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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Eukaryotic Evolution01:24

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The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Genomic DNA in Eukaryotes00:58

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Protein Complexes with Interchangeable Parts01:57

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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A Method to Study de novo Formation of Chromatin Domains
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Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

Viktorija Linkeviciute1, Owen J L Rackham2, Julian Gough3

  • 1Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; School of Biological Sciences, University of Edinburgh, Darwin Building, The King's Buildings, Edinburgh EH9 3BF, UK.

Biochimie
|May 19, 2015
PubMed
Summary
This summary is machine-generated.

Protein function significantly shapes genome evolution, with specific functions showing biases. Eukaryotic genomes, especially animal ones, prioritize complex signaling and regulation over metabolism.

Keywords:
Domain architecturesEukaryotic genomesEvolutionFunction

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Understanding how protein function influences genome evolution is crucial.
  • The concept of 'architecture plasticity potential' (APP) offers a new perspective.
  • APP measures the capacity of protein domains to form distinct architectures.

Purpose of the Study:

  • Introduce and quantify 'architecture plasticity potential' (APP) for protein domain sets.
  • Analyze the evolutionary dynamics of protein domain architectures across eukaryotic genomes.
  • Investigate the relationship between functional evolution and genome complexity.

Main Methods:

  • Developed a scoring metric to quantify APP for domain sets.
  • Applied the APP metric to a phylogenetic tree of eukaryotic genomes.
  • Compared functional evolution patterns across different species and lineages.

Main Results:

  • Functional involvement in genome evolution is highly selective, not random.
  • Eukaryotic genomes, particularly in animals, show a bias towards expanding signaling and regulatory functions at the expense of metabolic processes.
  • Differential evolution of transcriptional regulation and a unique role for channel regulators were observed, detectable via APP.

Conclusions:

  • Architecture plasticity potential provides novel insights into the significance of protein function in eukaryotic genome evolution.
  • The study reveals specific evolutionary trends in functional domain composition across eukaryotes.
  • Findings highlight the selective nature of functional evolution and its impact on genome complexity.