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opencc-zeroOct 2023View details →

Data from: Convergent rates of protein evolution identify novel targets of sexual selection in primates

Sexual selection is the differential reproductive success of individuals, resulting from competition for mates, mate choice, or success in fertilization. In primates, this selective pressure often leads to the development of exaggerated traits which play a role in sexual competition and successful reproduction. In order to gain insight into the mechanisms driving the development of sexually selected traits, we used an unbiased genome-wide approach across 21 primate species to correlate individual rates of protein evolution to relative testes size and sexual dimorphism in body size, two anatomical hallmarks of sexual selection in mammals. Among species with presumed high levels of sperm competition, we detected strong conservation of testes-specific proteins responsible for spermatogenesis and ciliary form and function. In contrast, we identified accelerated evolution of female reproductive proteins expressed in the vagina, cervix, and fallopian tubes in these same species. Additionally, we found accelerated protein evolution in lymphoid tissue, indicating that adaptive immune functions may also be influenced by sexual selection. This study demonstrates the distinct complexity of sexual selection in primates revealing contrasting patterns of protein evolution between male and female reproductive tissues.

opencc-zeroNov 2023View details →

Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5' to guanine (G) on the same coding strand, and if the C is methylated, then C→T and G→A mutations occur at an elevated rate relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2 affinity in high-altitude birds. Using a data set of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, demonstrating that mutation bias can influence outcomes of molecular adaptation.

zenodo40/100

Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins

This repository contains files that accompany the Schoelmerich et al. (2022) bioRxiv preprint. These files include - all Borg proteins used for protein family clustering (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/all_Borg_proteins.fasta">all_Borg_proteins.fasta</a>) - 37 additional aaTR-proteins from manually curated Borg contigs (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/37_Borg_aaTR-proteins.fasta?versionId=bfdfe7b6-e3b5-48b8-b7e6-a20304097e7d">37_Borg_aaTR-proteins.fasta</a>) - IQ-TREE of Borg DNA polymerases and reference sequences from doi: 10.1093/nar/gkaa760 (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/DNAPolB_iqtree.treefile?versionId=c588a98c-822d-4a2f-a92d-7dcb3b1675f0">DNAPolB_iqtree.treefile</a>) - Borg Sm ribonucleoprotein sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/21_Borg_Sm_ribonucleoproteins.fasta">21_Borg_Sm_ribonucleoproteins.fasta</a>) - Borg MHC sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/14_Borg_MHC_proteins.fasta">14_Borg_MHC_proteins.fasta</a>) - AlphaFold2 predicted structural models of Borg Sm ribonucleoproteins and MHCs with aaTRs

opencc-by-4.0May 2022View details →

publicMay 2025View details →

Data from: The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family

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publicNov 2023View details →

Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

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publicOct 2023View details →

Data from: Convergent rates of protein evolution identify novel targets of sexual selection in primates

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opencc-by-4.0Dec 2023View details →

the supplementary of Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates

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opencc-by-4.0Mar 2022View details →

Data from: Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an "Allosterized" Enzyme using Evolution Guided Punctual Mutations

This data accompanies the paper entitled Protein Conformational Space at the Edge of Allostery: Turning a Non-allosteric Malate Dehydrogenase into an “Allosterized” Enzyme using Evolution Guided Punctual Mutations The zip archive contains the results of molecular dynamics simulations of the 4 systems investigated in the paper: wt of A. ful MalDH and three mutants. Each system has been simulated at two temperatures, 300 K and 340 K. Starting configurations of the proteins after equilibration are provided for all the systems in GRO Gromos87 format. Trajectories with the positions of the proteins every 100 ps are provided for all the systems in XTC gromacs format.

opencc-zeroMay 2022View details →

Evolution of a novel female reproductive strategy in Drosophila melanogaster populations subjected to long term protein restriction

Reproductive output is often constrained by availability of macronutrients, especially protein. Long term protein restriction, therefore, is expected to select for traits maximizing reproduction even under nutritional challenge. We subjected four replicate populations of Drosophila melanogaster to a complete deprivation of yeast supplement, thereby mimicking a protein restricted ecology. Following 24 generations, compared to their matched controls, females from experimental populations showed increased reproductive output early in life, both in presence and absence of yeast supplement. The observed increase in reproductive output was without associated alterations in egg size, development time, pre-adult survivorship, body mass at eclosion, and lifespan of the females. Further, selection was ineffective on lifelong cumulative fecundity. However, females from experiment regime were found to have a significantly faster rate of reproductive senescence following the attainment of the reproductive peak early in life. Therefore, adaptation to yeast deprivation ecology in our study involved a novel reproductive strategy whereby females attained higher reproductive output early in life followed by faster reproductive aging. To the best of our knowledge, this is one of the cleanest demonstration of optimization of fitness by fine tuning of reproductive schedule during adaptation to a prolonged nutritional deprivation.

opencc-by-4.0Aug 2019View details →

Protein interaction networks are substantially rewired across evolution

Complete data and source code deposit for Protein interaction networks are substantially rewired across evolution.

opencc-by-4.0Nov 2024View details →

Docking data for "The evolution of the SARS-CoV-2 spike protein for differential usage of the host transmembrane serine proteases entry pathway"

The dataset includes predicted complexes of the SARS-CoV-2 Spike protein (specifically at the S2' cleavage site) with Hepsin and TMPRSS2 proteins. It contains data on three variants: Wuhan, Delta, and Omicron BA.1. Compressed folders: -357596-DeltaHepsin.tgz -357597-DeltaTMPRSS2.tgz -360039-WuhanHepsin.tgz -360042-TMPRSSWuhan.tgz -392981-TMPRSS-BA1_all.tgz -392982-Hepsin-BA-all.tgz Each compressed folder contains the following: -Initial structures in pdb format -Output complexes in pdb format -Clusters in pdb format -Protocols -Parameters -Scoring files   Protein-protein docking  Molecular docking between the SARS-CoV-2 S protein of Wuhan, Delta (PDB: 7W92, [DOI: 10.1038/s41467-022-28528-w]), and BA.1 (PDB: 7XO5, [DOI: 10.1038/s41422-022-00672-4]) and the human proteases TMPRSS2 (PDB: 8HD8, [DOI: 10.1038/s41467-023-42527-5]) and Hepsin (PDB: 1Z8G, [DOI: 10.1042/BJ20041955]) was performed using the HADDOCK v2.5-2024.03 webserver ([DOI: 10.1021/ja026939x], [DOI: 10.1016/j.jmb.2015.09.014]). Missing loops in the protein structures were reconstructed using Modeller v10.5 ([DOI: 10.1006/jmbi.1993.1626]). Every heteroatom was removed from the reference structures. The relaxed atomistic coordinates for each S protein variant were derived via all-atom molecular dynamics (MD) simulations. These simulations were performed using AMBER22 with the FF19SB force fields and the pmemd.cuda module for enhanced performance ([DOI: 10.1021/acs.jcim.3c01153], [DOI: 10.1021/jz501780a], [DOI:10.1021/ct400314y]). For the Wuhan variant the S protein was retrieved from our previous modeling study [DOI: 10.1039/D0NR03969A] where for Delta and BA.1, ecah S protein was placed in a dodecahedral box, extending 20 Å beyond the solute in every cartesian direction, and solvated with the four-site OPC water model ([DOI: 10.1021/jz501780a]). The systems were neutralized with counterions, specifically one Cl− ion for the Delta variant and three Cl- ions for the BA.1 variant. To remove local clashes, a geometric optimization was performed using the steepest descent algorithm for 5000 cycles. The MD equilibration process consisted of several stages. First, temperature equilibration in the NVT ensemble was performed by gradually increasing the temperature through steps of 150, 200, 250, 300, and finally 310 K, each lasting 200 ps. During this phase, position restraints were applied to the heavy atoms of the proteins, with progressively decreasing spring constants of 5.0, 4.0, 3.0, and 1.0 kcal mol−1 Å−2, facilitating gradual relaxation. This was followed by a 1 ns equilibration at 310 K in the NPT ensemble without restraints. For production MD, the simulations were run in the NPT ensemble with periodic boundary conditions and Particle Mesh Ewald (PME) method ([DOI: 10.1063/5.0040966], [DOI: 10.1021/ct9001015]) using a grid spacing of 1.0 Å for long-range electrostatics. Non-bonded interactions were modeled with a Lennard-Jones potential using a 9Å cutoff. Temperature control was maintained using Langevin dynamics ([DOI: 10.1021/ct800573m]) with a collision frequency of 4.0 ps−1, and pressure control was managed by the Monte Carlo barostat ([DOI: 10.1016/j.cplett.2003.12.039]) with a 2.0 ps relaxation time at 1 bar. Bond constraints on hydrogen atoms were applied using the SHAKE algorithm ([DOI: 10.1016/0021-9991(77)90098-5]), and the hydrogen mass repartitioning scheme was applied via ParmEd ([DOI: 10.1371/journal.pcbi.1005659]), enabling a 4 fs integration time step ([DOI: 10.1021/ct5010406]). Each protein complex was simulated for a total of 20 ns. For the Wuhan variant, the 3D coordinates were retrieved from [DOI: 10.5281/zenodo.3817446]. The active interaction region on the spike protein was defined as the cleavage site (residues P809-R815). For TMPRSS2 and Hepsin, the active sites were defined based on their catalytic residues: H296, D345, D435, S441, S460, and G462 for TMPRSS2, and H203, D257, D347, A348, and S353 for Hepsin. These specific regions were selected to guide the docking process and maximize biologically relevant interactions. Docking clusters were analyzed by selecting those with the lowest interaction energies for further structural analysis. To evaluate binding accuracy, native contacts between the S protein and proteases were computed using the contact map analysis based on the OV+rCSU method ([DOI: 10.12693/APhysPolA.145.S9, 10.1021/acs.jctc.6b00986]), which allows for a precise identification of critical stabilizing interactions, both specific and non-specifics. High-frequency contacts, defined as those appearing in over 70% of the generated models, were highlighted as key determinants of protein-protein recognition, providing insight into the most stable and consistent interactions across docking configurations.

opencc-zeroAug 2021View details →

Data from: Detailed characterization of the UMAMITs proteins provides insight into their evolution, amino acid transport properties, and role in the plant

Amino acid transporters play a critical role in distributing amino acids within the cell compartments and between the plant organs. Despite this importance, relatively few amino acid transporter genes have been characterized and their role elucidated with certainty. Two main families of proteins encode amino acid transporters in plants: the Amino Acid-Polyamine-Organocation superfamily, containing mostly importers, and the Usually Multiple Acids Move In and out Transporter family, apparently encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively. Knowledge on UMAMITs is scarce, based on six Arabidopsis genes and a handful of genes from other species. To get insight into the role of the members of this family and provide data to be used for future characterization, we studied the evolution of the UMAMITs in plants, and determined the functional properties, the structure, and the localization of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are essentially localized at the tonoplast or the plasma membrane, and that most of them are able to export amino acids from the cytosol, confirming a role in intra- and inter-cellular amino acid transport. As an example, this set of data was used to hypothesize the role of a few AtUMAMITs in the plant and the cell.

opencc-by-4.0Sep 2021View details →

Supplementary Dataset for Trenner et al. 2022: Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling

This record contains additional information and a supplementary dataset of sequence alignment files and phylograms that support the publication: Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. 2022. Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling. (submitted to Annual Review of Plant Biology) Included files: Additional information.pdf This file contains Supplementary Methods and References. Supp_Fig1_Ubox_full_protein_maximum_likelihood_phylogram_linear.pdf A multiple protein sequence alignment by MAFFT of 1121 U-box protein sequences from 21 species and four outgroup sequences containing a RING finger domain (A. thaliana RBX1, A. thaliana RMA1, S. cerevisiae RAD18, Homo sapiens TRAF6 ) was used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL.   Supp_Fig2_Ubox_domain_maximum_likelihood_phylogram_linear.pdf In order to analyse specifically the evolution of the U-box domain, the U-box domain of the final 1121 U-box protein sequences as well as the RING finger domain of the four outgroup sequences were isolated and aligned by MAFFT. The U-box domain alignment was then used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL. This tree was used to interpret the evolutionary history of U-box proteins in the main text.   MAFFT_alignment _1121seqs_Ubox_full_protein_plus_4seqs_RING_outgroup.fasta Multiple protein sequences alignment by MAFFT of 1121 U-box full length protein sequences and four RING finger protein sequences, FASTA formatted.   MAFFT_alignment _1121seqs_Ubox_domain_plus_4seqs_RING_outgroup.fasta Multiple protein sequences alignment by MAFFT of U-box domain sequences of 1121 U-box protein and four RING finger domain sequences of outgroup sequences, FASTA formatted.   Ubox_protein_sequences_information.xlsx Spreadsheet with sequence ID information and source databases.

opencc-by-4.0Sep 2021View details →

Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein

Data underlying the figures in the publication “Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein”, published in ACS Catal. 2021, 11, 17, 10705–10712. https://pubs.acs.org/doi/10.1021/acscatal.1c02405 Table of contents: 1. Dataset; Excel file with the experimental data for figures 2a, 2b, 3b and 5, plus protocol for in vivo catalysis, sequencing data and the selection for rescreening.

opencc-zeroSep 2023View details →

Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family

Early metazoan evolution was characterized by the expansion of many gene families involved in novel multicellularity-related functions, like the Tudor family. In eukaryotes, Tudor genes are numerous and heterogeneous, mostly associated with gene expression regulation. However, the family underwent a lineage-specific expansion in animals, with novel elements almost exclusively involved in the germline-specific regulation of retrotransposons through piRNAs (as spatiotemporal regulators of the key-element Piwi, another previously supposedly animal-specific gene). In the present analysis, we used online-available proteomes for a total of 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, and we confirmed the apomorphic expansion of piRNA-related Tudor genes in animals. However, we could also interestingly observe the presence of elements of the piRNA pathway, both Tudor and Piwi genes, in some Ichthyosporea species, suggesting that some elements of the pathway were already present in the last common ancestor of Holozoa. Moreover, we observed an outstanding variability (34-fold) of Tudor gene number both between and within metazoan phyla, that could be associated with convergent genomic and phenotypic evolutions. Expansions were usually sided by whole genome duplications and/or life history traits such as parthenogenesis, possibly leading to the expansion of retrotransposon silencing pathways. Reductions were instead mostly associated with overall phenotypic and genomic simplifications, like almost all endoparasites of our dataset. Lastly, we phylogenetically tested a previously proposed model for the evolution of the three possible secondary structures of the Tudor domains and we could mostly (but not completely) confirm the model.