Partial Gene Duplication and the Formation of Novel Genes

Toll-Riera, Macarena; Laurie, Steve; Radó-Trilla, Núria; Albà, Mar

doi:10.5772/21846

Cited by 6 publications

(2 citation statements)

References 69 publications

(51 reference statements)

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“…Species- or lineage-specific orphan genes are defined by their lack of homologues in other species. They may arise by rearrangements of already existing coding sequences, often including partially duplicated genes and/or transposable elements ( Zhang et al 2004 ; Toll-Riera et al 2009 , 2011 ), or completely de novo from previously noncoding genomic regions ( Levine et al 2006 ; Cai et al 2008 ; Heinen et al 2009 ; Knowles and McLysaght 2009 ; Toll-Riera, Laurie, Radó-Trilla and Albà 2011 ; Tautz and Domazet-Lošo 2011 ; Wu et al 2011 ; Reinhardt et al 2013 ; McLysaght and Hurst 2016 ). The latter process is facilitated by the high transcriptional turnover of the genome, which continuously produces transcripts that can potentially acquire new functions and become novel protein coding genes ( Zhao et al 2014 ; Ruiz-Orera et al 2015 ; Neme and Tautz 2016 ).…”

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confidence: 99%

New Genes and Functional Innovation in Mammals

Villanueva‐Cañas

Ruiz-Orera

Agea

et al. 2017

Genome Biology and Evolution

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The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

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Section: Introductionmentioning

confidence: 99%

New Genes and Functional Innovation in Mammals

Villanueva‐Cañas

Ruiz-Orera

Agea

et al. 2017

Genome Biology and Evolution

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“…Gene duplication is common in molecular evolution and is thought to be a major mechanism underlying the emergence of new protein function. , For example, duplication of the eight-strand outer membrane β-barrel protein OmpX produces a functional 16-stranded barrel Omp2x, suggesting gene duplication is a simple way to create pores of different diameters . In addition to complete gene duplication, partial gene duplications are also observed; sequence alignments of evolutionarily related proteins commonly show short insertions or deletions, and these have been estimated to be only ∼10-fold less common than point mutations. , Several groups have analyzed how insertions and deletions (indels) can lead to new folds and functions. − For example, Mollet and Delley discovered that a spontaneous partial duplication of an internal sequence in β-galactosidase could restore the activity of a deletion mutant of that enzyme . Very short duplications or amino acid repeats in protein sequences also occur, for example, via replication slippage, and can also lead to altered protein function as with the poly Q repeats observed in huntingtin …”

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Duplication of a Single Strand in a β-Sheet Can Produce a New Switching Function in a Photosensory Protein

et al. 2018

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Duplication of a single β-strand that forms part of a β-sheet in photoactive yellow protein (PYP) was found to produce two approximately isoenergetic protein conformations, in which either the first or the second copy of the duplicated β-strand participates in the β-sheet. Whereas one conformation (big-loop) is more stable at equilibrium in the dark, the other conformation (long-tail) is populated after recovery from blue light irradiation. By appending a recognition motif (E-helix) to the C-terminus of the protein, we show that β-strand duplication, and the resulting possibility of β-strand slippage, can lead to a new switchable protein-protein interaction. We suggest that β-strand duplication may be a general means of introducing two-state switching activity into protein structures.

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