Biology subjects

O'Halloran, T. V.

Publications and source records attributed to O'Halloran, T. V..

12 recordsLinked to original sources

bioRxiv2026

Blank Spectrum Correction as a Robust Solution to Artifacts in Quantitative X-ray Fluorescence Mapping

X-ray fluorescence microscopy (XFM) continues to develop as a powerful quantitative technique for high resolution, label-free, elemental mapping of biological, environmental, and material samples. Methods for rigorously fitting spectra, increasing throughput, accounting for background signals, and deconvoluting overlapping emission lines continue to evolve. We show here that quantitative fits of XFM data obtained after removing a baseline, calculated by connecting peak edges, can be unexpectedly dependent upon acquisition dwell-time and spectral aggregation leading to differences in apparent elemental content. Using mouse preimplantation embryos and ovarian follicles as model samples, we demonstrate how these variables influence quantitative comparisons between samples. We find that subtracting an empirically measured blank spectrum instead of a baseline provides quantitative XFM elemental mapping results that are independent of dwell time and spectral aggregation dependencies.

biophysics↗

bioRxiv2026

Client distribution between Chlamydomonas FDX1 and FDX2 in carbon, nitrogen and sulfur assimilation

Plant-type ferredoxins (Fd) comprise small, soluble protein families that distribute electrons from photosystem I to various client proteins within the chloroplast stroma. In Chlamydomonas reinhardtii, the major, constitutively expressed FDX1/PetF supports Fd-NADP+ reductase (FNR) in NADPH production. The highly similar FDX2 is present only when its preferred nitrogen (N) source ammonium is absent, supplying Fd-dependent nitrite reductase (NiR) for nitrate/nitrite assimilation. Surprisingly, despite accumulating to [~]10% of FDX1 abundance and preferential interaction with NiR, fdx2 mutants are asymptomatic when grown on nitrate, requiring to additionally deplete FDX1 for growth to be halted. A fdx1 knockout itself appears lethal, severe fdx1 knockdowns have reduced growth rates both in phototrophic and photoheterotrophic conditions, independent of the N source. Transcriptome analyses of fdx1 mutants revealed expression patterns similar to sulfur (S) deficient algae, and fdx1 strains have a reduced total cellular S content. S assimilation requires Fd-dependent sulfite reductase (SiR) activity, an enzyme distantly related to FDX2 client NiR. Expression defects are partially alleviated; growth and S content are less impacted with FDX2 expression. Our mutant analysis shows the two major Fds in Chlamydomonas focus on a specific subset of Fd-dependent metabolism, mostly supplying Fd-dependent enzymes involved in macronutrient assimilation (C/N/S).

plant biology↗

bioRxiv2026

On-slide Preparation of Caenorhabditis elegans Towards Quantitative, High-Resolution LA-ICP-TOF Mass Spectrometry Imaging

Metal homeostasis is a complex process wherein essential metals serving structural, catalytic and regulatory roles are acquired, trafficked, and exported once they are present in excess. Understanding changes in metal content and localization in heterogenous tissue types is critical to understanding fundamental physiology as well as a growing number of disease states. Laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) imaging is a powerful technique for untargeted quantitation and mapping of metals in biological systems. While the nematode Caenorhabditis elegans (C. elegans) is a well-established model organism for fundamental biological research and metal-based diseases, there have been few reports of mass spectrometry-based imaging of C. elegans, mostly due to challenges preparing samples that maintain the native distribution of the elements. In this study, we developed an embedding, quantitation and imaging workflow that preserves C. elegans using 3D-printed uniform layer media application tools (ULMATs). Multiple embedding media were evaluated, and petrolatum, commercially known as Vaseline, stood out for its performance in preserving C. elegans for imaging applications. Worms were subjected to microscopy and LA-ICP-TOF-MS imaging where we achieved a 2-m spatial resolution by over-sampling laser shots during ablation. Quantitative elemental maps were obtained using a series of gelatin standards that were sectioned at a 40-m thickness to closely mimic the average tissue ablation depth of a Day 1 gravid adult C. elegans. Our results establish a new workflow for comprehensive elemental profiling of C. elegans using LA-ICP-TOF-MS, which holds high potential for future spatial metal biology research with C. elegans. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/698490v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7c66c5org.highwire.dtl.DTLVardef@13f4934org.highwire.dtl.DTLVardef@1df3215org.highwire.dtl.DTLVardef@512fd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

CIA5 INTERACTS WITH THE ZINC CHAPERONE ZNG3 TO BALANCECARBON AND ZINC METABOLISM

Carbon and zinc (Zn) metabolism are intrinsically connected in phototrophs, as crucial components involved in CO2 assimilation, like carbonic anhydrases, are highly abundant Zn proteins. Utilizing these and other proteins, the eukaryotic green algae Chlamydomonas reinhardtii can maintain phototrophic growth in low CO2 environments by inducing a carbon concentrating mechanism (CCM). In this work we show that Chlamydomonas dynamically increases its Zn content to accommodate the higher intracellular Zn demand in low CO2 environments. This increase requires the presence of Cia5, a major regulator of the CCM in Chlamydomonas. How Cia5 regulates expression of thousands of low CO2-inducible genes remains enigmatic, its transcript and protein abundance is unchanged in different CO2 environments, even in the presence of an additional reduced carbon source, acetate. We show here that the Cia5 protein is not present in Zn-limitation, despite CIA5 transcription being unchanged. We used a CRISPR knock-in approach to express Cia5-HA from its endogenous locus and used two independent Cia5-HA expressing strains for affinity purification and identified a protein belonging to a conserved family of metal binding GTPases, ZNG3, as a constitutive interaction partner. Like Cia5, ZNG3 is constitutively expressed, co-expressed with Cia5 along the diurnal cycle and is Cia5-dependently induced in low CO2 environments. Surprisingly, zng3 mutants do not phenocopy cia5 mutants and grow well in low CO2 conditions. Instead, zng3 mutants are unable to grow like wildtype if excess carbon is available in the form of high CO2 or acetate. Transcriptomics of wildtype and zng3 mutants grown with different carbon sources revealed that transcriptional induction of the majority of genes involved in the CCM is maintained in low CO2 grown zng3 mutants, while the degree of induction in a subset of LCI genes is reduced (HLA3, CAH4 and CAH5). Genes encoding proteins involved in plastid quality control were induced in zng3 mutants grown on acetate and high CO2, as well as other, related metallochaperones. We hypothesize that Zn trafficking towards the plastid is mis regulated in zng3 mutants resulting in protein mis-metalation and unfolding. Taken together, we propose that ZNG3 and Cia5 coordinate Zn and CO2 metabolism, affecting intracellular Zn trafficking and modulate the CO2 response.

plant biology↗

bioRxiv2025

Inorganic profiles of preimplantation embryos reveal a role for zinc in blastocyst development

Elements such as iron, copper and zinc play essential roles in the mammalian oocyte, egg, and embryo, however among these metals, zinc plays unique regulatory roles. Temporal fluctuations in zinc concentrations drive reproductive milestones such as meiotic resumption, egg activation, and initiation of the mitotic cell cycle. Roles for zinc in late preimplantation embryo development, have not been well characterized. Using a quantitative element approach we report the inorganic profiles of mouse embryos progressing through the late blastocyst stage. We find that blastocysts, like oocytes and eggs, and distinct to somatic cells, maintain higher levels of zinc than copper and iron. All three of these essential metals are more abundant in the inner cell mass, which contains the population of pluripotent stem cells that give rise to the fetus, relative to the trophectoderm which gives rise to the placenta and extraembryonic tissues. To test whether zinc abundance was associated with mitotic progress and cell fate lineage, we perturbed zinc homeostasis during blastocyst formation by artificially raising intracellular zinc concentrations with zinc pyrithione. This treatment during the morula-to-blastocyst transition when cell fate lineages emerge resulted in an elevation of zinc in the ICM. This treatment did not impact cell number but did increase expression of the pluripotency and epiblast marker, Nanog. These results demonstrate that the inorganic profiles of the late preimplantation embryo retain elemental hallmarks of earlier developmental stages and perturbation of zinc levels alters pluripotency gene expression in the blastocyst. In BriefZinc plays important regulatory roles during oocyte maturation, fertilization and early embryo development; however, the role of zinc in the late preimplantation embryo is unknown. In this study, inorganic profiling of mouse embryos reveal zinc levels are higher than copper and iron in the late blastocyst and zinc supplementation during the morula-to-blastocyst alters expression of pluripotency marker, Nanog.

developmental biology↗

bioRxiv2025

Targeting the selectivity filter to drastically alter the activity and substrate spectrum of a promiscuous metal transporter

d-Block metal transporters play a crucial role in maintaining the homeostasis of life-essential trace elements and are attractive targets for protein engineering aimed to selectively enriching or excluding metals in living organisms. However, systematic efforts to engineer these transporters have been hindered by limited understanding of their transport mechanism and substrate specificity. In this study, we applied a focused-screen approach to human ZIP8, a promiscuous d-block divalent metal transporter, by systematically changing three key residues that form the selectivity filter at the entrance of the transport pathway. Screening a library of 48 constructs using an ICP-MS-based transport assay, we identified variants with significantly altered transport activities and/or substrate preferences. The E343D variant exhibited dramatically enhanced activity for all tested metal substrates, a shift in substrate preference, and an expanded substrate spectrum including the non-substrate metals VO2+ and Cu2+. Additionally, we identified lead ion (Pb2+) as a substrate of wild-type ZIP8. These findings suggest that the ZIP fold is highly adaptable and amenable for transporting a wide range of metals with diverse physicochemical properties, making it a promising scaffold to generate novel metal transporters for applications.

biochemistry↗

bioRxiv2025

Non-redundant cardiolipin synthases support membrane integrity and stress resilience in Bacteroides fragilis

Gut-resident bacteria must tolerate diverse membrane-disrupting agents, including bile acids, to maintain colonization. Cardiolipin is an anionic phospholipid that supports membrane integrity and stress resilience in many bacteria. However, cardiolipin synthases remain poorly characterized in the Bacteroidota, a dominant phylum of the human gut microbiota. The prevalent gut commensal Bacteroides fragilis encodes two predicted cardiolipin synthases, ClsA and ClsB. We previously identified both cls genes as bile-acid fitness factors in B. fragilis P207, but the individual contributions of ClsA and ClsB to cell physiology had remained undefined. Here we combine targeted gene deletion with high-resolution lipidomics, metabolomics, and elemental mass spectrometry to show that the two enzymes have non-redundant functions in the cell. Cardiolipin is a minor lipid in the B. fragilis membrane, and both Cls enzymes contribute to its production. clsA and clsB differ in growth-phase expression, in their effects on cell morphology, and in their associated cardiolipin species. Loss of each enzyme also produces distinct changes in fitness under several membrane-perturbing stresses and in the broader cellular metabolome, including compound classes with documented bioactivity in mammalian hosts. In contrast to the acute ion-gradient disruption caused by the secondary bile acid deoxycholate, deletion of both synthases did not measurably alter steady-state intracellular ion levels under standard growth conditions, indicating that cardiolipin loss does not perturb basal ion homeostasis under these conditions. Together, these results define non-redundant roles for two cardiolipin synthases in a common member of the human gut microbiota. ImportanceInflammatory bowel diseases affect millions of people worldwide. The gut bacterium Bacteroides fragilis is a normal member of the human intestinal microbiota that can also bloom to high abundance in inflamed guts. To survive within the gut, B. fragilis must maintain the integrity and function of its cell membrane. In this study, we characterize the functional role of two B. fragilis genes that contribute to the synthesis of the membrane lipid, cardiolipin. We find that the two cardiolipin synthase genes are not functionally interchangeable; each impacts the cells lipid pool in distinct ways and contributes differently to how B. fragilis responds to membrane stress. Our work provides insight into how a common gut bacterium adapts to conditions encountered in the intestine, and improves understanding of membrane biology in this important group of gut microbes.

microbiology↗

bioRxiv2025

Multifunctional bending magnet beamline with a capillary optic for X-ray fluorescence studies of metals in tissue sections

Scanning fluorescence X-ray microscopy lets one non-destructively and quantitatively map the distribution of most biologically-important metals in cells and tissues. For studies on large-scale tissues and organs, a spatial resolution of several micrometers is often sufficient; in this case, bending magnets at synchrotron light sources provide abundant X-ray flux. We describe here the use of bending magnet beamline 8-BM-B at the Advanced Photon Source (APS) with two distinct microscopy stations: a pre-existing one with Kirkpatrick-Baez (KB) mirror optics for slightly higher throughput and the ability to accommodate samples tens of centimeters across, and a new prototype station with an axially-symmetric, single-bounce, capillary optic with slightly less flux, but slightly higher fluence (which affects achievable resolution at low metal concentration) and higher spatial resolution. The KB station provides{delta} res = 10.5 {micro}m spatial resolution at a per-pixel exposure time of tdwell = 100 ms and a fluence per time of 5.8x 107 photons /({micro}m2 {middle dot}s), while the prototype capillary station provides{delta} res = 6.3 {micro}m at tdwell = 50 ms and a fluence per time of 6.1x 107 photons ({micro}m2 {middle dot}s). We used image power spectral density to estimate the achieved spatial resolution{delta} res from individually acquired images, with{delta} res depending-on the optic, the fluorescence signal strength of the sample being imaged, and the method used to process raw fluorescence spectral data.

biophysics↗

bioRxiv2025

Autoimmune regulator deficiency causes sterile epididymitis and impacts male fertility through disruption of inorganic physiology

Autoimmune regulator (AIRE), a transcription factor expressed by medullary thymic epithelial cells, is required for shaping the self-antigen tolerant T cell receptor repertoire. Humans with mutations in AIRE suffer from Autoimmune Polyglandular Syndrome Type 1 (APS-1). Among many symptoms, men with APS-1 commonly experience testicular insufficiency and infertility, but the mechanisms causing infertility are unknown. Using an Aire-deficient mouse model, we demonstrate that male subfertility is caused by sterile epididymitis characterized by immune cell infiltration and extensive fibrosis. In addition, we reveal that the presence of autoreactive immune cells and inflammation in epididymides of Aire-deficient mice are required for iron (Fe) deposition in the interstitium, which is brought on by macrophages. We further demonstrate that male subfertility is associated with a decrease in metals zinc (Zn), copper (Cu), and selenium (Se) which serve as cofactors in several antioxidant enzymes. We also show increase in DNA damage of epididymal sperm of Aire-/- animals as a key contributing factor to subfertility. The absence of Aire results in autoimmune attack of the epididymis leading to fibrosis, Fe deposition, and Cu, Zn and Se imbalance, ultimately resulting in sperm DNA damage and subfertility. These results highlight the requirement of Aire to promote immune tolerance throughout the epididymis, disruption of which causes an imbalance of inorganic elements with resulting consequence on male fertility. Key pointsBreakdown of epididymal self-tolerance promotes disruption of inorganic elements. Autoimmunity causes interstitial fibrosis resulting in sperm DNA damage and subfertility. Elevated interstitial iron and macrophages contribute to fibrosis.

pathology↗

bioRxiv2024

A co-conserved gene pair supports Caulobacter iron homeostasis during chelation stress

Synthetic metal chelators are widely used in industrial, clinical, and agricultural settings, leading to their accumulation in the environment. We measured the growth of Caulobacter crescentus, a soil and aquatic bacterium, in the presence of the ubiquitous chelator ethylenediaminetetraacetic acid (EDTA) and found that it restricts growth by lowering intracellular iron levels. Using barcoded transposon sequencing, we identified an operonic gene pair, cciT-cciO, that is required to maintain iron homeostasis in laboratory media during EDTA challenge. cciT encodes one of four TonB-dependent transporters that are regulated by the ferric uptake repressor (Fur) and stands out among this group of genes in its ability to support Caulobacter growth across diverse media conditions. The function of CciT strictly requires cciO, which encodes a cytoplasmic FeII dioxygenase-family protein. Our results thus define a functional partnership between an outer membrane iron receptor and a cytoplasmic dioxygenase that are broadly co-conserved in Proteobacteria. We expanded our analysis to natural environments by examining the growth of mutant strains in freshwater from two lakes, each with biochemical and geochemical profiles that differ markedly from standard laboratory media. In lake water, Caulobacter growth did not require cciT or cciO and was less affected by EDTA treatment. This result aligns with our observation that EDTA toxicity is influenced by common forms of biologically chelated iron and the spectrum of free cations present in the medium. Our study defines a conserved iron acquisition system in Proteobacteria and bridges laboratory-based physiology studies with real-world conditions. IMPORTANCEMetal-chelating chemicals are widely used across industries, including as preservatives in the food sector, but their full impact on microbial physiology is not well understood. We identified two genes, cciT and cciO, that function together to support Caulobacter crescentus iron balance when cells are exposed to the common synthetic chelator, EDTA. CciT is an outer membrane transporter and CciO is a dioxygenase-family protein that are mutually conserved in many bacteria, including several human pathogens, where mutations in cciT homologs are linked to clinical resistance to the siderophore antibiotic, cefiderocol. This study identifies a conserved genetic system that supports iron homeostasis during chelation stress and illuminates the iron acquisition versatility and stress resilience of Caulobacter in freshwater environments.

microbiology↗

bioRxiv2024

Determination of metal ion transport rate of human ZIP4 using stable zinc isotopes

The essential microelement zinc is absorbed in the small intestine mainly by the zinc transporter ZIP4, a representative member of the Zrt/Irt-like protein (ZIP) family. ZIP4 is reportedly upregulated in many cancers, making it a promising oncology drug target. To date, there have been no reports on the turnover number of ZIP4, which is a crucial missing piece of information needed to better understand the transport mechanism. In this work, we used a non-radioactive zinc isotope, 70Zn, and inductively coupled plasma mass spectrometry (ICP-MS) to study human ZIP4 (hZIP4) expressed in HEK293 cells. Our data showed that 70Zn can replace the radioactive 65Zn as a tracer in kinetic evaluation of hZIP4 activity. This approach, combined with the quantification of the cell surface expression of hZIP4 using biotinylation or surface-bound antibody, allowed us to estimate the apparent turnover number of hZIP4 to be in the range of 0.08-0.2 s-1. The turnover numbers of the truncated hZIP4 variants are significantly smaller than that of the full-length hZIP4, confirming a crucial role for the extracellular domain in zinc transport. Using 64Zn and 70Zn, we measured zinc efflux during the cell-based transport assay and found that it has little effect on the zinc import analysis under these conditions. Finally, we demonstrated that use of laser ablation (LA) ICP-TOF-MS on samples applied to a solid substrate significantly increased the throughput of the transport assay. We envision that the approach reported here can be applied to the studies of metal transporters beyond the ZIP family.

biochemistry↗

bioRxiv2022

Zur and Zinc Increase Expression of E. coli Ribosomal Protein L31 Through RNA-Mediated Repression of the Repressor L31p

Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way enteric bacteria respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal subunits. Here, we report the discovery and mechanistic basis for the ability of Zur to up-regulate expression of the ribosomal protein L31 in response to zinc in E. coli. Through genetic mutations and reporter gene assays, we find that Zur achieves the up-regulation of L31 through a double repression cascade by which Zur first represses the transcription of L31p, a zinc-lacking paralogue of L31, which in turn represses the translation of L31. Mutational analyses show that translational repression by L31p requires an RNA hairpin structure within the l31 mRNA and involves the N-terminus of the L31p protein. This work uncovers a new genetic network that allows bacteria to respond to host-induced nutrient limiting conditions through a sophisticated ribosomal protein switching mechanism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/493739v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@6a6281org.highwire.dtl.DTLVardef@6942f7org.highwire.dtl.DTLVardef@ab7ce8org.highwire.dtl.DTLVardef@957d55_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗