Rizzato F, Zamuner S, Pagnani A, Laio A. A common root for coevolution and substitution rate variability in protein sequence evolution. Sci Rep. 2019;9(1):18032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Echave J, Wilke CO. Biophysical models of protein evolution: understanding the patterns of evolutionary sequence divergence. Annu Rev Biophys. 2017;46:85–103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Yang JR. Determinants of the rate of protein sequence evolution. Nat Rev Genet. 2015;16(7):409–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Serohijos AW, Rimas Z, Shakhnovich EI. Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep. 2012;2(2):249–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lobkovsky AE, Wolf YI, Koonin EV. Universal distribution of protein evolution rates as a consequence of protein folding physics. Proc Natl Acad Sci U S A. 2010;107(7):2983–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ. The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A. 2009;106(18):7273–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol. 2004;186(19):6575–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolf YI, Carmel L, Koonin EV. Unifying measures of gene function and evolution. Proc Biol Sci. 2006;273(1593):1507–15.
CAS
PubMed
PubMed Central
Google Scholar
Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008;134(2):341–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lannergard J, Kristensen BM, Gustafsson MC, Persson JJ, Norrby-Teglund A, Stalhammar-Carlemalm M, Lindahl G. Sequence variability is correlated with weak immunogenicity in Streptococcus pyogenes M protein. Microbiologyopen. 2015;4(5):774–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lemey P, Rambaut A, Pybus OG. HIV evolutionary dynamics within and among hosts. AIDS Rev. 2006;8(3):125–40.
PubMed
Google Scholar
Marchi J, Lassig M, Mora T, Walczak AM. Multi-lineage evolution in viral populations driven by host immune systems. Pathogens. 2019;8(3):115.
Article
PubMed Central
Google Scholar
Luksza M, Lassig M. A predictive fitness model for influenza. Nature. 2014;507(7490):57–61.
Article
CAS
PubMed
Google Scholar
Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct. 2006;1:34.
Article
PubMed
PubMed Central
CAS
Google Scholar
Burroughs AM, Aravind L. Identification of uncharacterized components of prokaryotic immune systems and their diverse eukaryotic reformulations. J Bacteriol. 2020;202(24):e00365-20.
Article
PubMed
PubMed Central
Google Scholar
Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct. 2012;7:18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Makarova KS, Wolf YI, Karamycheva S, Koonin EV. A unique gene module in Thermococcales Archaea centered on a hypervariable protein containing immunoglobulin domains. Front Microbiol. 2021;12:721392.
Article
PubMed
PubMed Central
Google Scholar
Makarova KS, Wolf YI, Koonin EV. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009;4:19.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roux S, Paul BG, Bagby SC, Nayfach S, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Gruninger RJ, Hallam SJ, et al. Ecology and molecular targets of hypermutation in the global microbiome. Nat Commun. 2021;12(1):3076.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yi X, Kazlauskas R, Travisano M. Evolutionary innovation using EDGE, a system for localized elevated mutagenesis. PLoS ONE. 2020;15(4):e0232330.
Article
CAS
PubMed
PubMed Central
Google Scholar
Medhekar B, Miller JF. Diversity-generating retroelements. Curr Opin Microbiol. 2007;10(4):388–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006;6:29.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lemmon AR, Moriarty EC. The importance of proper model assumption in bayesian phylogenetics. Syst Biol. 2004;53(2):265–77.
Article
PubMed
Google Scholar
Buckley TR. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst Biol. 2002;51(3):509–23.
Article
PubMed
Google Scholar
Buckley TR, Cunningham CW. The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Mol Biol Evol. 2002;19(4):394–405.
Article
CAS
PubMed
Google Scholar
Esterman ES, Wolf YI, Kogay R, Koonin EV, Zhaxybayeva O. Evolution of DNA packaging in gene transfer agents. Virus Evol. 2021;7(1):veab015.
Article
PubMed
PubMed Central
Google Scholar
Heinze S, Kornberger P, Gratz C, Schwarz WH, Zverlov VV, Liebl W. Transmating: conjugative transfer of a new broad host range expression vector to various Bacillus species using a single protocol. BMC Microbiol. 2018;18(1):56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Leigh JA, Albers SV, Atomi H, Allers T. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev. 2011;35(4):577–608.
Article
CAS
PubMed
Google Scholar
Staroscik AM, Hunnicutt DW, Archibald KE, Nelson DR. Development of methods for the genetic manipulation of Flavobacterium columnare. BMC Microbiol. 2008;8:115.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nakashima N, Tamura T. Isolation and characterization of a rolling-circle-type plasmid from Rhodococcus erythropolis and application of the plasmid to multiple-recombinant-protein expression. Appl Environ Microbiol. 2004;70(9):5557–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Markillie LM, Varnum SM, Hradecky P, Wong KK. Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants. J Bacteriol. 1999;181(2):666–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Makarova KS, Wolf YI, Koonin EV. Archaeal clusters of orthologous genes (arCOGs): an update and application for analysis of shared features between thermococcales, methanococcales, and methanobacteriales. Life (Basel). 2015;5(1):818–40.
CAS
Google Scholar
Sojo V, Dessimoz C, Pomiankowski A, Lane N. Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life. Mol Biol Evol. 2016;33(11):2874–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Puigbo P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol. 2014;12:66.
Article
PubMed
PubMed Central
Google Scholar
Favrot L, Blanchard JS, Vergnolle O. Bacterial GCN5-related N-acetyltransferases: from resistance to regulation. Biochemistry. 2016;55(7):989–1002.
Article
CAS
PubMed
Google Scholar
Struck AW, Thompson ML, Wong LS, Micklefield J. S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications. ChemBioChem. 2012;13(18):2642–55.
Article
CAS
PubMed
Google Scholar
Schubert HL, Blumenthal RM, Cheng X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci. 2003;28(6):329–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bichara M, Wagner J, Lambert IB. Mechanisms of tandem repeat instability in bacteria. Mutat Res. 2006;598(1–2):144–63.
Article
CAS
PubMed
Google Scholar
Meszaros B, Erdos G, Dosztanyi Z. IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 2018;46(W1):W329–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP. Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc Natl Acad Sci U S A. 2005;102(25):8933–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samson RY, Obita T, Freund SM, Williams RL, Bell SD. A role for the ESCRT system in cell division in archaea. Science. 2008;322(5908):1710–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang C, Phillips APR, Wipfler RL, Olsen GJ, Whitaker RJ. The essential genome of the crenarchaeal model Sulfolobus islandicus. Nat Commun. 2018;9(1):4908.
Article
PubMed
PubMed Central
CAS
Google Scholar
Samson RY, Obita T, Hodgson B, Shaw MK, Chong PL, Williams RL, Bell SD. Molecular and structural basis of ESCRT-III recruitment to membranes during archaeal cell division. Mol Cell. 2011;41(2):186–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol. 2012;4(12):1223–44.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev. 2019;43(1):19–52.
Article
CAS
PubMed
Google Scholar
Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, et al. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci. 2017;12:46.
Article
PubMed
PubMed Central
CAS
Google Scholar
Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, et al. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS ONE. 2007;2(9):e955.
Article
PubMed
PubMed Central
CAS
Google Scholar
Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2021;49(D1):D274–81.
Article
CAS
PubMed
Google Scholar
Udupa KS, O’Cain PA, Mattimore V, Battista JR. Novel ionizing radiation-sensitive mutants of Deinococcus radiodurans. J Bacteriol. 1994;176(24):7439–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dulermo R, Onodera T, Coste G, Passot F, Dutertre M, Porteron M, Confalonieri F, Sommer S, Pasternak C. Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library. PLoS ONE. 2015;10(4):e0124358.
Article
PubMed
PubMed Central
CAS
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5(3):e9490.
Article
PubMed
PubMed Central
CAS
Google Scholar
Steinegger M, Soding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35(11):1026–8.
Article
CAS
PubMed
Google Scholar
Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21(7):951–60.
Article
PubMed
Google Scholar
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427–32.
Article
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567–80.
Article
CAS
PubMed
Google Scholar
Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol. 1998;6:122–30.
CAS
PubMed
Google Scholar
Wootton JC, Federhen S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 1996;266:554–71.
Article
CAS
PubMed
Google Scholar
Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T. GLOOME: gain loss mapping engine. Bioinformatics. 2010;26(22):2914–5.
Article
CAS
PubMed
Google Scholar
Henikoff S, Henikoff JG. Performance evaluation of amino acid substitution matrices. Proteins. 1993;17(1):49–61.
Article
CAS
PubMed
Google Scholar
Parzen E. On estimation of a probability density function and mode. Ann Math Stat. 1962;33(3):1065–76.
Article
Google Scholar
Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, et al. Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Proc Natl Acad Sci U S A. 2019;116(34):16987–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Persi E, Wolf YI, Koonin EV. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins. Nat Commun. 2016;7:13570.
Article
CAS
PubMed
PubMed Central
Google Scholar
Persi E, Horn D. Systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution. PLoS Comput Biol. 2013;9(11):e1003346.
Article
PubMed
PubMed Central
CAS
Google Scholar
Felicori L, Jameson KH, Roblin P, Fogg MJ, Garcia-Garcia T, Ventroux M, Cherrier MV, Bazin A, Noirot P, Wilkinson AJ, et al. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners. Nucleic Acids Res. 2016;44(1):449–63.
Article
CAS
PubMed
Google Scholar
Simonetti A, Marzi S, Billas IM, Tsai A, Fabbretti A, Myasnikov AG, Roblin P, Vaiana AC, Hazemann I, Eiler D, et al. Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Proc Natl Acad Sci U S A. 2013;110(39):15656–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daniel J, Maamar H, Deb C, Sirakova TD, Kolattukudy PE. Mycobacterium tuberculosis uses host triacylglycerol to accumulate lipid droplets and acquires a dormancy-like phenotype in lipid-loaded macrophages. PLoS Pathog. 2011;7(6):e1002093.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, et al. The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics. 2010;11(2):167–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res. 2016;44(18):8525–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ran F, Gadura N, Michels CA. Hsp90 cochaperone Aha1 is a negative regulator of the Saccharomyces MAL activator and acts early in the chaperone activation pathway. J Biol Chem. 2010;285(18):13850–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Radauer C, Lackner P, Breiteneder H. The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. BMC Evol Biol. 2008;8:286.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hall CL, Lytle BL, Jensen D, Hoff JS, Peterson FC, Volkman BF, Kristich CJ. Structure and dimerization of IreB, a negative regulator of cephalosporin resistance in Enterococcus faecalis. J Mol Biol. 2017;429(15):2324–36.
Article
CAS
PubMed
PubMed Central
Google Scholar