AniProtDB: A Collection of Consistently Generated Metazoan Proteomes for Comparative Genomics Studies

Barreira, Sofia N; Nguyen, Anh‐Dao; Fredriksen, Mark T; Wolfsberg, Tyra G.; Moreland, Russell; Baxevanis, Andreas D

doi:10.1093/molbev/msab165

Cited by 8 publications

(6 citation statements)

References 28 publications

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“…Gene CDS were directly extracted from mRNA sequences (transcripts) downloaded from the October 2020 release of AniProtDB ( Barreira et al 2021 ). A reciprocal blastp was performed ( e -value 1 × 10 −3 ) to select orthologs.…”

Section: Methodsmentioning

confidence: 99%

Evolution is not Uniform Along Coding Sequences

Bricout

Weil

Stroebel

et al. 2023

Molecular Biology and Evolution

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Amino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. Notably, amino-acids located at the surface of proteins are known to evolve more rapidly than those in the core. In particular, amino-acids at the N- and C-termini of protein sequences are likely to be more exposed than those at the core of the folded protein due to their location in the peptidic chain, and they are known to be less structured. Because of these reasons, we would expect that amino-acids located at protein termini would evolve faster than residues located inside the chain. Here we test this hypothesis and found that amino acids evolve almost twice as fast at protein termini compared to those in the centre, hinting at a strong topological bias along the sequence length. We further show that the distribution of solvent-accessible residues and functional domains in proteins readily explain how structural and functional constraints are weaker at their termini, leading to the observed excess of amino-acid substitutions. Finally, we show that the specific evolutionary rates at protein termini may have direct consequences, notably misleading in silico methods used to infer sites under positive selection within genes. These results suggest that accounting for positional information should improve evolutionary models.

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Section: Methodsmentioning

confidence: 99%

Evolution is not Uniform Along Coding Sequences

Bricout

Weil

Stroebel

et al. 2023

Molecular Biology and Evolution

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“…In addition to p53 variations, it has been hypothesized that an accumulation of differentially expressed, modified, and activated (by PTMs) p53 pools, collectively or synergistically regulate the response to specific stresses in the cell ( Khoury and Bourdon 2011 ). These PTMs are suggested to have evolved as a result of coevolutionary cues of the p53–MDM2 interactions during the transition from (1) an ancestral early branching invertebrate system (prevertebrate) ( Barreira et al 2021 ) to (2) a derived mammalian vertebrate system ( Karakostis et al 2016 ; Karakostis and Fahraeus 2019 ).…”

Section: Introductionmentioning

confidence: 99%

The Elephant Evolved p53 Isoforms that Escape MDM2-Mediated Repression and Cancer

Padariya

Jooste

Hupp

et al. 2022

Molecular Biology and Evolution

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The p53 tumour suppressor is a transcription factor with roles in cell development, apoptosis, oncogenesis, ageing and homeostasis in response to stresses and infections. p53 is tightly regulated by the MDM2 E3 ubiquitin ligase. The p53-MDM2 pathway has co-evolved, with MDM2 remaining largely conserved while the TP53 gene morphed into various isoforms. Studies on pre-vertebrate ancestral homologues revealed the transition from an environmentally-induced mechanism activating p53 to a tightly regulated system involving cell signaling. The evolution of this mechanism depends on structural changes in the interacting protein motifs. Elephants such as Loxodonta africana constitute ideal models to investigate this co-evolution as they are large and long-living as well as having 20 copies of TP53 isoformic sequences expressing a variety of BOX-I MDM2-binding motifs. Collectively, these isoforms would enhance sensitivity to cellular stresses, such as DNA damage, presumably accounting for strong cancer defenses and other adaptations favouring healthy ageing. Here we investigate the molecular evolution of the p53-MDM2 system by combining in silico modelling and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction while forming distinct pools of cell-signalling. The methodology used demonstrates, for the first time, that in silico docking simulations can be used to explore functional aspects of elephant p53 isoforms. Our observations elucidate structural and mechanistic aspects of p53 regulation, facilitate understanding of complex cell signalling and suggest testable hypotheses of p53 evolution referencing Peto’s Paradox.

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“…The remaining 25% includes almost all representatives of tardigrades, annelids, nematodes, acoels, and some representatives of other phyla (see Table S1). As we want to maximize the taxon representation of animal lineages while keeping datasets of high quality, we lowered the threshold value to 70% in these cases, a value that has been previously used in other studies, as these values may indeed represent biological features of the genomes of these lineages (Barreira et al, 2021). As an exception, after this new threshold, 8 animal and 2 outgroup transcriptome assemblies have been included with a slightly lower BUSCO score due to their taxonomic relevance (e.g., they were the only representatives of their lineage, such as in the case of the hagfish).…”

Section: Methodsmentioning

confidence: 99%

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

Martínez-Redondo,

Vargas-Chávez,

Eleftheriadi

et al. 2024

Preprint

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Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (1) we include data from all animal phyla where public data is available, (2) we provide gene annotations from genomes obtained using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.

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AniProtDB: A Collection of Consistently Generated Metazoan Proteomes for Comparative Genomics Studies

Cited by 8 publications

References 28 publications

Evolution is not Uniform Along Coding Sequences

Evolution is not Uniform Along Coding Sequences

The Elephant Evolved p53 Isoforms that Escape MDM2-Mediated Repression and Cancer

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

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