Biology subjects

Copping, J.

Publications and source records attributed to Copping, J..

3 recordsLinked to original sources

bioRxiv2025

Exploring marine habitat restoration opportunities and blue carbon sequestration potential in the United Kingdom

Nature-based solutions (NbS), including blue carbon ecosystems, are crucial to meeting Net-Zero targets. The UKs Net-Zero 2050 strategy, alongside terrestrial measures, prioritises large-scale offshore wind development, creating opportunities to integrate marine NbS into Net-Zero plans. Consequently, aligning decarbonisation targets with conservation goals demands marine spatial planning and adaptive Marine Protected Area (MPA) networks. While estimates suggest UK marine systems store [~]244 million tonnes of organic carbon, sequestration potentials remain poorly quantified. We developed marine spatial plans for the UK and estimated carbon sequestration potentials. We divided the UK Exclusive Economic Zone into four zones (Open, Conservation, Oil, and Energy) using Marxan with Zones under two scenarios: (1) Existing MPAs locked-in, and (2) Unconstrained. Conservation Zones were defined as regions with minimal human activity. Planning incorporated 14 features: four species distribution models (SDMs), including the first UK-wide maerl SDMs, habitat suitability maps for subtidal macroalgae, and relevant stakeholder maps, such as offshore wind and oil fields. Conservation zones overlapped with >70% of current MPAs and complemented them by isolating biodiversity from anthropogenic activities, such as ports, without compromising renewable energy targets. We estimated sequestration rates of 533 - 625 kt C yr-1, with restoration contributing an additional 0.11 - 0.12 kt C yr-1 by 2040. These results provide evidence for embedding marine NbS into national strategies such as the UK Marine Strategy, while highlighting the need to address gaps in marine carbon dynamics to enable effective spatial planning and alignment with voluntary carbon markets to bridge climate finance gaps.

ecology↗

bioRxiv2024

On the function of TRAP substrate-binding proteins: conformational variation of the sialic acid binding protein SiaP

Tripartite ATP-independent periplasmic (TRAP) transporters are analogous to ABC transporters in that they use a substrate-binding proteins to scavenge metabolites (e.g., N-acetylneuraminate) and deliver them to the membrane components for import. TRAP substrate-binding proteins are thought to bind the substrate using a two-state (open and closed) induced-fit mechanism. We solved the structure of the TRAP N-acetylneuraminate substrate-binding protein from Aggregatibacter actinomycetemcomitans (AaSiaP) in both the open ligand-free and closed liganded conformations. Surprisingly, we also observed an intermediate conformation, where AaSiaP is mostly closed and is bound to a non-cognate ligand, acetate, which hints at how N-acetylneuraminate binding stabilises a fully closed state. AaSiaP preferentially binds N-acetylneuraminate (KD = 0.4 {micro}M) compared to N-glycolylneuraminate (KD = 4.4 {micro}M), which is explained by the closed-N-acetylneuraminate bound structure. Small-angle X-ray scattering data alongside molecular dynamics simulations suggest the AaSiaP adopts a more open state in solution than in crystal. However, the open unliganded conformation can also sample closed conformations. Molecular dynamics simulations also demonstrate the importance of water molecules for stabilising the closed conformation. Although our data is consistent with an induced fit model of binding, it is likely that the open unliganded conformation encompasses multiple states capable of binding substrate. The mechanism by which the ligand is released for import remains to be determined.

biochemistry↗

bioRxiv2022

Structure and mechanism of the tripartite ATP-independent periplasmic (TRAP) transporter

In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential carboxylate- and sulfonate-containing nutrients into the cytoplasm. Unlike other secondary active transporters, TRAP transporters cannot receive their substrates directly, but do so indirectly via a secreted soluble substrate-binding protein. How a sodium-driven secondary active transporter is strictly coupled to a passenger-carrying substrate-binding domain is poorly understood. Here, we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 [A] resolution. SiaM has 12-TMs that come together to form a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium-coupled elevator transporter VcINDY. Interestingly, the SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, indicating TRAP transporters may operate as monomers, rather than the typically observed oligomers. We have identified the Na+ and sialic acid binding sites in SiaM and confirmed a strict dependence on the substrate-binding protein SiaP for uptake. We have determined the SiaP crystal structure that, together with co-evolution driven docking studies, provides a molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We conclude that TRAP proteins are conceptually a marriage between an ABC importer and a secondary active transporter, which we describe herein as an elevator-with-an-operator mechanism.

molecular biology↗