Biology subjects

Zahn, M.

Publications and source records attributed to Zahn, M..

5 recordsLinked to original sources

bioRxiv2026

Characterization of heterogeneous bioinformatics training needs in the AI era

Bioinformatics training providers serve heterogeneous audiences, a challenge sharpened by fast-evolving technologies such as generative artificial intelligence (AI). Analyzing training-needs surveys in aggregate can mask this heterogeneity. We present a network-based clustering protocol that groups respondents by the similarity of their Likert-type topic ratings: respondents form a Spearman correlation network, and community detection groups them into learner profiles with shared training needs, independent of demographics. We demonstrate the protocol on the 2026 SIB Swiss Institute of Bioinformatics (SIB) training needs survey (n=260), covering topics, barriers, and formats. We identified four interpretable learner profiles: AI and data, infectious disease genomics, functional genomics, and biochemistry, imaging & AI. Each had distinct topic priorities, barriers, and format preferences that an aggregate analysis hides. For example, LLM-based knowledge extraction ranked 2nd overall but only 16th in the infectious disease genomics profile, whereas phylogenetics ranked 17th overall but first there. Across profiles, AI/LLM skills and reproducible data practices were in high demand, whereas AI-assisted learning was, unexpectedly, the least preferred format. Because the protocol requires only a shared Likert scale, it is reusable for other training-needs assessments; the implementation is openly available. Profile-based curricula can target each group's topics, formats, and barriers.

bioinformatics↗

bioRxiv2026

Engineering a cytochrome P450 O-demethylase for the bioconversion of hardwood lignin

Lignin is a promising alternative to petroleum as a feedstock for the chemical industry. Emergent strategies for lignin valorization involve tandem processes in which biomass is chemo-catalytically fractionated followed by biotransformation of the depolymerized lignin by microbial cell factories. A rate-limiting step in this biotransformation is O-demethylation of the lignin-derived monomers. The reductive catalytic fractionation of hardwood biomass generates high yields of two classes of monomers: 4-alkylguaiacols and 4-alkylsyringols. To better understand the biotransformation of these monomers, we studied AgcA, a cytochrome P450, and AgcB, the cognate reductase, that together catalyze the O-demethylation of 4-alkylguaiacols. A 1.82 [A] resolution crystal structure of AgcAEP4 from Rhodococcus rhodochrous EP4 in complex with 4-ethylguaiacol identified residues Leu78, Ala293 and Phe166 as potential specificity determinants. Substitution of Ala293 and Leu78 decreased the specificity of AgcAEP4 for alkylguaiacols. Substitution of Phe166 yielded a variant that bound 4-propylsyringol but did not transform it. In contrast, the corresponding variant in the Rhodococcus aromaticivorans RHA1 homolog, AgcARHA1 Y166A, catalyzed the O-demethylated of both methoxy groups of 4-propylsyringol with a kcat/Km of 8500 M-1 s-1 for the first O-demethylation, nearly 7-fold higher than WT AgcARHA1. A strain of RHA1 harboring the variant did not grow on 4-propylsyringol but consumed it at approximately the same rate as 4-propylguaiacol and transformed some of it to pentanoyl-CoA, consistent with metabolism via the meta-cleavage pathway that catabolizes 4-alkylguaiacols. These studies improve our understanding of a critical lignin-degrading enzyme system and facilitate its efficient implementation into biocatalysts. SignificanceLignin is a highly abundant source of aromatic carbon and a promising alternative to petroleum to generate materials. Fulfilling this promise depends on technological advances in areas such as catalytic fractionation and biocatalysis. Catalytic fractionation of hardwood biomass generates mixtures of aromatics enriched in 4-propylguaiacol and 4-propylsyringol. Here, we biochemically and structurally characterized a cytochrome P450 that initiates 4-propylguaiacol catabolism. Informed by the structure, we engineered the enzyme to have dual activity on both 4-propylguaiacol and 4-propylsyringol, and implemented this enzyme into a bacterial biocatalyst. Metabolomic analysis of this strain provided insights into the catabolism of both aromatics. Overall, these findings greatly facilitate the engineering of P450s and bacteria to biocatalytically upgrade lignin.

biochemistry↗

bioRxiv2025

Engineering surface electrostatics affords control over morphological preference, synergy, and activity in polymer degrading enzymes

The biocatalytic recycling of plastics, such as polyethylene terephthalate (PET), promises a sustainable alternative to our present open-loop cycles. Engineering of PET-hydrolases for this purpose has focused on improving activity near the glass-transition temperature of the polymer by increasing their thermostability, neglecting other features of the protein-polymer system that affect enzymatic activity. Here, we isolate the effect of electrostatics on the activity of a thermophilic PETase by rationally redesigning its surface charge, while preserving its thermodynamic properties. The enzyme variant, SfInv, shows orders of magnitude improvements in binding affinity and in activity towards untreated plastic films, with inverted morphological preference. When combined, the wildtype enzyme and SfInv act synergistically, revealing an entirely new mechanism for cooperative activities driven by complimentary electrostatic interactions at the PET surface. These findings highlight unexplored avenues in improving PETase function through the control of morphological preference or introduction of protein cooperativity by exploiting protein electrostatics.

biochemistry↗

bioRxiv2020

Insights into glycan import by a prominent gut symbiont

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the {beta}2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to [~]2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

microbiology↗

bioRxiv2018

A multidisciplinary approach towards identification of novel antibiotic scaffolds for Acinetobacter baumannii

Research efforts to discover potential new antibiotics for Gram-negative bacteria suffer from high attrition rates due to the synergistic action of efflux systems and the limited permeability of the outer membrane (OM). One potential strategy to overcome the OM permeability barrier is to identify small molecules that are natural substrates for abundant OM channels, and to use such compounds as scaffolds for the design of efficiently-permeating antibacterials. Here we present a multidisciplinary approach to identify such potential small-molecule scaffolds. Focusing on the pathogenic bacterium Acinetobacter baumannii, we use OM proteomics to identify DcaP as the most abundant channel under various conditions that are relevant for infection. High-resolution X-ray structure determination of DcaP surprisingly reveals a trimeric, porin-like structure and suggests that dicarboxylic acids are potential transport substrates. Electrophysiological experiments and allatom molecular dynamics simulations confirm this notion and provide atomistic information on likely permeation pathways and energy barriers for several small molecules, including a clinically-relevant {beta}-lactamase inhibitor. Our study provides a general blueprint for the identification of molecular scaffolds that will inform the rational design of future antibacterials.

microbiology↗