Biology subjects

Payne, R.

Publications and source records attributed to Payne, R..

6 recordsLinked to original sources

bioRxiv2026

FTO separation-of-function mutations alter m6A versus m6Am demethylation selectivity on RNA

The RNA demethylase FTO erases N6-methyladenosine (m6A) and cap-associated N6,2'-O-dimethyladenosine (m6Am) modifications. However, the molecular basis of its substrate selectivity and the biological effects of m6A versus m6Am demethylation in cells remain poorly understood. Here we report two engineered FTO separation-of-function mutants to selectively demethylate either m6A or m6Am modifications on RNA. While investigating the propensity of FTO active site residues to undergo self-hydroxylation, we found that mutations of FTO residue L203 resulted in impaired m6A demethylation but retained wild-type levels of m6Am demethylation, and that FTO L203A could function as a selective m6Am demethylase. Conversely, building on our recent work that identified conserved aromatic residues on FTO involved in mRNA 5' cap recognition, we found that the FTO H232A/W278A double mutant efficiently demethylates m6A modifications while exhibiting substantially impaired m6Am demethylation, making it a selective m6A demethylase. Together, these complementary FTO variants represent the first set of engineered mutations that shift FTO demethylation selectivity between m6A and m6Am substrates. These tools enable selective enzymatic removal of m6A or m6Am modifications in vitro for sequencing applications, and may facilitate understanding of FTO-mediated m6A versus m6Am demethylation in cellular and disease model systems.

biochemistry↗

bioRxiv2026

Molecular basis of promiscuous chemokine-engagement by the Duffy antigen receptor

The Duffy blood group antigen, encoded by a seven transmembrane protein known as Duffy Antigen Receptor for Chemokines (DARC), or Atypical Chemokine Receptor 1 (ACKR1), serves as a key receptor for the malarial parasite, Plasmodium vivax, on erythrocytes. DARC exhibits remarkable functional divergence compared to prototypical chemokine receptors and other G protein-coupled receptors (GPCRs) as it does not engage canonical signal-transducers such as G-proteins, GPCR regulatory kinases (GRKs), and {beta}-arrestins. DARC is a highly promiscuous receptor interacting with several homeostatic and inflammatory C-C and C-X-C subtype chemokines, and similar to other chemokine receptors, these interactions are modulated by post-translational tyrosine sulfation in the N-terminus. A single nucleotide polymorphism in DARC leading to Gly42Asp substitution forms the basis for Fya vs. Fyb Duffy blood group antigen classification with differential impact on Plasmodium vivax infection and cancer progression. However, the molecular basis of promiscuous chemokine-binding by DARC and the modulation by receptor sulfation and Fya/Fyb allelic variation remains unclear. Here, we design a sortase-mediated chemical-ligation strategy to generate purified DARC with naturally-occurring tyrosine sulfation at the N-terminus, and determine high-resolution cryo-EM structures in complex with a C-C type chemokine, CCL7, and a C-X-C type chemokine, CXCL8. We observe that similar to CCL7, CXCL8 engages with DARC primarily through the N-terminus of the receptor, which is in stark contrast with the two-site binding mechanism displayed by other chemokine receptors. Interestingly, the E-L-R motif in CXCL8 engages a pseudo-R-D motif in DARC leading to superficial engagement unlike CXCR2, a prototypical chemokine receptor sharing the same agonist. Moreover, tyrosine sulfation and Fyb allelic variation leads to a repositioning of the receptor N-terminus on the core domain of CXCL8, resulting in distinct interaction network imparting greater binding affinity. Taken together, our study presents novel insights into promiscuous chemokine-binding to DARC, tyrosine sulfation-mediated fine-tuning of chemokine engagement, and a generalizable sortase-mediated chemical-ligation platform applicable to other chemokine receptors.

biochemistry↗

bioRxiv2023

Contextual and Combinatorial Structure in Sperm Whale Vocalisations

Sperm whales (Physeter macrocephalus) are long-lived and highly social mammals that engage in complex group behaviours, including navigation, foraging, and child-rearing. During these behaviours, sperm whales communicate primarily using sequences of short bursts of clicks with varying inter-click intervals, known as codas. Past research has identified around 150 discrete coda types globally, with 21 in the Caribbean. A subset of these have been shown to encode information about caller and clan identity. However, almost everything else about the sperm whale communication system, including basic questions about its structure and information-carrying capacity, remains unknown. In this study, we show that codas exhibit contextual and combinatorial structure with key similarities to aspects of human language and other primate communication systems. First, we report previously undescribed variations in coda structure that are sensitive to the conversational context in which they occur. We call these rubato and ornamentation, by analogy to musical terminology. These variations are systematically controlled and imitated across individual whales. Second, we show that coda types are not defined by arbitrary sequences of inter-click intervals, but instead form a combinatorial coding system in which rubato and ornamentation combine with two categorical, context-independent features that we call rhythm and tempo to give rise to a large inventory of distinguishable codas. In a dataset of 8,719 codas from the sperm whales of the Eastern Caribbean clan, this sperm whale phonetic alphabet makes it possible to systematically explain observed variability in coda structure. Sperm whale vocalisations are more expressive and structured than previously believed, and are built from a repertoire comprising nearly an order of magnitude more distinguishable codas. These results show contextsensitive and combinatorial vocalisation systems extend beyond humans, and can appear in an organism with a divergent evolutionary lineage and vocal apparatus.

animal behavior and cognition↗

bioRxiv2020

Strongly coupled transmembrane mechanisms control MCU-mediated mitochondrial Ca2+ uptake

Ca2+ uptake by mitochondria regulates bioenergetics, apoptosis, and Ca2+ signaling. The primary pathway for mitochondrial Ca2+ uptake is the mitochondrial calcium uniporter (MCU), a Ca2+-selective ion channel in the inner mitochondrial membrane. MCU-mediated Ca2+ uptake is driven by the sizable inner-membrane potential generated by the electron-transport chain. Despite the large thermodynamic driving force, mitochondrial Ca2+ uptake is tightly regulated to maintain low matrix [Ca2+] and prevent opening of the permeability transition pore and cell death, while meeting dynamic cellular energy demands. How this is accomplished is controversial. Here we define a regulatory mechanism of MCU-channel activity in which cytoplasmic Ca2+ regulation of intermembrane space-localized MICU1/2 is controlled by strongly-coupled Ca2+-regulatory mechanisms localized across the membrane in the mitochondrial matrix. Ca2+ that permeates through the channel pore regulates Ca2+ affinities of coupled inhibitory and activating sensors in the matrix. Ca2+ binding to the inhibitory sensor within the MCU amino-terminus closes the channel despite Ca2+ binding to MICU1/2. Conversely, disruption of the interaction of MICU1/2 with the MCU complex abolishes matrix Ca2+ regulation of channel activity. Our results demonstrate how Ca2+ influx into mitochondria is tuned by coupled Ca2+-regulatory mechanisms on both sides of the inner mitochondrial membrane.

biophysics↗

bioRxiv2020

Nonclassical testosterone signaling through ZIP9 renders melanoma more aggressive in males than in females

Melanoma and most other cancers occur more frequently, and have worse prognosis, in males compared with females. Though sex steroids are thought to be involved, classical androgen and estrogen receptors are not detectable in most melanomas. Here we show that testosterone promotes melanoma proliferation by activating ZIP9 (SLC39A9), a zinc transporter that is not intentionally targeted by available therapeutics, but is widely expressed in human melanoma. This testosterone activity requires zinc influx, MAPK activation and YAP1 nuclear translocation. We demonstrate that FDA approved inhibitors of the classical androgen receptor also inhibit ZIP9, and thereby antagonize the pro-tumorigenic effects of testosterone in melanoma. In male mice, androgen receptor inhibitors suppressed growth of ZIP9-expressing melanomas, but had no effect on isogenic melanomas lacking ZIP9, nor on melanomas in females. These data suggest that ZIP9 might be effectively targeted in melanoma and other cancers by repurposing androgen receptor inhibitors that are currently approved only for prostate cancer. SignificanceMelanoma outcomes are worse in males than in females. Some of this difference is driven by testosterone signaling through ZIP9, a nonclassical testosterone receptor. Drugs that target AR can be repurposed to block ZIP9, and inhibit melanoma in males.

cancer biology↗

bioRxiv2019

CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family of remodellers. We demonstrate that the binding energy for CHD4-nucleosome complex formation - even in the absence of nucleotide - triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4-6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. We propose a mechanism for nucleosome sliding based on these and published data.

biochemistry↗