Biology subjects

Walsh, N.

Publications and source records attributed to Walsh, N..

3 recordsLinked to original sources

bioRxiv2024

Darwin's Naturalization Conundrum explained by gradients of environmental stress and disturbance

Darwins Naturalization Conundrum (DNC) states that non-native species closely related to the native community are either more likely to succeed because shared adaptations help them overcome environmental filtering, or less likely to succeed because of strong competition with their native relatives. Despite extensive research, no general patterns have so far emerged. One reason may be that the relative importance of competition and environmental filtering depends on environmental conditions. To test this hypothesis, we conducted a global assessment of DNC examining patterns of phylogenetic relatedness of non-native plant species to the native community along gradients of elevation and anthropogenic disturbance in mountains. Phylogenetic distance of non-native to native species decreased with increasing elevation and in disturbed plant communities. Our results help resolve DNC by showing that the environmental context sets expectations for patterns of relatedness between non-native and native species and helps illuminate the ecological and evolutionary processes generating these patterns.

ecology↗

bioRxiv2024

Cryo-EM captures the coordination of long-range allostery and asymmetric electron transfer by a bi-copper cluster in the nitrogenase-like DPOR complex

Enzymes that catalyze long-range electron transfer reactions are often structurally evolved to possess two symmetrical halves. The functional advantages and mechanistic principles for such architecture remain a mystery. Using Cryo-EM we capture snapshots of the nitrogenase-like Dark-operative Protochlorophyllide Oxidoreductase (DPOR) enzyme during substrate recognition and turnover. The structures reveal that asymmetry is enforced upon substrate binding and leads to an allosteric inhibition of protein-protein interactions and electron transfer in one half. Residues that form a conduit for electron transfer are aligned in one half while misaligned in the other. An ATP-turnover coupled switch is triggered once electron transfer is accomplished in one half and relayed through a bi-copper cluster at the oligomeric interface, leading to activation of enzymatic events in the other. The findings provide a mechanistic blueprint for regulation of asymmetric long-range electron transfer. One-Sentence SummaryA bi-copper cluster coordinates electron transfer for substrate reduction in the nitrogenase-like DPOR enzyme and the structures reveal how allostery and asymmetry are enacted over 100[A] and utilized for sequential electron transfer.

biochemistry↗

bioRxiv2024

Cyanamide-inducible expression of homing nuclease I-SceI for iterative genome engineering and parallel promoter characterisation in Saccharomyces cerevisiae

In synthetic biology, microbial chasses including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale. Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements, such as the galactose-inducible (GAL) promoter in S. cerevisiae. Here, we prototyped the cyanamide-induced I-SceI-mediated double-strand DNA breaks (DSBs) for selectable marker recycling in yeast metabolic engineering. We further combined cyanamide-induced I-SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter replacement, which simplified the molecular cloning procedure for promoter characterisation in S. cerevisiae. We then characterised three tetracycline-inducible promoters of differential strength, a non-leaky {beta}-estradiol-inducible promoter, cyanamide-inducible DDI2 promoter, bidirectional MAL32/MAL31 promoters, and five pairs of bidirectional GAL1/GAL10 promoters. Overall, alternative regulatory controls for genome engineering tools are important for the construction of complexed genotypes in microbial systems for synthetic biology and metabolic engineering applications.

synthetic biology↗