Reconstruction of biochemical networks in microorganisms

被引：621

作者：

Feist, Adam M. ^{[1
]}

Herrgard, Markus J. ^{[1
,2
]}

Thiele, Ines ^{[1
]}

Reed, Jennie L. ^{[3
]}

Palsson, Bernhard O. ^{[1
,4
]}

机构：

[1] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[2] Synthet Genom, La Jolla, CA 92037 USA

[3] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA

[4] Univ Iceland, Ctr Syst Biol, IS-101 Reykjavik, Iceland

来源：

NATURE REVIEWS MICROBIOLOGY | 2009年 / 7卷 / 02期

基金：

美国国家卫生研究院;

关键词：

SMALL NONCODING RNAS; ESCHERICHIA-COLI METABOLISM; TRANSCRIPTION FACTOR; SYSTEMS-APPROACH; GENE-EXPRESSION; IN-VITRO; SACCHAROMYCES-CEREVISIAE; PLASMODIUM-FALCIPARUM; BIOMASS COMPOSITION; HIGH-THROUGHPUT;

D O I：

10.1038/nrmicro1949

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Systems analysis of metabolic and growth functions in microbial organisms is rapidly developing and maturing. Such studies are enabled by reconstruction, at the genomic scale, of the biochemical reaction networks that underlie cellular processes. The network reconstruction process is organism specific and is based on an annotated genome sequence, high-throughput network-wide data sets and bibliomic data on the detailed properties of individual network components. Here we describe the process that is currently used to achieve comprehensive network reconstructions and discuss how these reconstructions are curated and validated. This Review should aid the growing number of researchers who are carrying out reconstructions for particular target organisms.

引用

页码：129 / 143

页数：15

共 133 条

[21] Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts [J].

Cho, Byung-Kwan ;

Knight, Eric M. ;

Barrett, Christian L. ;

Palsson, Bernhard O. .

GENOME RESEARCH, 2008, 18 (06) :900-910

[22] Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms [J].

Christie, KR ;

Weng, S ;

Balakrishnan, R ;

Costanzo, MC ;

Dolinski, K ;

Dwight, SS ;

Engel, SR ;

Feierbach, B ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Issel-Tarver, L ;

Nash, R ;

Sethuraman, A ;

Starr, B ;

Theesfeld, CL ;

Andrada, R ;

Binkley, G ;

Dong, Q ;

Lane, C ;

Schroeder, M ;

Botstein, D ;

Cherry, JM .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D311-D314

[23] Identifying transcription factor functions and targets by phenotypic activation [J].

Chua, Gordon ;

Morris, Quaid D. ;

Sopko, Richelle ;

Robinson, Mark D. ;

Ryan, Owen ;

Chan, Esther T. ;

Frey, Brendan J. ;

Andrews, Brenda J. ;

Boone, Charles ;

Hughes, Timothy R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (32) :12045-12050

[24] Integrating high-throughput and computational data elucidates bacterial networks [J].

Covert, MW ;

Knight, EM ;

Reed, JL ;

Herrgard, MJ ;

Palsson, BO .

NATURE, 2004, 429 (6987) :92-96

[25] Distinct physiological states of Plasmodium falciparum in malaria-infected patients [J].

Daily, J. P. ;

Scanfeld, D. ;

Pochet, N. ;

Le Roch, K. ;

Plouffe, D. ;

Kamal, M. ;

Sarr, O. ;

Mboup, S. ;

Ndir, O. ;

Wypij, D. ;

Levasseur, K. ;

Thomas, E. ;

Tamayo, P. ;

Dong, C. ;

Zhou, Y. ;

Lander, E. S. ;

Ndiaye, D. ;

Wirth, D. ;

Winzeler, E. A. ;

Mesirov, J. P. ;

Regev, A. .

NATURE, 2007, 450 (7172) :1091-U15

[26]

Deitsch K, 2007, AM J TROP MED HYG, V77, P201

[27] Toward the automated generation of genome-scale metabolic networks in the SEED [J].

DeJongh, Matthew ;

Formsma, Kevin ;

Boillot, Paul ;

Gould, John ;

Rycenga, Matthew ;

Best, Aaron .

BMC BIOINFORMATICS, 2007, 8 (1)

[28]

Dickinson J., 2004, METABOLISM MOL PHYSL

[29] Dynamics of replication-independent histone turnover in budding yeast [J].

Dion, Michael F. ;

Kaplan, Tommy ;

Kim, Minkyu ;

Buratowski, Stephen ;

Friedman, Nir ;

Rando, Oliver J. .

SCIENCE, 2007, 315 (5817) :1405-1408

[30] A mathematical model for prokaryotic protein synthesis [J].

Drew, DA .

BULLETIN OF MATHEMATICAL BIOLOGY, 2001, 63 (02) :329-351

← 1 2 3 4 5 6 7 8 9 10 →