynthetic gene expression at frontal zones. DA and expression of dabA, the gene encoding the first committed step of DA biosynthesis, were higher in association with recently upwelled water that supplied nutrients for growth and DA biosynthesis. Detection of subtle variations in dab gene expression in response to environmental variation provide a window into the ecological dynamics underpinning major toxic events. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/562961v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1c1f554org.highwire.dtl.DTLVardef@d16b02org.highwire.dtl.DTLVardef@c856e1org.highwire.dtl.DTLVardef@bfd248_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health.

microbiology↗

bioRxiv2022

A Universal Language for Finding Mass Spectrometry Data Patterns

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.

bioinformatics↗

bioRxiv2021

Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors

The identity and biological activity of most metabolites still remain unknown. A key bottleneck in the full exploration of this tremendous source of new structures and pharmaceutical activities is the compound purification needed for bioactivity assignments of individual compounds and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we developed a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry, and simultaneous detection of protein binding via native mass spectrometry. While screening for new protease inhibitors from an environmental cyanobacteria community, native metabolomics revealed 30 cyclodepsipeptides as chymotrypsin binders. Mass spectrometry-guided purification then allowed for the full structure elucidation of four new specialized metabolites via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy. Together with the evaluation of biological activities, our results identified the rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as promising approach for drug discovery, chemical ecology, and chemical biology studies.

systems biology↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗

bioRxiv2020

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

bioinformatics↗

bioRxiv2020

Magnetotactic bacteria accumulate a large pool of iron distinct from their magnetite crystals

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that form intracellular nanoparticles of magnetite (Fe3O4) or greigite (Fe3S4) in a genetically controlled manner. Magnetite and greigite synthesis requires MTB to transport a large amount of iron from the environment which is subsequently concentrated in organelles called magnetosomes for crystal precipitation and maturation. X-ray absorption analysis of MTB suggests that the intracellular iron is mainly contained within the crystals, thus preventing potential toxic effects of free iron. In contrast, recent mass spectrometry studies suggest that MTB may contain a large amount of iron that is not precipitated in crystals. Here, we attempt to resolve these descrepancies by performing chemical and magnetic assays to quantify the different iron pools in the magnetite-forming strain Magnetospirillum magneticum AMB-1 cultivated at varying iron concentrations. AMB-1 mutants showing defects in crystal precipitation were also characterized following the same approach. All results show that magnetite represents at most 30 % of the total intracellular iron under our experimental conditions. We further examined the iron speciation and subcellular localization in AMB-1 using the fluorescent indicator FIP-1 that is designed for detection of labile Fe(II). Staining with this probe suggests that unmineralized reduced iron is found in the cytoplasm and associated with magnetosomes. Our results demonstrate that, under our experimental conditions, AMB-1 is able to accumulate a large pool of iron distinct from magnetite. Finally, we discuss the biochemical and geochemical implications of these results. ImportanceMagnetotactic bacteria (MTB) are a group of microorganisms producing iron-based intracellular magnetic crystals. They represent a model system for studying iron homeostasis and biomineralization in bacteria. MTB contain an important mass of iron, about 10 to 100 higher than other bacterial model such as Escherichia coli, suggesting efficient iron uptake and storage systems. Accordingly, MTB have been proposed to significantly impact the iron biogeochemical cycle in sequestering a large amount of soluble iron into crystals. Recently, several studies proposed that MTB could also accumulate iron in a reservoir distinct from their crystals. Here, we present a chemical and magnetic methodology for quantifying the fraction of the total cellular iron contained in the magnetic crystals of the magnetotactic strain Magnetospirillum magneticum AMB-1. Comparison of the mass of iron contained in the different cellular pools showed that most of the bacterial iron is not contained in AMB-1 crystals. We then adapted protocols for the fluorescent detection of Fe(II) in bacteria, and showed that iron could be detected outside of crystals using fluorescence assays. This work suggests a more complex picture for iron homeostasis in MTB than previously thought. Because iron speciation controls its solubility, our results also provide important insights into the geochemical impact of MTB. A large pool of unmineralized iron in MTB could be more easily released in the environment than magnetite, thus limiting iron sequestration into MTB crystals.

microbiology↗

bioRxiv2019

Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds

Metals are essential for the molecular machineries of life, and microbes have evolved a variety of small molecules to acquire, compete for, and utilize metals. Systematic methods for the discovery of metal-small molecule complexes from biological samples are limited. Here we describe a two-step native electrospray ionization mass spectrometry method, in which double-barrel post-column metal-infusion and pH adjustment is combined with ion identity molecular networking, a rule-based informatics workflow. This method can be used to identify metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion features with the same chromatographic profiles. As this native metal metabolomics approach can be easily implemented on any liquid chromatography-based mass spectrometry system, this method has the potential to become a key strategy for elucidating and understanding the role of metal-binding molecules in biology.

biochemistry↗

bioRxiv2019

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

bioinformatics↗