Biology subjects

Pulsford, S. B.

Publications and source records attributed to Pulsford, S. B..

3 recordsLinked to original sources

bioRxiv2026

The modular evolution of chitinases is governed by coevolution of auxiliary and catalytic domains

The modular architecture of multi-domain enzymes is a key source of functional diversity. GH18 chitinases exemplify this, possessing a variety of auxiliary domains that have been postulated to underpin their role as essential global nutrient cyclers. However, there is no evolutionary framework that accounts for vast the assortment of domain compositions observed across the protein family. Here, we map the sequence space of nearly 40,000 bacterial chitinases, integrating phylogenetics with a quantitative analysis of domain promiscuity to decode their evolutionary history. We reveal that diversification follows distinct trajectories: enzymes necessary for environmental chitin scavenging evolve via high modular plasticity and structural elaboration of the catalytic core, whereas sequences required for specialized, essential developmental roles fix their domain architecture to fulfill lineage-specific physiological roles. By resolving how domain accretion co-evolves with catalytic scaffolds, this work provides a framework for understanding how multi-domain enzymes adapt to complex environments.

evolutionary biology↗

bioRxiv2023

Leveraging ancestral sequence reconstruction for protein representation learning

Protein language models (PLMs) convert amino acid sequences into the numerical representations required to train machine learning (ML) models. Many PLMs are large (>600 M parameters) and trained on a broad span of protein sequence space. However, these models have limitations in terms of predictive accuracy and computational cost. Here, we use multiplexed Ancestral Sequence Reconstruction (mASR) to generate small but focused functional protein sequence datasets for PLM training. Compared to large PLMs, this local ancestral sequence embedding (LASE) produces representations 10-fold faster and with higher predictive accuracy. We show that due to the evolutionary nature of the ASR data, LASE produces smoother fitness landscapes in which protein variants that are closer in fitness value become numerically closer in representation space. This work contributes to the implementation of ML-based protein design in real-world settings, where data is sparse and computational resources are limited.

bioinformatics↗

bioRxiv2023

Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP

Cyanobacterial CO2 concentrating mechanisms (CCMs) sequester a globally significant proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in [a]-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present the first structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate (RuBP), and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial [a]-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of -carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage. One-Sentence SummaryThe carboxysomal carbonic anhydrase, CsoSCA, is allosterically activated by the Rubisco substrate RuBP, revealing a novel mechanism controlling key enzyme activity in cyanobacterial -carboxysomes.

molecular biology↗