Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

被引:350
作者
Pál, C
Papp, B
Lercher, MJ
机构
[1] European Mol Biol Lab, D-69012 Heidelberg, Germany
[2] Eotvos Lorand Univ, MTA, Theoret Biol & Ecol Res Grp, H-1117 Budapest, Hungary
[3] Univ Manchester, Fac Life Sci, Manchester M13 9PT, Lancs, England
[4] Univ Bath, Dept Biol & Biochem, Bath BA2 7AY, Avon, England
基金
匈牙利科学研究基金会;
关键词
D O I
10.1038/ng1686
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Numerous studies have considered the emergence of metabolic pathways(1), but the modes of recent evolution of metabolic networks are poorly understood. Here, we integrate comparative genomics with flux balance analysis to examine (i) the contribution of different genetic mechanisms to network growth in bacteria, (ii) the selective forces driving network evolution and (iii) the integration of new nodes into the network. Most changes to the metabolic network of Escherichia coli in the past 100 million years are due to horizontal gene transfer, with little contribution from gene duplicates. Networks grow by acquiring genes involved in the transport and catalysis of external nutrients, driven by adaptations to changing environments. Accordingly, horizontally transferred genes are integrated at the periphery of the network, whereas central parts remain evolutionarily stable. Genes encoding physiologically coupled reactions are often transferred together, frequently in operons. Thus, bacterial metabolic networks evolve by direct uptake of peripheral reactions in response to changed environments.
引用
收藏
页码:1372 / 1375
页数:4
相关论文
共 30 条
[21]   Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli [J].
Rison, SCG ;
Teichmann, SA ;
Thornton, JM .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 318 (03) :911-932
[22]   RegulonDB (version 4.0):: transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 [J].
Salgado, H ;
Gama-Castro, S ;
Martínez-Antonio, A ;
Díaz-Peredo, E ;
Sánchez-Solano, F ;
Peralta-Gil, M ;
Garcia-Alonso, D ;
Jiménez-Jacinto, V ;
Santos-Zavaleta, A ;
Bonavides-Martínez, C ;
Collado-Vides, J .
NUCLEIC ACIDS RESEARCH, 2004, 32 :D303-D306
[23]   Metabolites: a helping hand for pathway evolution? [J].
Schmidt, S ;
Sunyaev, S ;
Bork, P ;
Dandekar, T .
TRENDS IN BIOCHEMICAL SCIENCES, 2003, 28 (06) :336-341
[24]   Analysis of optimality in natural and perturbed metabolic networks [J].
Segrè, D ;
Vitkup, D ;
Church, GM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (23) :15112-15117
[25]   Quantifying modularity in the evolution of biomolecular systems [J].
Snel, B ;
Huynen, MA .
GENOME RESEARCH, 2004, 14 (03) :391-397
[26]   Genomes in flux: The evolution of archaeal and proteobacterial gene content [J].
Snel, B ;
Bork, P ;
Huynen, MA .
GENOME RESEARCH, 2002, 12 (01) :17-25
[27]   Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins [J].
Taoka, M ;
Yamauchi, Y ;
Shinkawa, T ;
Kaji, H ;
Motohashi, W ;
Nakayama, H ;
Takahashi, N ;
Isobe, T .
MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (08) :780-787
[28]   The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli [J].
Teichmann, SA ;
Rison, SCG ;
Thornton, JM ;
Riley, M ;
Gough, J ;
Chothia, C .
JOURNAL OF MOLECULAR BIOLOGY, 2001, 311 (04) :693-708
[29]   Marginal fitness contributions of nonessential genes in yeast [J].
Thatcher, JW ;
Shaw, JM ;
Dickinson, WJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (01) :253-257
[30]   STRING: known and predicted protein-protein associations, integrated and transferred across organisms [J].
von Mering, C ;
Jensen, LJ ;
Snel, B ;
Hooper, SD ;
Krupp, M ;
Foglierini, M ;
Jouffre, N ;
Huynen, MA ;
Bork, P .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D433-D437