One billion years of bZIP transcription factor evolution: Conservation and change in dimerization and DNA-binding site specificity

被引:135
作者
Amoutzias, G. D. [1 ]
Veron, A. S.
Weiner, J., III
Robinson-Rechavi, M.
Bornberg-Bauer, E.
Oliver, S. G.
Robertson, D. L.
机构
[1] Univ Manchester, Fac Life Sci, Manchester, Lancs, England
[2] Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland
[3] Swiss Inst Bioinformat, Lausanne, Switzerland
[4] Univ Munster, Bioinformat Div, Inst Evolut & Biodivers, Sch Biol Sci, D-4400 Munster, Germany
基金
英国生物技术与生命科学研究理事会;
关键词
bZIP; dimerization; transcription factor; molecular evolution; network; bilateria;
D O I
10.1093/molbev/msl211
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 genomic era has revealed that the large repertoire of observed animal phenotypes is dependent on changes in the expression patterns of a finite number of genes, which are mediated by a plethora of transcription factors (TFs) with distinct specificities. The dimerization of TFs can also increase the complexity of a genetic regulatory network manifold, by combining a small number of monomers into dimers with distinct functions. Therefore, studying the evolution of these dimerizing TFs is vital for understanding how complexity increased during animal evolution. We focus on the second largest family of dimerizing TFs, the basic-region leucine zipper (bZIP), and infer when it expanded and how bZIP DNA-binding and dimerization functions evolved during the major phases of animal evolution. Specifically, we classify the metazoan bZIPs into 19 families and confirm the ancient nature of at least 13 of these families, predating the split of the cnidaria. We observe fixation of a core dimerization network in the last common ancestor of protostomes-deuterostomes. This was followed by an expansion of the number of proteins in the network, but no major dimerization changes in interaction partners, during the emergence of vertebrates. In conclusion, the bZIPs are an excellent model with which to understand how DNA binding and protein interactions of TFs evolved during animal evolution.
引用
收藏
页码:827 / 835
页数:9
相关论文
共 47 条
  • [1] Convergent evolution of gene networks by single-gene duplications in higher eukaryotes
    Amoutzias, GD
    Robertson, DL
    Oliver, SG
    Bornberg-Bauer, E
    [J]. EMBO REPORTS, 2004, 5 (03) : 274 - 279
  • [2] Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network
    Amoutzias, Gregory D.
    Bornberg-Bauer, Erich
    Oliver, Stephen G.
    Robertson, David L.
    [J]. BMC GENOMICS, 2006, 7 (1)
  • [3] Evolutionary genomics of nuclear receptors: From twenty-five ancestral genes to derived endocrine systems
    Bertrand, W
    Brunet, FG
    Escriva, H
    Parmentier, G
    Laudet, V
    Robinson-Rechavi, M
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2004, 21 (10) : 1923 - 1937
  • [4] The gain and loss of genes during 600 million years of vertebrate evolution
    Blomme, Tine
    Vandepoele, Klaas
    De Bodt, Stefanie
    Simillion, Cedric
    Maere, Steven
    Van de Peer, Yves
    [J]. GENOME BIOLOGY, 2006, 7 (05)
  • [5] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Boeckmann, B
    Bairoch, A
    Apweiler, R
    Blatter, MC
    Estreicher, A
    Gasteiger, E
    Martin, MJ
    Michoud, K
    O'Donovan, C
    Phan, I
    Pilbout, S
    Schneider, M
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 365 - 370
  • [6] Computational approaches to identify leucine zippers
    Bornberg-Bauer, E
    Rivals, E
    Vingron, M
    [J]. NUCLEIC ACIDS RESEARCH, 1998, 26 (11) : 2740 - 2746
  • [7] TOO MANY LEUCINE ZIPPERS
    BRENDEL, V
    KARLIN, S
    [J]. NATURE, 1989, 341 (6243) : 574 - 575
  • [8] Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    Brenner, SE
    Chothia, C
    Hubbard, TJP
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (11) : 6073 - 6078
  • [9] The ProDom database of protein domain families: more emphasis on 3D
    Bru, C
    Courcelle, E
    Carrre, S
    Beausse, Y
    Dalmar, S
    Kahn, D
    [J]. NUCLEIC ACIDS RESEARCH, 2005, 33 : D212 - D215
  • [10] Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
    Danchin, EGJ
    Gouret, P
    Pontarotti, P
    [J]. BMC EVOLUTIONARY BIOLOGY, 2006, 6 (1)