Biology subjects

Scadden, J.

Publications and source records attributed to Scadden, J..

2 recordsLinked to original sources

bioRxiv2024

Easy come, easier go: mapping the loss of flagellar motility across the tree of life

Bacterial swimming is mostly powered by the bacterial flagellar motor and the number of proteins involved in the flagellar motor can vary. Quantifying the proteins present in flagellar motors from a range of species delivers insight into how motility has changed throughout history and provides a platform for estimating from its genome whether a species is likely to be motile. We conducted sequence and structural homology searches for 54 flagellar pathway proteins across 11,365 bacterial genomes and developed a classifier with up to 95% accuracy that could predict whether a strain was motile or not. We then mapped the evolution of flagellar motility across the GTDB bacterial tree of life. We confirmed that the last common bacterial ancestor had flagellar motility and that the rate of loss of this motility was four-fold higher than the rate of gain. We showed that the presence of filament protein homologues was highly phylogenetically correlated with motility and that all species classified as motile contained at least one filament homologue. We calculated the rate of gain and loss for each flagellar protein and that the filament protein FliC was highly correlated with motility across the tree of life. We then measured the correlation of each flagellar motor protein with FliC and showed that the filament, rotor, and rod and hook proteins were all highly correlated with FliC, and thus with motility. We calculated the differential rates of gain and loss for each flagellar protein and quantified which genomes encoded for partial sets of flagellar proteins, indicating potential pathways by which motility could be lost. Overall, we show that filament, rod and hook and rotor proteins are conserved when flagellar motility is preserved and that the presence or absence of a FliC homologue is a good, simple predictor of whether or not a species has flagellar motility.

microbiology↗

bioRxiv2024

Rescue of bacterial motility using two and three-species FliC chimeras

The bacterial flagellar filament acts as a propeller to drive most bacterial swimming. The filament is made of flagellin, known as FliC in Escherichia coli. FliC consists of four domains, the highly conserved core D0 and D1 domains and the hypervariable outer D2 and D3 domains. The size and structure of the outer domains varies, being completely absent in some bacterial species. Here, we sought to identify outer domains from various species that are compatible with the ability of E. coli K-12 FliC to form filaments capable of supporting motility. We calculated a phylogeny of 210 representative flagellin amino acid sequences and generated a series of FliC variants, including outer-domain-deleted forms and eleven chimeric FliC mutants using domains from E. coli K-12, Salmonella Typhimurium, Pseudomonas aeruginosa, Collimonas fungivorans, Helicobacter mustelae and Mesorhizobium sp. ORS3359 in various combinations. Notably, two of the chimeric fliC mutants rescued motility in a fliC-disrupted E. coli K-12 strain, both of which contained the S. Typhimurium D2 domain. Overall, we demonstrate that, while most FliC chimeras did not support motility, interchangeability of the outer domains can produce filaments that provide motility, providing insights to guide the design of synthetic flagellins. ImportanceFlagellin is a key protein forming the filament of the bacterial flagellar motor which powers most bacterial swimming. Flagellin can have hypervariable domains which can alter motility in different environments and provide immune evasion. Here we engineered two flagellin chimeras that could drive motility. This indicates that the flagellin outer domains can be exchanged, to some degree, allowing us to refine rational design approaches for engineering of bacterial swimming. Our work shows the challenges to overcome when combining flagellins from different species and provides evidence that domain switched flagellins can form filaments.

microbiology↗