Biology subjects

Philip, J. S.

Publications and source records attributed to Philip, J. S..

4 recordsLinked to original sources

bioRxiv2026

A Specific Ancestral Sequence Reconstruction of Flagellin Can Drive Motility in Salmonella enterica but not Escherichia coli

The bacterial flagellar filament, built from thousands of flagellin subunits, is essential for flagellar motility. Here, we aimed to use ancestral sequence reconstruction (ASR) to generate conservative, ancestral flagellin sequences that surround the divergency point between Escherichia and Salmonella species and tested their ability to restore motility in flagellin deleted Escherichia coli and Salmonella Typhimurium. Only one (N131) out of three candidates restored motility in S. Typhimurium but not E. coli, despite high structural similarity to native FliC/FljB. S. Typhimurium expressing N131 showed reduced motility relative to wild-type Salmonella FliC, alongside increased tumbling frequency. Serial passage across swim plates produced a derivative, N131.10, containing a single flagellin mutation (M144I), with a larger swim ring diameter but also increased tumbling frequency. Comparison of structural interaction networks among the residues of S. Typhimurium LT2 FliC with those of other filament proteins showed that non-motile candidates (N132 and N134) carried substitutions that disrupted key core-domain atomic interactions. These results demonstrate that flagellar filament assembly tolerates only limited sequence variation and that this capacity for tolerance differs between E. coli and S. Typhimurium despite their close phylogenetic relationship.

microbiology↗

bioRxiv2026

Evolutionary Coupling of Flagellar Motility and Type VI Secretion Systems Across Bacteria

Bacteria use both motility and antagonism to compete in spatially structured environments, but whether these traits evolve together across broad bacterial diversity remains unclear. We developed a spatial kin-competition model predicting that motility should couple robustly with contact-dependent weapons by increasing encounter rates with competitors, whereas coupling with diffusible weapons should be weaker and context-dependent. To test these predictions, we performed a comprehensive analysis of 11,365 bacterial genomes across the Tree of Life (ToL). By utilising large-scale homology-based searches, we annotated flagellar, T6SS, and bacteriocin components and then applied phylogenetic comparative models to examine evolutionary associations. T6SS presence was strongly associated with flagellar motility: T6SS-positive lineages were predominantly flagellated, and BayesTraits supported a dependent model of FliC and T6SS evolution. In contrast, bacteriocins showed no detectable evolutionary coupling with flagellar motility. Transition-rate analyses further indicated that T6SS gain was strongly biased towards motile lineages, even though T6SS loss was common overall. These results support an asymmetric macroevolutionary relationship between bacterial motility and antagonism, in which flagellar motility is robustly coupled to contact-dependent competition but not to diffusible antagonistic systems.

evolutionary biology↗

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↗

bioRxiv2020

Structural and Functional Implications of Non-synonymous Mutations in the Spike protein of 2,954 SARS-CoV-2 Genomes

Protein-protein interactions between virus and host are crucial for infection. SARS-CoV-2, the causative agent of COVID-19 pandemic is an RNA virus prone to mutations. Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. Yet, how this binding interface evolves as virus acquires mutations during pandemic remains elusive. Here, using a high fidelity bioinformatics pipeline, we analysed 31,403 SARS-CoV-2 genomes across the globe, and identified 444 non-synonymous mutations that cause 49 distinct amino acid substitutions in the RBD. Molecular phylogenetic analysis suggested independent emergence of these RBD mutants during pandemic. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. Comparative structure analysis using binding interface from mouse that prevents SARS-CoV-2 entry uncovered minimal molecular determinants in RBD necessary for the formation of stable interface. We identified that interfacial interaction involving amino acid residues N487 and G496 on either ends of the binding scaffold are indispensable to anchor RBD and are well conserved in all SARS-like corona viruses. All other interactions appear to be required to locally remodel binding interface with varying affinities and thus may decide extent of viral transmission and disease outcome. Together, our findings propose the modalities and variations in RBD-ACE2 interface formation exploited by SARS-CoV-2 for endurance. ImportanceCOVID-19, so far the worst hit pandemic to mankind, started in January 2020 and is still prevailing globally. Our study identified key molecular arrangements in RBD-ACE2 interface that help virus to tolerate mutations and prevail. In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. The minimal molecular requirements for the formation of RBD-ACE2 interface predicted using in silico structure models may help precisely design neutralizing antibodies, vaccines and therapeutics. Our study also proposes the significance of understanding evolution of protein interfaces during pandemic.

evolutionary biology↗