Evolution After<i>and</i>Before Gene Duplication?

Sikosek, Tobias; Bornberg‐Bauer, Erich

doi:10.1002/9780470619902.ch6

Cited by 7 publications

(3 citation statements)

References 114 publications

(136 reference statements)

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“…De novo protein emergence provides the genome with great innovative potential to explore the hitherto unexplored sequence space (McLysaght and Hurst 2016;Tautz and Domazet-Lošo 2011;Weisman and Eddy 2017;Van Oss and Carvunis 2019;Rödelsperger et al 2019). In comparison to other known mechanisms of protein emergence that rely on recycling of conserved genetic elements, like duplication (Ohno 1970;Sikosek and Bornberg-Bauer 2010) or gene fusion (Dohmen et al 2020), de novo genes emerge from non-coding regions of the genome (Bornberg-Bauer et al 2021). De novo proteins are shorter on average than new proteins emerging through duplication (Montañés et al 2023) and have low expression that is often restricted to specific tissues or conditions (Heames, J. Schmitz, et al 2020;Wu and Knudson 2018;J.…”

Section: Introductionmentioning

confidence: 99%

High-throughput selection of humande novo-emerged sORFs with high folding potential

Aubel,

Buchel,

Heames

et al. 2024

Preprint

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De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Forster resonance energy transfer (FRET) combined with Fluorescence-activated cell sorting (FACS) we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.

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Section: Introductionmentioning

confidence: 99%

High-throughput selection of humande novo-emerged sORFs with high folding potential

Aubel,

Buchel,

Heames

et al. 2024

Preprint

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“…This evolutionary stability is consistent with the possibility that the function of sult1st6a may be common to those in other fish species. In contrast, there are little clues about the function of sult1st6y but might be explained by a sort of neofunctionalization among possible evolutionary mechanisms of duplicated genes [ 46 ]: sult1st6y could have been immune from the original role of sult1st6 as a redundant copy, leading to the gain of a new function related to sex development under relaxed selection. Here, it is assumed that some mutations may have occurred in the regulatory region of sult1st6y , which changes the expression pattern but not the enzymatic function itself as estrogen sulfotransferase.…”

Section: Discussionmentioning

confidence: 99%

Prediction of the Sex-Associated Genomic Region in Tunas (Thunnus Fishes)

Nakamura

Higuchi

Kumon

et al. 2021

International Journal of Genomics

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Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.

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“…De novo protein emergence provides the genome with great innovative potential to explore the hitherto unexplored sequence space ( Tautz and Domazet-Lošo 2011 ; McLysaght and Hurst 2016 ; Weisman and Eddy 2017 ; Rödelsperger et al 2019 ; Van Oss and Carvunis 2019 ). In comparison to other known mechanisms of protein emergence that rely on recycling of conserved genetic elements, like duplication ( Ohno 1970 ; Sikosek and Bornberg-Bauer 2010 ) or gene fusion ( Dohmen et al 2020 ), de novo genes emerge from noncoding regions of the genome ( Bornberg-Bauer et al 2021 ). De novo proteins are shorter on average than new proteins emerging through duplication ( Montañés et al 2023 ) and have low expression that is often restricted to specific tissues or conditions ( Wu and Knudson 2018 ; Heames et al 2020 ; Schmitz et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential

Aubel,

Buchel,

Heames

et al. 2024

Genome Biology and Evolution

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De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Förster resonance energy transfer combined with Fluorescence-activated cell sorting we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.

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Evolution AfterandBefore Gene Duplication?

Cited by 7 publications

References 114 publications

High-throughput selection of humande novo-emerged sORFs with high folding potential

High-throughput selection of humande novo-emerged sORFs with high folding potential

Prediction of the Sex-Associated Genomic Region in Tunas (Thunnus Fishes)

High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential

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