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Trends Genet
FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands. Electronic address:
Published: May 2014
Environmental changes can not only trigger a regulatory response, but also impose evolutionary pressures that can modify the underlying regulatory network. Here, we review recent approaches that are beginning to disentangle this complex interplay between regulatory and evolutionary responses. Systematic genetic reconstructions have shown how evolutionary constraints arise from epistatic interactions between mutations in fixed environments. This approach is now being extended to more complex environments and systems. The first results suggest that epistasis is affected dramatically by environmental changes and, hence, can profoundly affect the course of evolution. Thus, external environments not only define the selection of favored phenotypes, but also affect the internal constraints that can limit the evolution of these phenotypes. These findings also raise new questions relating to the conditions for evolutionary transitions and the evolutionary potential of regulatory networks.
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http://dx.doi.org/10.1016/j.tig.2014.04.003 | DOI Listing |
Adv Sci (Weinh)
March 2025
State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
Evolutionary constraints significantly limit the diversity of naturally occurring enzymes, thereby reducing the sequence repertoire available for enzyme discovery and engineering. Recent breakthroughs in protein structure prediction and de novo design, powered by artificial intelligence, now enable to create enzymes with desired functions without solely relying on traditional genome mining. Here, a computational strategy is demonstrated for creating new-to-nature polyethylene terephthalate hydrolases (PET hydrolases) by leveraging the known catalytic mechanisms and implementing multiple deep learning algorithms and molecular computations.
View Article and Find Full Text PDFBio Protoc
March 2025
Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
The limited standards for the rigorous and objective use of mitochondrial genomes (mitogenomes) can lead to uncertainties regarding the phylogenetic relationships of taxa under varying evolutionary constraints. The mitogenome exhibits heterogeneity in base composition, and evolutionary rates may vary across different regions, which can cause empirical data to violate assumptions of the applied evolutionary models. Consequently, the unique evolutionary signatures of the dataset must be carefully evaluated before selecting an appropriate approach for phylogenomic inference.
View Article and Find Full Text PDFSci Rep
March 2025
School of Cyber Science and Engineering, Ningbo University of Technology, Ningbo, 315211, Zhejiang, China.
The evolution of cyber-physical systems (CPS) is inevitable. Traditional graph and hypergraph modeling and analysis methods can only describe one-dimensional evolutionary information, making it difficult to directly apply them to the modeling and analysis of CPS evolution processes that involve two-dimensional space. To address this issue, this paper proposes a Bigraph model for CPS that incorporates positional constraints.
View Article and Find Full Text PDFBiosystems
March 2025
Department of Physics, National Institute of Technology, Durgapur, W.B., India. Electronic address:
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing, given the inherent difficulties in the simultaneous and localized prebiotic synthesis of all four monomers of progenitors of RNA/DNA from common precursors on early Earth. Excluding the scenario where a two-letter alphabet genome eventually expanded to include two more letters to code for more amino acids on teleological grounds, we show here that a replicatively superior heteropolymer sequence in an RNA-world-like scenario would have to be composed of at least four letters in order to predictably fold into a specific secondary structure, and hence must have out-competed the two-letter alphabet genomes.
View Article and Find Full Text PDFCurr Opin Struct Biol
March 2025
Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. Electronic address:
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences that comprise intrinsically disordered regions. We here review developments in the study of sequence-ensemble-function relationships of disordered proteins that exploit or are used to train machine learning models.
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