Biology subjects

Waters, M. T.

Publications and source records attributed to Waters, M. T..

5 recordsLinked to original sources

bioRxiv2025

Ecological coherence in abundance dynamics across terrestrial and marine assemblages

Understanding how communities respond to environmental change requires assessing not just overall variability but also the structure of co-variation among taxa. We frame this idea under the Ecological Coherence (EC) framework, which generalizes previous notions such as community synchrony or coherence. EC captures the structure of co-responses among taxa within assemblages and can be expressed through two complementary objects: (1) the co-response matrix C, which contains all pairwise correlations between taxa and can be used to identify clusters of taxa with coherent responses as well as the contributions of individual species to community-wide coherence; and (2) the EC distribution, which summarizes the overall profile of co-responses by capturing their shape, spread, and central tendency across the community. By combining these two views, EC moves beyond single summary metrics and provides a richer picture of how coherence is organized within communities. Analyzing the EC distribution across 341 terrestrial and 105 marine assemblages worldwide, we found a general prevalence of weak correlations and a few strong, directional correlations. We also found that it varies with community composition, sampling effort, and biogeographic region. Moreover, the C matrix consistently identified a small subset of taxa with strong correlations to many others, suggesting a promising path to detecting those that may play central roles in amplifying or buffering community responses to environmental change. Our findings on EC pave the way for deeper investigations into what drives the diversity of ecological responses to environmental changes and how it shapes community dynamics, while also underscoring the need for strategically distributing ecological monitoring across trophic guilds and functional roles.

ecology↗

bioRxiv2025

Structural and functional characterisation of a reconstructed ancestral strigolactone receptor

Strigolactones are phytohormones that regulate shoot branching and promote root interactions with arbuscular mycorrhizal fungi. In seed plants, strigolactone perception begins with the enzyme-receptor DWARF14 (D14), an /{beta}-hydrolase that is believed to have evolved via gene duplication from the karrikin receptor, KARRIKIN INSENSITIVE2 (KAI2). D14 and KAI2 are highly homologous at the sequence and structural levels, and both proteins bind and cleave similar butenolide compounds. Nevertheless, the two signalling pathways are distinct, as the activity of one receptor cannot compensate for the loss of the other. Here, we apply ancestral sequence reconstruction to generate a D14 protein representative of seed plants to study the evolution of substrate specificity, and to explore desirable traits for protein engineering. We describe the structure, as well as the in vitro and in planta activity of ancestral D14, showing that substrate specificity does not meaningfully differ from that of Arabidopsis thaliana D14. We also demonstrate that ancestral D14 shows higher recombinant yields, greatly increased thermostability, and enhanced catalytic activity relative to D14 from A. thaliana. This work provides insight into the evolution of phytohormone signalling and presents a robust scaffold for the application of D14-type proteins in synthetic biology. SIGNIFICANCE STATEMENTAncestral sequence reconstruction of the strigolactone receptor DWARF14 (D14) reveals that its substrate specificity has remained largely conserved in seed plants. Additionally, the ancestral reconstruction exhibits superior recombinant yields, thermostability, and catalytic activity relative to Arabidopsis thaliana D14, providing both evolutionary insights and promising utility for synthetic biology applications.

plant biology↗

bioRxiv2023

Perception of butenolides by Bacillus subtilis via the α/β-hydrolase RsbQ

The regulation of behavioural and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi1-3. DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous receptors that perceive strigolactones and karrikins, respectively, and that hydrolyse their ligands to effect signal transduction4-7. RsbQ, a homologue of D14 and KAI2 from the Gram-positive bacterium Bacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB ({sigma}B)8,9. However, the molecular function of RsbQ is unknown. Here we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilised by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signalling function of RsbQ in vivo, with dGR24 being 10-fold more potent. Application of dGR24 to B. subtilis phenocopied loss-of-function rsbQ mutations and led to a significant down-regulation of {sigma}B-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signalling compounds between plants and bacteria to help shape rhizosphere communities.

microbiology↗

bioRxiv2022

Structure-guided investigations into HMG-CoA reductase as a herbicide target

Decades of intense herbicide use has led to resistance in weeds. Without innovative weed management practices and new herbicidal modes of action, the unabated rise of herbicide resistance will undoubtedly place further stress upon food security. HMGR (3-hydroxy-3-methylglutaryl-coenzyme A reductase) is the rate limiting enzyme of the eukaryotic mevalonate pathway successfully targeted by statins to treat hypercholesterolemia in humans. As HMGR inhibitors have been shown to be herbicidal, HMGR could represent a new mode of action target for the development of herbicides. Here we present the crystal structure of a HMGR from Arabidopsis thaliana (AtHMG1) which exhibits a wider active site than previously determined structures from different species. This plant conserved feature enabled the rational design of specific HMGR inhibitors, for which we engineered a tolerance trait through sequence analysis of fungal gene clusters. These results suggest HMGR to be a viable herbicide target modifiable to provide a tolerance trait.

plant biology↗

bioRxiv2018

Divergent receptor proteins confer responses to different karrikins in two ephemeral weeds

Wildfires can encourage the establishment of invasive plants by releasing potent germination stimulants, such as karrikins. Seed germination of Brassica tournefortii, a noxious weed of Mediterranean climates, is strongly stimulated by KAR1, which is the archetypal karrikin produced from burning vegetation. In contrast, the closely-related yet non-fire-associated ephemeral Arabidopsis thaliana is unusual because it responds preferentially to KAR2. The /{beta}-hydrolase KARRIKIN INSENSITIVE2 (KAI2) is the putative karrikin receptor identified in Arabidopsis. Here we show that B. tournefortii differentially expresses three KAI2 homologues, and the most highly-expressed homologue is sufficient to confer enhanced responses to KAR1 relative to KAR2 when expressed in Arabidopsis. We further identify two variant amino acid residues near the KAI2 active site that explain the ligand selectivity, and show that this combination has arisen independently multiple times within dicots. Our results suggest that duplication and diversification of KAI2 proteins could confer upon weedy ephemerals and potentially other angiosperms differential responses to chemical cues produced by environmental disturbance, including fire.

plant biology↗