ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability

Abstract

The ancestral sequence reconstruction (ASR) is a molecular evolution techniquethat provides applications to a variety of fields such as biotechnology and biomedicine. To infer ancestral sequences with realistic biological properties, the accuracy of ASR methods is crucial. We previously developed an ASR framework for proteins, called ProtASR, which is based on our site-specific stability-constrained substitution (SCS) model with selection on protein folding stability against both unfolding and misfolding. This model improved the empirical substitution models traditionally applied in ASR without increasing the computational complexity.However, it adopted a global exchangeability matrix, an approximation that we overcome here by considering site-specific exchangeability matrices based on the Halpern-Bruno approach.2. Here we present ProtASR2, a new version of our ASR framework that implements novel SCS models of protein evolution, namely mean-field (MF) and wild-type (WT). ProtASR2 under MF and WT SCS models outperforms empirical models andprevious SCS models in terms of goodness of fit and site-specific distributions of amino acids. Importantly, the framework infers ancestral sequences with more realistic predicted folding stability with respect to simulated sequences, while empirical, CAT and other SCS models tend to overestimate the folding stability. We applied ProtASR2 to explore the evolution of two protein families present in diverse Prokaryota and found fluctuations of protein stability over time in both families. ProtASR2 is available from https ://github.com/migue laren as/protasr and the new SCS models are also available from https ://github.com/ ugoba s/protevol. 4. Use of ProtASR2 will allow more realistic inferences of ancestral proteins in terms of folding stability with respect to those based on traditional empirical and CAT substitution models of protein evolution. K E Y W O R D Sancestral protein reconstruction, ancestral sequence reconstruction, molecular adaptation, molecular evolution, phylogenetics, protein evolution, protein folding stability, protein sequences | 249Methods in Ecology and Evoluঞon ARENAS ANd BASTOLLA

Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction

“…We analyzed the prokaryotic protein families D-ala D-ala ligases and Thioredoxins I (TRXB; table 1 ) as illustrative real examples. These protein families, available from the PFAM database ( table 1 ), include a putative group of homologs from many bacterial species ( Bastolla et al 2004 ) with extant sequences longer than 200 amino acids that allow well-supported phylogenetic reconstructions ( Arenas et al 2017 ; Arenas and Bastolla 2020 ) and also have been previously analyzed with ASR ( Perez-Jimenez et al 2011 ; Meziane-Cherif et al 2012 ; Ingles-Prieto et al 2013 ). We realigned the sequences with MAFFT ( Katoh and Standley 2013 ) as a prudent procedure.…”

ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation

“…ProteinEvolver is based on previous coalescent simulators ( Arenas and Posada, 2007 ; Arenas and Posada, 2010 ) and has been widely used and validated (e.g. Arenas and Bastolla, 2020 ; Arenas et al , 2013 ; Arenas et al , 2017 ; Pascual-Garcia et al , 2019 ). The simulations are parameterized sampling from the user-specified prior distributions ( Supplementary Table S1 ) and, conveniently, can run in parallel on multicore computers.…”

“…In this concern, it is known that accounting for the best fitting substitution model of protein evolution is convenient for evolutionary inferences (e.g. Arenas and Bastolla, 2020 ; Bordner and Mittelmann, 2014 ; Lemmon and Moriarty, 2004 ) although there is a recent discussion concerning its specific application to phylogenetic tree reconstructions ( Spielman, 2020 ). In any case, accounting for the substitution model of evolution that best fits the data in the estimation of the recombination rate with probabilistic methods was found necessary ( Lopes et al , 2014 ).…”

HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models

“…Substitution models of molecular evolution are well established in a variety of phylogenetic methods to obtain accurate inferences of past evolutionary processes [ 1 ]. At the protein level, substitution models are frequently applied in evolutionary biology to infer phylogenetic trees [ 2 , 3 ], ancestral sequences [ 4 , 5 ] and selection [ 6 , 7 ], among other applications [ 1 , 8 ]. The current substitution models of protein evolution can be classified roughly into two categories.…”