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Klasberg, S, Bitard-Feildel, T, Callebaut, I and Bornberg-Bauer, E
Origins and Structural Properties of Novel and De Novo Protein Domains During Insect Evolution.
FEBS Journal, 2018

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Over long time scales, protein evolution is characterized by modular rear-
rangements of protein domains. Such rearrangements are mainly caused by
gene duplication, fusion and terminal losses. To better understand domain
emergence mechanisms we investigated 32 insect genomes covering a speci-
ation gradient ranging from ~ 2 to ~ 390 mya. We use established domain
models and foldable domains delineated by hydrophobic cluster analysis
(HCA), which does not require homologous sequences, to also identify
domains which have likely arisen de novo, that is, from previously noncod-
ing DNA. Our results indicate that most novel domains emerge terminally
as they originate from ORF extensions while fewer arise in middle arrange-
ments, resulting from exonization of intronic or intergenic regions. Many
novel domains rapidly migrate between terminal or middle positions and
single- and multidomain arrangements. Young domains, such as most
HCA-defined domains, are under strong selection pressure as they show
signals of purifying selection. De novo domains, linked to ancient domains
or defined by HCA, have higher degrees of intrinsic disorder and disorder-
to-order transition upon binding than ancient domains. However, the cor-
responding DNA sequences of the novel domains of de novo origins could
only rarely be found in sister genomes. We conclude that novel domains
are often recruited by other proteins and undergo important structural
modifications shortly after their emergence, but evolve too fast to be char-
acterized by cross-species comparisons alone.