Rooting the Ribosomal Tree of Life

被引:47
作者
Fournier, Gregory P. [1 ]
Gogarten, J. Peter [1 ]
机构
[1] Univ Connecticut, Dept Mol & Cell Biol, Storrs, CT 06269 USA
基金
美国国家科学基金会;
关键词
tree of life; ribosome; genetic code; ancestral reconstruction; TRANSFER-RNA SYNTHETASE; MULTIPLE SEQUENCE ALIGNMENT; UNIVERSAL TREE; GENETIC-CODE; AMINO-ACIDS; PROKARYOTIC EVOLUTION; PHYLOGENETIC ANALYSIS; ESCHERICHIA-COLI; ORIGIN; EUKARYOTES;
D O I
10.1093/molbev/msq057
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The origin of the genetic code and the rooting of the tree of life (ToL) are two of the most challenging problems in the study of life's early evolution. Although both have been the focus of numerous investigations utilizing a variety of methods, until now, each problem has been addressed independently. Typically, attempts to root the ToL have relied on phylogenies of genes with ancient duplications, which are subject to artifacts of tree reconstruction and horizontal gene transfer, or specific physiological characters believed to be primitive, which are often based on subjective criteria. Here, we demonstrate a unique method for rooting based on the identification of amino acid usage biases comprising the residual signature of a more primitive genetic code. Using a phylogenetic tree of concatenated ribosomal proteins, our analysis of amino acid compositional bias detects a strong and unique signal associated with the early expansion of the genetic code, placing the root of the translation machinery along the bacterial branch.
引用
收藏
页码:1792 / 1801
页数:10
相关论文
共 65 条
  • [1] ESCHERICHIA-COLI SERYL-TRANSFER-RNA SYNTHETASE RECOGNIZES TRNA(SER) BY ITS CHARACTERISTIC TERTIARY STRUCTURE
    ASAHARA, H
    HIMENO, H
    TAMURA, K
    NAMEKI, N
    HASEGAWA, T
    SHIMIZU, M
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 236 (03) : 738 - 748
  • [2] The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny
    Baldauf, SL
    Palmer, JD
    Doolittle, WF
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (15) : 7749 - 7754
  • [3] Prokaryotic evolution and the tree of life are two different things
    Bapteste, Eric
    O'Malley, Maureen A.
    Beiko, Robert G.
    Ereshefsky, Marc
    Gogarten, J. Peter
    Franklin-Hall, Laura
    Lapointe, Francois-Joseph
    Dupre, John
    Dagan, Tal
    Boucher, Yan
    Martin, William
    [J]. BIOLOGY DIRECT, 2009, 4 : 34
  • [4] Benson DA, 2013, NUCLEIC ACIDS RES, V41, pD36, DOI [10.1093/nar/gkn723, 10.1093/nar/gkp1024, 10.1093/nar/gkw1070, 10.1093/nar/gkr1202, 10.1093/nar/gkx1094, 10.1093/nar/gkl986, 10.1093/nar/gkq1079, 10.1093/nar/gks1195, 10.1093/nar/gkg057]
  • [5] A site- and time-heterogeneous model of amino acid replacement
    Blanquart, Samuel
    Lartillot, Nicolas
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2008, 25 (05) : 842 - 858
  • [6] Parallel adaptations to high temperatures in the Archaean eon
    Boussau, Bastien
    Blanquart, Samuel
    Necsulea, Anamaria
    Lartillot, Nicolas
    Gouy, Manolo
    [J]. NATURE, 2008, 456 (7224) : 942 - U74
  • [7] A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
    Brooks, DJ
    Fresco, JR
    Singh, M
    [J]. BIOINFORMATICS, 2004, 20 (14) : 2251 - 2257
  • [8] Evolution of amino acid frequencies in proteins over deep time: Inferred order of introduction of amino acids into the genetic code
    Brooks, DJ
    Fresco, JR
    Lesk, AM
    Singh, M
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2002, 19 (10) : 1645 - 1655
  • [9] Increased frequency of cysteine, tyrosine, and phenylalanine residues since the last universal ancestor
    Brooks, DJ
    Fresco, JR
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (02) : 125 - 131
  • [10] ROOT OF THE UNIVERSAL TREE OF LIFE BASED ON ANCIENT AMINOACYL-TRANSFER-RNA SYNTHETASE GENE DUPLICATIONS
    BROWN, JR
    DOOLITTLE, WF
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (07) : 2441 - 2445