Toward accessible bioinformatic tools for analyzing residue coevolution and sequence-fitness relationships in Fluc family proteins
Creators: name: Baudelaire, Fox
Publisher: name: My University
Year: 2023
Subjects: subject: membrane protein
subject: bioinformatics
subject: evolutionary couplings
subject: ion channel
subject: fitness landscape
subject: structural biology
subject: Biology
subject: Science

description: Members of the Fluc family of membrane channel proteins, found in all three domains of biological classification, allow organisms to prevent the buildup of fluoride ion inside cells and thereby counteract fluoride toxicity. Export through these proteins is passive yet extremely selective for the substrate. Like nearly all membrane proteins, Fluc protomers exhibit internal repeat symmetry, which is thought to result from either the association of structurally similar domains or gene duplication. Gene duplication events are of special significance to the Fluc family because duplication is considered the earliest mechanism of major genetic variation that allowed for topologically distinct Fluc channels to evolve. In prokaryotes, the Fluc channels assemble as proper dimers and may have a dual topology (monomer is equally capable of insertion in either of two orientations with respect to the membrane) or a fixed topology (monomer is biased towards one orientation). Fixed-topology channels are obligate Fluc heterodimers thought to have arisen due to sequence divergence in the two copies of Fluc-encoding gene following a duplication event. In eukaryotes, the homologous FEX family proteins are monomeric, but retain a pseudosymmetry suggestive of a gene fusion event in an ancestor, joining two previously separate copies of Fluc-encoding gene. Accordingly, the dual-topology state is considered the ancestral phenotype; the more subfunctionalized phenotypes evolved later. Multiple independent gene duplications in the Fluc family have been retained over evolutionary time, and the Fluc/FEX proteins as a whole are thought to have undergone a general, three-step evolutionary trajectory: (1) gene duplication, (2) sequence divergence, and (3) gene fusion. With attention to ease of access and other principles of software development, the present work develops computational tools using Python and R for two purposes: evaluating the bias in membrane protein orientation for each member of a diverse set of prokaryotic Fluc homologs and quantifying mutational tolerance in Fluc residues from computed statistical correlations between likely pairs of co-evolving residues. For the latter of these ends, we apply the validated computational framework EVcouplings to Fluc-Bpe, the dual-topology Fluc channel found in Bordetella pertussis whose structure and function have become well characterized in recent years. We generate a single-site substitution matrix that illustrates the effects of amino acid substitution for nearly the entirety of the Fluc-Bpe primary sequence and we describe means by which this result may be validated by experiment. Having estimated prima facie the mutational lability of the Fluc-Bpe sequence space, we consider paralog dynamics to posit a more detailed yet provisional narrative of the evolution of post-duplication Fluc topologies. We stress the importance of further studies in the elaboration and testing of this narrative, including efforts to chart the Fluc evolutionary pathway in phylogenetic terms. Finally, we draw attention to particular limitations of the adaptationist paradigm in evolutionary theory and we advise nuance in the modeling of sequence-fitness relationships using the fitness landscape metaphor that is prominently used throughout the discipline.