Biology subjects

Wright, J. J.

Publications and source records attributed to Wright, J. J..

7 recordsLinked to original sources

bioRxiv2026

A modular mechanism determines the proton-pumping stoichiometry of respiratory complex I

Respiratory complex I, a crucial metabolic enzyme, uses the reducing potential of NADH to pump protons across energy-transducing membranes, but its mechanism of catalysis remains unknown. Here, guided by detailed structural information, we combine targeted mutagenesis and biophysical analyses to define the proton-pumping pathways in the three antiporter-like (proton-pumping) subunits of complex I from Paracoccus denitrificans and Escherichia coli. In Pd-CI, a four-proton pump, one of the three proton-uptake pathways is inactive, reconciling the four-proton/three-subunit mismatch. In Ec-CI two pathways are inactive - and Ec-CI pumps only two protons. We define the structural determinants for redox-coupled proton uptake, establish a mechanistic framework for proton pumping, and reveal how the proton-pumping stoichiometry has been adapted to deliver efficient energy conservation in diverse bioenergetic environments.

biochemistry↗

bioRxiv2026

Conformational gating at histidine junctions coordinates proton translocation in respiratory complex I

Respiratory complex I, a central enzyme in cellular metabolism, converts the free energy of NADH oxidation into a transmembrane proton-motive force to drive ATP synthesis, but the molecular mechanisms by which it couples redox catalysis to vectorial proton translocation remain unresolved. Here, we present high-resolution cryo-EM structures of complex I from Bos taurus captured under conditions designed to change the protonation states of residues in the membrane domain. Our structures reveal conformational rearrangements at key pathway junctions that reconfigure proton-transfer connections. In ND5, helical rearrangements switch the connectivity of histidine-248 between proton-uptake and proton-output pathways. In ND4, rotameric changes of histidine-220 alternately enable proton uptake or lateral proton transfer along the membrane domain. Combined with molecular simulations, our structures define gating mechanisms that impose directionality on proton transfer reactions and provide a framework for proton-coupled energy transduction in complex I.

biochemistry↗

bioRxiv2026

Chromosome-level genome assembly of the Endangered scaly-sided merganser Mergus squamatus with insight into its demographic history

The scaly-sided merganser, Mergus squamatus, is an Endangered piscivorous duck which has been declining since the late 1900s due to habitat loss, over-hunting, and climate change. Despite being a species of global conservation concern and subject to ex- and in-situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 307 scaffolds, 64 of which are anchored into 35 chromosomes, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified [~]15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modelling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this threatened species.

genomics↗

bioRxiv2023

Structural basis of a regulatory switch in mammalian complex I

Respiratory complex I powers oxidative phosphorylation in mammalian mitochondria by using the reducing potential of NADH to reduce ubiquinone-10 and drive protons across the inner mitochondrial membrane. High-resolution cryoEM structures have provided a molecular framework for complex I catalysis, but controversies about how to assign functional properties to the states identified in single-particle analyses are preventing progress on its energy-converting mechanism. Here, we combine precise biochemical definition with high-resolution cryoEM structures in the phospholipid bilayer of coupled vesicles and show that the closed and open states observed in mammalian complex I preparations are components of the deactive transition that occurs during ischaemia. Populations of the cryoEM open state and biochemical deactive state match exactly. Deactivation switches the enzyme off, converting the closed state that is capable of rapid, reversible catalysis into an open, dormant state that is unable to start up in reverse. The deactive state is switched back on by slow priming reactions with NADH and ubiquinone-10. Thus, by developing a versatile membrane system to unite structure and function, we define the role of large-scale conformational transitions in complex I and establish a new gold standard for structure-based investigations of catalysis by energy-coupled proteins.

biochemistry↗

bioRxiv2022

Cryo-EM structures reveal ubiquinone-10 binding to mitochondrial complex I and conformational transitions associated with Q-site occupancy

Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, structures of Q10-bound states have remained elusive. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the active (ready-to-go) resting state (plus a matching substrate-free structure) and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the deactive resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.

biochemistry↗

bioRxiv2021

RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

A hallmark of type 2 diabetes (T2D), a major cause of world-wide morbidity and mortality, is dysfunction of insulin-producing pancreatic islet {beta} cells1-3. T2D genome-wide association studies (GWAS) have identified hundreds of signals, mostly in the non-coding genome and overlapping {beta} cell regulatory elements, but translating these into biological mechanisms has been challenging4-6. To identify early disease-driving events, we performed single cell spatial proteomics, sorted cell transcriptomics, and assessed islet physiology on pancreatic tissue from short-duration T2D and control donors. Here, through integrative analyses of these diverse modalities, we show that multiple gene regulatory modules are associated with early-stage T2D {beta} cell-intrinsic defects. One notable example is the transcription factor RFX6, which we show is a highly connected {beta} cell hub gene that is reduced in T2D and governs a gene regulatory network associated with insulin secretion defects and T2D GWAS variants. We validated the critical role of RFX6 in {beta} cells through direct perturbation in primary human islets followed by physiological and single nucleus multiome profiling, which showed reduced dynamic insulin secretion and large-scale changes in the {beta} cell transcriptome and chromatin accessibility landscape. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs, and individuals and thus we anticipate this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits with GWAS data.

cell biology↗

bioRxiv2021

Functional basis of electron transport within photosynthetic complex I

Photosynthesis and respiration rely upon a proton gradient to produce ATP. In photosynthesis, the Respiratory Complex I homologue, Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes, and is fundamental to bioenergetics in photosynthetic bacteria and some higher plant cell types. However, little is known about the PS-CI molecular mechanism and attempts to understand its function have previously been frustrated by its large size and high lability. Here, we overcome these challenges by pushing the limits in sample size and spectroscopic sensitivity, to determine arguably the most important property of any electron transport enzyme - the reduction potentials of its cofactors, in this case the iron-sulphur clusters of PS-CI, and unambiguously assign them to the structure using double electron-electron resonance (DEER). We have thus determined the bioenergetics of the electron transfer relay and provide insight into the mechanism of PS-CI, laying the foundations for understanding of how this important bioenergetic complex functions.

biophysics↗