Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genusEucalyptus

2014 ◽  
Vol 206 (4) ◽  
pp. 1328-1336 ◽  
Author(s):  
Anna R. Kersting ◽  
Eshchar Mizrachi ◽  
Erich Bornberg-Bauer ◽  
Alexander A. Myburg
Keyword(s):  
Adaptive Radiation ◽  
Protein Domain ◽  
Domain Evolution ◽  
Protein Domain Evolution

scholarly journals The Nature of Protein Domain Evolution: Shaping the Interaction Network

2010 ◽  
Vol 11 (5) ◽  
pp. 368-376 ◽  
Author(s):  
Christoph P. Bagowski ◽  
Wouter Bruins ◽  
Aartjan J.W. te Velthuis
Keyword(s):  
Interaction Network ◽  
Protein Domain ◽  
Domain Evolution ◽  
Protein Domain Evolution

scholarly journals Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190088 ◽  
Author(s):  
David López-Escardó ◽  
Xavier Grau-Bové ◽  
Amy Guillaumet-Adkins ◽  
Marta Gut ◽  
Michael E. Sieracki ◽  
...  
Keyword(s):  
Single Cell ◽  
Sister Group ◽  
Genomic Diversity ◽  
Protein Domain ◽  
Clear Understanding ◽  
Single Cell Genomics ◽  
Genome Data ◽  
New Genes ◽  
Protein Domain Evolution ◽  
Rearrangement Processes

Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals Gene Content Evolution in the Arthropods

2018 ◽  
Author(s):  
Gregg W.C. Thomas ◽  
Elias Dohmen ◽  
Daniel S.T. Hughes ◽  
Shwetha C. Murali ◽  
Monica Poelchau ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Large Scale ◽  
Gene Families ◽  
Protein Domain ◽  
Whole Genome ◽  
Genome Sequences ◽  
Arthropod Evolution ◽  
Animal Diversity ◽  
Physiological Adaptations ◽  
Protein Domain Evolution

AbstractBackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.ResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality and chemoperception.ConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

scholarly journals The deep(er) roots of Eukaryotes and Akaryotes

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 112
Author(s):  
Ajith Harish ◽  
David Morrison
Keyword(s):  
Phylogenetic Signal ◽  
Protein Domains ◽  
Protein Domain ◽  
Root Node ◽  
Molecular Features ◽  
Phylogenetic Reconstructions ◽  
Universal Common Ancestor ◽  
Evolutionary Relatedness ◽  
Protein Domain Evolution ◽  
Phylogenetic Character

Background: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics. The root-node or the universal common ancestor (UCA) divides descendants into organismal domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA and that Asgard archaea are sister to other archaea, whereas the other proposes that eukaryotes emerged within archaea and places Asgard archaea sister to eukaryotes. Williams et al. (Nature Ecol. Evol. 4: 138–147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: We argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. Which 2D-ToL is better supported depends on which kind of molecular features – protein-domains or their component amino acids – are better for resolving common ancestors at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA. We believe the criticisms of 2D-ToL focus on superficial aspects of the data and reflects common misunderstandings of phylogenetic reconstructions using protein domains (folds).   Clarifications: Models of protein domain evolution support more reliable phylogenetic reconstructions. In contrast, even the best available amino acid substitution models fail to resolve the archaeal radiation, despite employing thousands of genes. Therefore, the primary domains Eukaryotes and Akaryotes are better supported in a 2D-ToL.

scholarly journals Selection on network dynamics drives differential rates of protein domain evolution

2015 ◽  
Author(s):  
Brian K Mannakee ◽  
Ryan N Gutenkunst
Keyword(s):  
Systems Biology ◽  
Evolutionary Rate ◽  
Network Dynamics ◽  
Protein Domain ◽  
Computational Systems Biology ◽  
Protein Activity ◽  
Phenotypic Effect ◽  
Reaction Rate Constants ◽  
Evolutionary Forces ◽  
Protein Domain Evolution

The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein's rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces.

Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain

2018 ◽  
Author(s):  
Sarah Klass ◽  
Matthew J. Smith ◽  
Tahoe Fiala ◽  
Jessica Lee ◽  
Anthony Omole ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Fusion Proteins ◽  
Organic Molecules ◽  
Intrinsically Disordered Protein ◽  
Protein Domain ◽  
Enzymatic Cleavage ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Self Assembling ◽  
Protein Tag

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

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