Biology subjects

Young, J.

Publications and source records attributed to Young, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Predicting cyanobacterial oxic diazotrophy and prioritizing candidate protein families beyond known Nif proteins

Diazotrophic cyanobacteria must reconcile oxygenic photosynthesis with the oxygen sensitivity of nitrogenase. Engineering studies have demonstrated nitrogenase activity in a non-diazotrophic cyanobacterium while highlighting the importance of accessory functions and oxygen management. Robust aerobic nitrogen fixation remains challenging, motivating systematic identification of candidate support functions beyond the canonical Nif machinery. We modeled nifHDK-defined diazotrophic potential from protein-family presence or absence in 426 cyanobacterial assemblies. Four classifiers evaluated with genus-blocked cross-validation achieved mean ROC AUCs of 0.853 to 0.893, with purity and genus-breadth filters fitted within training folds. Restricting the panel to 401 assemblies with current NCBI status gave AUCs of 0.806 to 0.881. Family-content logistic regression outperformed a genome-size-only baseline across ten genus partitions. Two inventories describe candidates across the full panel: 981 high-purity families and 473 families with positive residual associations (accompanied by three ubiquitous controls). Model importance orders the residual-association inventory. A separate heuristic score combines inventory membership with proteomics, condensate-driver ranks and genus-based morphotype proxies to prioritize 167 families for experiments. Proteomics annotations tracked detection opportunity; the condensate contrast between inventories attenuated after prevalence adjustment. These annotations help choose experiments but do not independently validate accessory functions. Protein-family content predicts nifHDK-defined diazotrophic potential, with performance sensitive to assembly inclusion, taxonomy, genome size and taxonomic weighting. The two candidate inventories distinguish high carrier purity from residual association, providing complementary resources for prioritizing previously uncharacterized functions associated with cyanobacterial oxic diazotrophy.

bioinformatics↗

bioRxiv2026

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

neuroscience↗

bioRxiv2026

Actin-related ACTL8 localizes to the nucleus and modulates locus-specific transcription through chromatin regulation

Actin-related proteins (Arps) are evolutionarily ancient and broadly expressed, yet some Arps evolved in mammals and acquired germline-specific expression. Here, we investigate the germline-specific Arp "Actin-like 8" (ACTL8), which is also misexpressed in multiple cancers with unexplored molecular roles. We show that ACTL8 surprisingly localizes to the nucleus of spermatogonia in human testes and breast and lung cancer cells. In breast cancer cells, ACTL8 misexpression alters transcriptional programs primarily in cell migration pathways, and ACTL8 depletion increases migration rate. Mechanistically, we find that ACTL8 interacts with KDM5B, an H3K4 demethylase and transcriptional repressor, and demonstrate that this interaction contributes to changes in migration. Consistent with this, ACTL8 loss increases H3K4me3 at genes associated with migration, indicating transcriptional activation. These findings establish ACTL8 as a novel nuclear Arp that plays a role in KDM5B-mediated transcriptional repression, providing insight into its function in chromatin regulation in cancer and potentially spermatogenesis.

cell biology↗

bioRxiv2026

Nitrogen-Responsive Extracellular Proteomics Reveals Evidence for a Novel Heterocyst-Specific Protein Secretion Pathway in Anabaena

Nitrogen availability is a major factor governing the physiology, ecology, and metabolism of cyanobacteria. Here, we performed a comparative extracellular proteomic analysis of Anabaena sp. PCC 7120 grown under nitrate-replete and diazotrophic conditions. Using LC-MS/MS, we identified 115 extracellular proteins in nitrate-grown cultures and 113 proteins under N2-fixing conditions. Remarkably, SignalP 6.0 predicted canonical signal peptides in only [~]22% of the identified proteins, suggesting that extracellular protein export in Anabaena predominantly occurs through non-classical secretion mechanisms, potentially involving extracellular vesicles or other unrecognized pathways. Six highly abundant extracellular proteins (Alr2938, Alr4550, Alr2328, All4121, Alr0528, and Alr0529) were detected under both nitrogen regimes. In contrast, All4337, Alr0608, and All3093 were preferentially enriched under nitrate-replete conditions, whereas Alr0267 and Alr1050 emerged among the most abundant extracellular proteins during diazotrophic growth. Notably, an Alr0267-GFP fusion protein was detected exclusively in heterocysts, the specialized N2-fixing cells of Anabaena, with GFP fluorescence concentrated at the cell periphery. The extracellular localization of Alr0267 is particularly intriguing because heterocysts are surrounded by specialized polysaccharide and glycolipid envelope layers that establish the microoxic environment required for nitrogenase activity. The apparent export of Alr0267 across these barriers provides evidence for a previously unrecognized heterocyst-associated protein secretion pathway. Together, these findings reveal a nitrogen-responsive extracellular proteome and provide the first evidence for heterocyst-specific extracellular protein secretion. This work advances our understanding of heterocyst biology and protein trafficking while laying a foundation for engineering Anabaena as a sustainable photosynthetic platform for secreting high-value proteins using sunlight, CO2, N2, and mineralized water.

molecular biology↗

bioRxiv2026

Nitrosomes: protein language modeling and live-cell imaging reveal condensate-like nitrogenase organization in heterocysts

Biological nitrogen fixation in some filamentous cyanobacteria occurs in heterocysts, yet the subcellular organization of nitrogenase in these cells remains poorly defined. Using fluorescence microscopy of living Anabaena sp. PCC 7120, we found that a NifH-GFP fusion forms discrete puncta restricted to mature heterocysts, whereas constitutively expressed GFP in vegetative cells and a nifB-linked GFP reporter remained diffuse. To contextualize this phenotype, we built a homology-aware cyanobacterial condensate-prioritization framework across 31,028 proteins from seven proteomes, integrating ESM-2 embeddings, 27 biophysical features, and 44 curated condensate-associated positives. Because direct positives remain limited, we present the model as a ranking resource rather than a calibrated classifier. Under a deliberately conservative nitrogenase-withheld analysis that removed nitrogenase-family labels and homologous clusters from the training data, NifH retained a median rank in the highest-scoring 4.8% of cyanobacterial proteins. catGRANULE 2.0 also assigned high scores to nitrogenase iron proteins, while having only modest rank concordance to the whole atlas. Together, these data identify heterocyst-restricted NifH-GFP puncta as evidence of sub-cellular spatial organization and provide a curated resource for prioritizing cyanobacterial condensate candidates, some of which are also important for nitrogen fixation.

molecular biology↗

bioRxiv2026

scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies

Longitudinal single-cell clinical studies enable tracking within-individual cellular dynamics, but methods for modeling temporal phenotypic changes and estimating power remain limited. We present scLASER, a framework detecting time-dependent cellular neighborhood dynamics and simulating longitudinal single-cell datasets for power estimation. Across benchmark experiments, scLASER shows consistently higher sensitivity than traditional cluster--based approaches, with particularly pronounced gains in rare cell types and non-linear temporal patterns. Applications to inflammatory bowel disease (95,813 cells, 38 patients) reveal treatment-responsive NOTCH3+ stromal trajectories with high cell type discrimination (AUC > 0.92), while analysis of COVID-19 data (188,181 cells, 84 patients) identifies three distinct axes of T cell activity (cytotoxic effector, NK immunoreceptor signaling, and interferon-stimulated gene programs) over disease progression. scLASER enables robust longitudinal single-cell analysis and optimization of study design. TeaserA new framework detects time-dependent cellular dynamics and enables power estimation for longitudinal clinical single-cell studies.

bioinformatics↗

bioRxiv2026

Cyclome: Large-scale replica-exchange dynamics of 930 cyclic peptide reveal thermal stability and critical metal-binding behavior

Cyclic peptides are recognized as versatile scaffolds for therapeutic and functional applications due to their structural stability and resistance to degradation. Despite this promise, systematic analysis and prediction of their thermal stability remain limited by fragmented data resources, inadequate sequence comparison methods, and the lack of cyclicity-aware computational models. We provide a comprehensive, multi-scale computational framework to characterize cyclic peptides. First, we unified four fragmented public repositories of cyclic peptides into a single largest curated resource of 930 cyclic peptides, Cyclome930. This integrates cyclic topology, sequence, experimental structural coordinates, and source organism annotations into a consistently featurized dataset. Cyclome930 thus expands the dataset of annotated cyclic peptides by [~]3.4 fold (from 276 to 930). Second, we developed a novel cyclic sequence alignment algorithm that explicitly accounts for rotational symmetry and knot topology, enabling more accurate scoring of sequence similarity than conventional linear alignments. Third, we investigate the thermal stability of cyclic peptides using extensive all-atom replica-exchange molecular dynamics (100ns; REMD) simulations, allowing conformational sampling across 298 K - 400 K and track its stress tensors with increasing temperature. Finally, these simulation-derived thermo-stability metrics were used to train a machine learning model to predict cyclic peptide melting points from sequence and topology (STop2Melt). Crucially, the model introduces cyclicity-aware embeddings derived from ESMc representations coupled with cyclic offset vector, capturing the peptides knot topology. STop2Melt achieved strong predictive performance on held-out peptides and outperforms baseline methods that neglect cyclic structure. Finally, we scored Cyclome930 (cyclic ligands) for critical mineral metal binding using a multi-classifier model (CritiCL). To our knowledge, Cyclome930 represents the first effort in peptide literature to integrate physics-based temperature ramped simulations, cyclic sequence similarity scoring, machine learning for thermal stability prediction and scoring them for critical metal binding. Cyclicity-aware computational toolchains (cyclome930.studio/) provide a foundational resource for computational design of stable cyclic peptide prototype libraries thereby annotating and expanding genomic islands linked to critical mineral recovery.

bioinformatics↗

bioRxiv2026

Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at the PICALM-EED locus for Alzheimer Disease

ObjectiveBoth the phosphatidylinositol binding clathrin assembly protein gene (PICALM) and the embryonic ectoderm development gene (EED) have been implicated as causal genes driving a genome-wide association for Alzheimer disease (AD) risk. We employed a new virtual approach using genome-wide chromatin interactions (Hi-C) called enhanced Hi-C Capture Analysis (eHiCA) to identify the genes and regulatory regions that are driving this important AD risk association. MethodsHi-C data from the frontal cortex of eight AD patients, as well as inducible pluripotent stem cell-derived microglia and spheroids of AD and control patients were used. We applied 14 eHiCA baits each containing a GWAS SNP to identify the cis regulatory interactions in this GWAS locus at a 5kb resolution. ResultsThe baits derived from the GWAS associated haplotype primarily interacted with the PICALM promoter and the large cis-regulatory elements cluster (CREe) lying upstream of the EED promoter. The EED promoter interacts with PICALM gene body and promoter region but not directly with the associated risk haplotype. Although the AD-associated variants segregate together as a haplotype in the population, each bait exhibited distinct functional chromatin interactions. InterpretationThe PICALM gene is the primary driver of the association in microglia along with the CREe locus. Different SNPs in a segregating haplotype can display different physical Hi-C interactions. This study demonstrates that eHiCA can help resolve the casual genes driving complex GWAS associations, opening new pathways to study Alzheimer disease and other disorders.

genomics↗

bioRxiv2025

Finding ancestry-specific chromatin architecture in Alzheimer's disease

Genetic risk for Alzheimers Disease (AD) varies across populations. We hypothesized that three-dimensional (3D) genome architecture variations could offer novel epigenetic understanding of ancestry-specific genetic risk. Herein, we performed Hi-C analyses of frontal cortex from APOE {varepsilon}4/{varepsilon}4 individuals with African (AF) or European (EU) ancestry who also had single nuclei ATAC-seq and RNA-seq data available. Ancestry-specific 3D genome architecture was found at both compartment and chromatin loop levels. EU genomes have more active compartments than AF genomes, consistent with our previous report of higher chromatin accessibility in EU than AF genome. Of the over one million chromatin loops identified by the DeepLoop pipeline, we called 12,082 putative EU-specific and 2885 putative AF- specific loops. The AF-specific loops are smaller (median size =158 kb) and likely represent promoter-enhancer interactions, while EU-specific loops are larger (median size = 496 kb) and enriched for CTCF loops. We found that differently expressed genes between AF and EU ancestries were significantly enriched at the putative ancestry-specific loop loci (Fisher-test; p<2.2x10-16; OR=5.13). High confidence HiC-QTLs (N=38) were identified after filtering with CTCF consensus sequence and chromatin accessibility-QTLs. Our study demonstrates variations in 3D genome structure between ancestries, which may contribute to the ancestry-specific genetic risk.

genetics↗

bioRxiv2025

Aberrant recursive splicing in a human disease locus

Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as does the role of recursive splicing (RS) in human disease. From analyses of rare copy number variants (CNVs) from almost one million individuals, we previously identified large, heterozygous deletions eliminating an RS site (RS1) in the first intron of CADM2 that conferred substantial risk for attention deficit hyperactivity disorder (ADHD) and other neurobehavioral traits. CADM2 encodes a neuronally expressed cell adhesion molecule that has repeatedly been associated with ADHD and numerous similar traits. To explore the molecular impact of RS ablation in CADM2, we used CRISPR to model patient deletions and to target a smaller region ([~]500 base pairs) containing RS1 in both human induced neurons (iNs) and rats. Transcriptome analyses in unedited iNs provided a catalog of CADM2 transcripts, including novel transcripts that retained RS exons. Intriguingly, ablating RS1 altered the gradient of RNA abundance across the first intron of CADM2, decreased the level of CADM2 expression, and impacted transcript usage. Decreased CADM2 expression was reflected in reduced exon usage downstream of the RS1 site and global alteration to genes involved in neuronal processes including synapse and axon development. Given the scale of our analyses and the widespread association of CADM2 with neurobehavioral traits, we sought to validate these findings using in vivo models and found that rodent models harboring Cadm2 RS1 deletions exhibited significant changes in relevant behaviors and functional brain connectivity. In summary, our analyses demonstrate a functional role for RS as a noncoding regulatory mechanism in a gene associated with a spectrum of neuropsychiatric and behavioral traits. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/666599v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@171156borg.highwire.dtl.DTLVardef@13553baorg.highwire.dtl.DTLVardef@bee7forg.highwire.dtl.DTLVardef@156f19e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genomics↗

bioRxiv2025

Electrocorticographic Detection of Speech Networks in Glioma-infiltrated Cortex

Direct cortical stimulation (DCS) is the clinical gold standard for identifying functional cortex in the human brain, which is essential for the safe removal of brain lesions. Defining the electro-physiological properties of DCS- positive cortical regions may facilitate the identification of critical language regions, thereby permitting safe glioma resections in communities without access. Leveraging a multicenter electrophysiologic dataset of DCS- positive language regions spatially matched with subdural arrays, we analyzed regions identified as functionally critical (DCS+) versus functionally non-critical (DCS-) during intraoperative language mapping. In IDH-mutant gliomas, DCS+ regions exhibited significantly greater speech-related neural activity and enhanced encoding and decoding of linguistic and semantic features. We demonstrate that resting-state classifiers distinguish DCS+ from DCS- regions in IDH-mutant tumors. Task-based and resting-state electrophysiologic distinctions were pathology-specific and not present in IDH-wildtype glioblastomas. These findings may accelerate DCS mapping by guiding surgeons to priority regions, improving efficiency, and patient outcomes.

neuroscience↗

bioRxiv2025

WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm

Human pluripotent stem cells (hPSCs) can be used as a scalable source of lymphocytes for adoptive cell therapies, contingent on the robust generation of definitive hematopoietic intermediates. Early WNT activation with CHIR99021 during mesoderm induction promoted the formation of KDR+ ALDH1A2+ mesodermal progenitors and subsequent generation of T cells in a retinoic acid (RA)-dependent manner. Integrated scRNA-seq and ATAC-seq defined a WNT-dependent developmental trajectory from hPSCs to KDR+ ALDH1A2+ mesoderm. Gene regulatory network modeling predicted HDAC2 and E-box transcription factors as regulators of RA-responsive mesodermal differentiation downstream of WNT. HDAC2 knockout impaired, while HDAC2 overexpression enhanced, KDR+ ALDH1A2+ progenitor formation. E-box factor manipulation had no discernible effect. An orthogonal chemical screen confirmed that HDAC2 inhibition suppressed KDR+ ALDH1A2+ mesodermal progenitors, whereas modulating histone methylation enhanced their formation. These findings reveal mechanisms by which WNT signaling promotes RA-responsive mesoderm and suggest methods to improve the generation of lymphocytes from hPSCs.

developmental biology↗

bioRxiv2025

Microbial communities in Caldicellulosiruptor spp. pretreatment vessels and anaerobic digesters fed dairy manure

Hyperthermophilic pretreatment with Caldicellulosiruptor species (EBP) increases substrate availability in anaerobic digestion, but the effect on downstream microbial community composition in industrial systems is not characterized. Changes in microbial communities were determined at an industrial facility processing dairy manure in a modified split-stream system with three reactor types: 1) EBP tanks at 70-72{degrees}C, 2) mesophilic Continuously Stirred Tank Reactors (CSTRs), and 3) mesophilic Induced Bed Reactors (IBRs) receiving combined CSTR and EBP effluent. All reactors had a two-day hydraulic retention time. Samples were collected weekly for 60 days. pH, volatile fatty acid and bicarbonate concentrations, COD, and methane yield were measured to assess tank environmental conditions. Microbial community compositions were obtained via 16S rRNA gene sequencing. EBP pretreatment increased acetate availability but led to a decline in the relative abundance of acetoclastic Methanosarcina species in downstream IBRs. Rather, syntrophic methanogens, e.g., Methanobrevibacter species, increased in relative abundance and became central to microbial co-occurrence networks, particularly in association with hydrogen-producing bacteria. Network analysis also demonstrated that these syntrophic relationships were tightly coordinated in pretreated digestate but absent in the untreated CSTRs. By promoting syntrophic methanogenesis while increasing acetate concentrations, EBP pretreatment requires system configurations that enable acetoclast retention to prevent acetate underutilization and maximize methane yields. ImportanceHyperthermophilic Caldicellulosiruptor pretreatment in anaerobic digestion increased acetate availability while suppressing acetoclastic methanogens and promoting robust syntrophic methanogenic networks. The results offer engineers microbial guidance essential for designing effective multi-stage industrial anaerobic digestion facilities employing EBP methods.

microbiology↗

bioRxiv2025

IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma

The glioblastoma tumor immune microenvironment (TIME) is an immunosuppressive barrier to therapy that encumbers glioblastoma responses to immune checkpoint inhibition (ICI). Immunosuppressive cytokines, pro-tumor myeloid cells, and exhausted T-cells are hallmarks of the glioblastoma TIME. Here we integrate spatial and single-cell analyses of patient-matched human glioblastoma samples before and after ICI with genetic, immunologic, single-cell, and pharmacologic studies in preclinical models to reveal that interleukin-6 (IL-6) inhibition reprograms the glioblastoma TIME to sensitize mouse glioblastoma to ICI and radiotherapy. Rare human glioblastoma patients who achieve clinical responses to ICI have lower pre-treatment IL-6 levels compared to glioblastomas who do not respond to ICI. Immune stimulatory gene therapy suppresses IL-6 tumor levels in preclinical murine models of glioblastoma. Furthermore, survival was longer in Il-6 knockout mice with orthotopic SB28 glioblastoma relative to wild-type mice. IL-6 blockade with a neutralizing antibody transiently sensitizes mouse glioblastoma to anti-PD-1 by increasing MHCII+ monocytes, CD103+ migratory dendritic cells (DCs), CD11b+ conventional DCs, and effector CD8+ T cells, and decreasing immunosuppressive Tregs. To translate these findings to a combination treatment strategy for recurrent glioblastoma patients, we show that IL-6 blockade plus ICI durably sensitizes mouse glioblastoma to high-dose radiotherapy.

cancer biology↗

bioRxiv2025

A genome wide CRISPR screen reveals novel determinants of long-lived plasma cell secretory capacity

Plasma cell subsets vary in their lifespans and ability to sustain humoral immunity. We conducted a genome-wide CRISPR-Cas9 screen in myeloma cells for factors that promote surface expression of CD98, a marker of longevity in mouse plasma cells. A large fraction of genes found to promote CD98 expression in this screen are involved in secretory and other vesicles, including subunits of the V-type ATPase complex. Genetic ablation and chemical inhibition of V-type ATPases in myeloma cells and primary plasma cells, respectively, reduced antibody secretion. Mouse and human long-lived plasma cells had greater numbers of acidified vesicles than their short-lived counterparts, and this correlated with increased antibody secretory capacity. The screen also revealed a requirement for the signaling adapter MYD88 in CD98 expression. Plasma cell-specific deletion of Myd88 led to reduced survival and antibody secretion by antigen-specific cells in vivo and unresponsiveness to BAFF and APRIL ex vivo. These data reveal novel regulators that link plasma cell secretory capacity and lifespan. SummaryLong-lived plasma cells rely on V-type ATPases, PI4K, DDX3X, and MYD88 signals for maximal secretory capacity and survival

immunology↗

bioRxiv2025

CellPhenoX: An eXplainable Cell-specific machine learning method to predict clinical Phenotypes using single-cell multi-omics

Single-cell technologies have enhanced our knowledge of molecular and cellular heterogeneity underlying disease. As the scale of single-cell datasets expands, linking cell-level phenotypic alterations with clinical outcomes becomes increasingly challenging. To address this, we introduce CellPhenoX, an eXplainable machine learning method to identify cell-specific phenotypes that influence clinical outcomes. CellPhenoX integrates classification models, explainable AI techniques, and a statistical framework to generate interpretable, cell-specific scores that uncover cell populations associated with relevant clinical phenotypes and interaction effects. We demonstrated the performance of CellPhenoX across diverse single-cell designs, including simulations, binary disease-control comparisons, and multi-class studies. Notably, CellPhenoX identified an activated monocyte phenotype in COVID-19, with expansion correlated with disease severity after adjusting for covariates and interactive effects. It also uncovered an inflammation-associated gradient in fibroblasts from ulcerative colitis. We anticipate that CellPhenoX holds the potential to detect clinically relevant phenotypic changes in single-cell data with multiple sources of variation, paving the way for translating single-cell findings into clinical impact.

bioinformatics↗

bioRxiv2024

An in-cell approach to evaluate E3 ligases for use in targeted protein degradation.

One of the major challenges in evaluating the suitability of potential [~]700 E3 ligases for target protein degradation (TPD) is the lack of binders specific to each E3 ligase. Here we apply genetic code expansion (GCE) to encode a tetrazine-containing non-canonical amino acid (Tet-ncAA) site-specifically into the E3 ligase, which can be conjugated with strained trans-cyclooctene (sTCO) tethered to a neo-substrate protein binder by click chemistry within living cells. The resulting E3 ligase minimally modified and functionalized in an E3-ligand free (ELF) manner, can be evaluated for TPD of the neo-substrate. We demonstrate that CRBN encoded with clickable Tet-ncAA, either in the known immunomodulatory drug (IMiD)-binding pocket or across surface, can be covalently tethered to sTCO-linker-JQ1 and recruit BRD2/4 for CRBN mediated degradation, indicating the high plasticity of CRBN for TPD. The degradation efficiency is dependent on location of the Tet-ncAA encoding on CRBN as well as the length of the linker, showing the capability of this approach to map the surface of E3 ligase for identifying optimal TPD pockets. This ELF-degrader approach has the advantages of not only maintaining the native state of E3 ligase, but also allowing the interrogation of E3 ligases and target protein partners under intracellular conditions and can be applied to any known E3 ligase.

cell biology↗

bioRxiv2024

YibN, a bona fide interactor of YidC with implications in membrane protein insertion and membrane lipid production

YidC, a prominent member of the Oxa1 superfamily, is essential for the biogenesis of the bacterial inner membrane, significantly influencing its protein composition and lipid organization. It interacts with the Sec translocon, aiding the proper folding of multi-pass membrane proteins. It also functions independently, serving as an insertase and lipid scramblase, augmenting the insertion of smaller membrane proteins while contributing to the organization of the bilayer. Despite the wealth of structural and biochemical data available, how YidC operates remains unclear. To investigate this, we employed proximity-dependent biotin labeling (BioID), leading to the identification of YibN as a crucial component within the YidC protein environment. We then demonstrated the association between YidC and YibN by affinity purification-mass spectrometry assays conducted on native membranes, with further confirmation using on-gel binding assays with purified proteins. Co-expression studies and in vitro assays indicated that YibN enhances the production and membrane insertion of YidC substrates, such as M13 and Pf3 phage coat proteins, ATP synthase subunit c, and various small membrane proteins like SecG. Additionally, the overproduction of YibN was found to stimulate membrane lipid production and promote inner membrane proliferation, perhaps by interfering with YidC lipid scramblase activity. Consequently, YibN emerges as a significant physical and functional interactor of YidC, influencing membrane protein insertion and lipid organization.

biochemistry↗