دورية أكاديمية
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mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.

التفاصيل البيبلوغرافية
العنوان: mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.
المؤلفون: Kuzminkova AA; Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia., Sokol AD; Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia., Ushakova KE; Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia., Popadin KY; Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland., Gunbin KV; Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia. genkvg@gmail.com.; Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia. genkvg@gmail.com.; Novosibirsk State University, Novosibirsk, Russia. genkvg@gmail.com.
المصدر: BMC evolutionary biology [BMC Evol Biol] 2019 Feb 26; Vol. 19 (Suppl 1), pp. 47. Date of Electronic Publication: 2019 Feb 26.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100966975 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2148 (Electronic) Linking ISSN: 14712148 NLM ISO Abbreviation: BMC Evol Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2001-
مواضيع طبية MeSH: Computational Biology* , Evolution, Molecular*, Mitochondrial Proteins/*genetics , Vertebrates/*genetics, Animals ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/metabolism ; Phylogeny ; Software ; Solvents/chemistry
مستخلص: Background: Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions. This provides a computationally fast alternative, based on comparison of evolutionary rates of amino acid replacements with the rates of RSA evolutionary changes in order to recognize any shifts in epistatic interaction.
Results: Based on RSA information, data randomization and phylogenetic approaches, we constructed a software pipeline, which can be used to analyze the evolutionary consequences of intra-protein epistatic interactions with relatively low computational time. We analyzed the evolution of 512 protein families tightly linked to mitochondrial function in Vertebrates and created "mtProtEvol", the web resource with data on protein evolution. In strict agreement with lifespan and metabolic rate data, we demonstrated that different functional categories of mitochondria-related proteins subjected to selection on accelerated and decelerated RSA rates in rodents and primates. For example, accelerated RSA evolution in rodents has been shown for Krebs cycle enzymes, respiratory chain and reactive oxygen species metabolism, while in primates these functions are stress-response, translation and mtDNA integrity. Decelerated RSA evolution in rodents has been demonstrated for translational machinery and oxidative stress response components.
Conclusions: mtProtEvol is an interactive resource focused on evolutionary analysis of epistatic interactions in protein families involved in Vertebrata mitochondria function and available at http://bioinfodbs.kantiana.ru/mtProtEvol /. This resource and the devised software pipeline may be useful tool for researchers in area of protein evolution.
References: Mol Biol Evol. 2009 Dec;26(12):2689-97. (PMID: 19687305)
Mol Biol Evol. 2008 Jul;25(7):1307-20. (PMID: 18367465)
Biol Lett. 2015 Oct;11(10):. (PMID: 26445980)
Genome Res. 2003 Nov;13(11):2498-504. (PMID: 14597658)
J Mol Biol. 1999 Mar 19;287(1):187-98. (PMID: 10074416)
BMC Bioinformatics. 2009 Oct 27;10:356. (PMID: 19860910)
Genome Biol. 2016 May 06;17(1):91. (PMID: 27154141)
Syst Biol. 2010 May;59(3):307-21. (PMID: 20525638)
BMC Evol Biol. 2009 Sep 08;9:225. (PMID: 19737395)
Syst Biol. 2020 Mar 1;69(2):249-264. (PMID: 31364711)
Syst Biol. 2017 Mar 01;66(2):232-255. (PMID: 27633354)
Nat Ecol Evol. 2017 Dec;1(12):1923-1930. (PMID: 29062121)
PeerJ. 2017 May 30;5:e3391. (PMID: 28584717)
Protein Sci. 2016 Jul;25(7):1204-18. (PMID: 26833806)
Proteins. 2018 Feb;86(2):218-228. (PMID: 29178386)
Curr Protoc Bioinformatics. 2016 Jun 20;54:1.30.1-1.30.33. (PMID: 27322403)
BMC Bioinformatics. 2014 Oct 24;15:341. (PMID: 25344302)
Mol Biol Evol. 2011 May;28(5):1661-73. (PMID: 21186190)
Evolution. 1984 Sep;38(5):1116-1129. (PMID: 28555784)
PLoS Comput Biol. 2016 Jul 12;12(7):e1004763. (PMID: 27404731)
Nucleic Acids Res. 2016 Jul 8;44(W1):W430-5. (PMID: 27112573)
Bioinformatics. 2015 Jan 1;31(1):143-5. (PMID: 25236461)
Math Biosci. 1998 Jan 1;147(1):63-91. (PMID: 9401352)
Nature. 2004 Jun 3;429(6991):558-62. (PMID: 15175752)
Mol Biol Evol. 2015 Feb;32(2):542-54. (PMID: 25415964)
Mol Biol Evol. 2013 Jan;30(1):36-44. (PMID: 22977116)
Nucleic Acids Res. 2016 Jan 4;44(D1):D1258-61. (PMID: 26432830)
PeerJ. 2018 Oct 5;6:e5549. (PMID: 30310736)
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20. (PMID: 20576703)
Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. (PMID: 18940867)
Mol Biol Evol. 2001 May;18(5):691-9. (PMID: 11319253)
Nature. 2012 Oct 25;490(7421):535-8. (PMID: 23064225)
Annu Rev Biophys. 2017 May 22;46:85-103. (PMID: 28301766)
Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3955-64. (PMID: 18852097)
Mol Biol Evol. 2010 Feb;27(2):371-84. (PMID: 19822637)
Bioinformatics. 2016 Nov 15;32(22):3501-3503. (PMID: 27412096)
Syst Biol. 2017 Nov 01;66(6):1054-1064. (PMID: 28057858)
Bioinformatics. 2010 Jul 1;26(13):1669-70. (PMID: 20472542)
Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761. (PMID: 29155950)
Syst Biol. 2016 Nov;65(6):997-1008. (PMID: 27121966)
Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430)
Bioinformatics. 2014 Sep 15;30(18):2592-7. (PMID: 24860169)
Bioinformatics. 2004 Dec 12;20(18):3481-9. (PMID: 15284106)
Proc Biol Sci. 2012 Aug 7;279(1740):3075-82. (PMID: 22456880)
Mol Biol Evol. 2008 Jun;25(6):1054-66. (PMID: 18319244)
Biol Chem. 2016 Jan;397(1):1-21. (PMID: 26351909)
BMC Evol Biol. 2018 Apr 4;18(1):46. (PMID: 29618314)
Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. (PMID: 27924014)
Nat Rev Genet. 2016 Feb;17(2):109-21. (PMID: 26781812)
Protein Sci. 2016 Jul;25(7):1168-78. (PMID: 26808055)
Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1352-9. (PMID: 22547823)
Nature. 2016 May 11;533(7603):397-401. (PMID: 27193686)
Comput Appl Biosci. 1992 Jun;8(3):275-82. (PMID: 1633570)
Mol Biol Evol. 2018 Mar 1;35(3):743-755. (PMID: 29294047)
فهرسة مساهمة: Keywords: Database; Epistatic interactions; Positive selection; Proteins; Residue solvent accessibilities
المشرفين على المادة: 0 (Mitochondrial Proteins)
0 (Solvents)
تواريخ الأحداث: Date Created: 20190301 Date Completed: 20190523 Latest Revision: 20231006
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6391778
DOI: 10.1186/s12862-019-1371-x
PMID: 30813887
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2148
DOI:10.1186/s12862-019-1371-x