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Molecular evolution is the area of evolutionary biology that studies evolutionary change at the level of the DNA sequence. It includes the study of rates of sequence change, relative importance of adaptive and neutral changes, and changes in genome structure.
Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are currently extracted from low-yielding daffodils. Here, authors pair biosensor-assisted screening with machine learning-guided protein design to rapidly engineer an improved Amaryllidaceae enzyme in a microbial host.
In Caenorhabditis tropicalis, selective expression of genetic alleles from one parent but not the other can arise from maternally inherited small transcripts acting via the PIWI-interacting RNA host defence pathway.
The authors analyse 8,790 prokaryotic pangenomes to identify the ecological variables associated with recent versus old horizontal gene transfer events, finding that gene transfers are more common among co-occurring, highly abundant or host-associated species.
By developing computational algorithms, the authors annotated translated open reading frames in five eukaryotes and found many stable peptides are encoded by putative ‘noncoding’ regions of genomes.
The reasons for epistasis, wherein mutations interact non-additively, are often not fully understood. Now it is found that shifting the rate-limiting step from substrate binding to the chemical reaction step during the directed evolution of β-lactamase correlates with epistasis.
In this Journal Club, Hajk-Georg Drost highlights a recent study by Pavlopoulos et al. that organizes proteins at tree-of-life scale using massively parallel graph-based clustering.
Carl G. de Boer highlights a recent paper by Lim et al. on the importance low-affinity transcription factor-binding sites for determining organismal phenotypes.
Li Zhao recalls a 2006 paper by Levine et al. that, by identifying a handful of de novo genes, outlined a potentially universal process of de novo gene birth and propelled forward this field of research.
A recent study demonstrated the existence of mutations that facilitate access to efficient evolutionary solutions. Here I discuss the implications of this finding and the potential to open a new chapter in the study of evolvability.