Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

© 2015 Avila-Herrera and Pollard. Background: When biomolecules physically interact, natural selection operates on them jointly. Contacting positions in protein and RNA structures exhibit correlated patterns of sequence evolution due to constraints impose

The role of visual adaptation in cichlid fish speciation

D. Shane Wright (1) , Ole Seehausen (2), Ton G.G. Groothuis (1), Martine E. Maan (1) (1) University of Groningen; GELIFES; EGDB(2) Department of Fish Ecology & Evolution, EAWAG Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum AND Institute of Ecology and Evolution, Aquatic Ecology, University of Bern.In less than 15,000 years, Lake Victoria cichlid fishes have radiated into as many as 500 different species. Ecological and sexual sel ection are thought to contribute to this ongoing speciation process, but genetic differentiation remains low. However, recent work in visual pigment genes, opsins, has shown more diversity. Unlike neighboring Lakes Malawi and Tanganyika, Lake Victoria is highly turbid, resulting in a long wavelength shift in the light spectrum with increasing depth, providing an environmental gradient for exploring divergent coevolution in sensory systems and colour signals via sensory drive. Pundamilia pundamila and Pundamilia nyererei are two sympatric species found at rocky islands across southern portions of Lake Victoria, differing in male colouration and the depth they reside. Previous work has shown species differentiation in colour discrimination, corresponding to divergent female preferences for conspecific male colouration. A mechanistic link between colour vision and preference would provide a rapid route to reproductive isolation between divergently adapting populations. This link is tested by experimental manip ulation of colour vision - raising both species and their hybrids under light conditions mimicking shallow and deep habitats. We quantify the expression of retinal opsins and test behaviours important for speciation: mate choice, habitat preference, and fo raging performance

Directed evolution of bioactive compounds: oxa(thia)zole-containing post-translationally modified peptides

Thiazole/Oxazole Modified Microcins (TOMMs) are a diverse class of post-translationally modified peptides including many bioactive compounds; a potential new source for drug discovery. Despite a limited understanding of the TOMM synthase heterotrimeric complex biosynthetic mechanism, a variable degree of substrate plasticity is present in the family. This makes them attractive targets for developing novel oxazole- and thiazole-containing compounds from synthetic peptides. Available annotation on complex members suggests the presence of different biochemical activities among homologous proteins, precluding the use of established prediction methods for identification of functional residues. A novel algorithm was developed (Normalised Shannon Entropy, NoSE) for functional prediction from sequence alignments containing mixed functions. NoSE was applied, along with established conservation- and coevolution-based metrics, to detect functional residues in the well-characterised bacterial Solute Binding Protein family, which could be validated against the extensively reported characterisation. The strategy was applied for functional residue prediction in the TOMM synthase complex and candidate functional residues were mutated in McbC dehydrogenase of Escherichia coli. Mutants were assessed using a bacterial growth inhibition bioassay and six out of sixteen mutations reduced TOMM production, demonstrating the value of employing a prediction strategy to improve characterization of proteins. Attempts at establishing an in vitro assay for TOMM biosynthesis were unsuccessful due to difficulties in protein expression and purification, as well as inconsistent assay results. Finally, a framework for directed evolution of length-variable proteins was developed, with the aim of engineering synthetic TOMM products. A method was developed for assembly of high-quality libraries at a low cost, along with a workflow for enriched motif detection in selection experiments. The approach was validated by isolating seven novel variants of the β-lactamase TEM-1 active on a non-cognate substrate. Together, the developed methods represent a foundation for establishing TOMM biosynthesis as a platform for discovery of novel bioactive compounds

Molecular Phylogenetics and Mitochondrial Evolution

The aim of the present Special Issue is to address the state-of-art of mitochondrial genomics and phylogenomics. Mitochondrial markers are widespread in phylogenetics; however, it is becoming increasingly clear that (i) many discordance issues arise with respect to nuclear markers and (ii) many features that are normally considered 'typical' for the mitochondrial genome are indeed highly unstable and unconserved