A protocol for generating a high-quality genome-scale metabolic reconstruction

被引:1158
作者
Thiele, Ines [1 ]
Palsson, Bernhard O. [1 ]
机构
[1] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA
基金
美国国家卫生研究院;
关键词
IN-SILICO MODELS; ESCHERICHIA-COLI; NETWORK ANALYSIS; SUBCELLULAR-LOCALIZATION; INFORMATION-SYSTEM; DATABASE RESOURCES; HIGH-THROUGHPUT; NATIONAL-CENTER; ANNOTATION; BACTERIAL;
D O I
10.1038/nprot.2009.203
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.
引用
收藏
页码:93 / 121
页数:29
相关论文
共 102 条
[1]   Global organization of metabolic fluxes in the bacterium Escherichia coli [J].
Almaas, E ;
Kovács, B ;
Vicsek, T ;
Oltvai, ZN ;
Barabási, AL .
NATURE, 2004, 427 (6977) :839-843
[2]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[3]   The RAST server: Rapid annotations using subsystems technology [J].
Aziz, Ramy K. ;
Bartels, Daniela ;
Best, Aaron A. ;
DeJongh, Matthew ;
Disz, Terrence ;
Edwards, Robert A. ;
Formsma, Kevin ;
Gerdes, Svetlana ;
Glass, Elizabeth M. ;
Kubal, Michael ;
Meyer, Folker ;
Olsen, Gary J. ;
Olson, Robert ;
Osterman, Andrei L. ;
Overbeek, Ross A. ;
McNeil, Leslie K. ;
Paarmann, Daniel ;
Paczian, Tobias ;
Parrello, Bruce ;
Pusch, Gordon D. ;
Reich, Claudia ;
Stevens, Rick ;
Vassieva, Olga ;
Vonstein, Veronika ;
Wilke, Andreas ;
Zagnitko, Olga .
BMC GENOMICS, 2008, 9 (1)
[4]   The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states [J].
Barrett, CL ;
Herring, CD ;
Reed, JL ;
Palsson, BO .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (52) :19103-19108
[5]   BRENDA, AMENDA and FRENDA: the enzyme information system in 2007 [J].
Barthelmes, Jens ;
Ebeling, Christian ;
Chang, Antje ;
Schomburg, Ida ;
Schomburg, Dietmar .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D511-D514
[6]   Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox [J].
Becker, Scott A. ;
Feist, Adam M. ;
Mo, Monica L. ;
Hannum, Gregory ;
Palsson, Bernhard O. ;
Herrgard, Markus J. .
NATURE PROTOCOLS, 2007, 2 (03) :727-738
[7]   A SIMPLE AND RELIABLE METHOD FOR THE DETERMINATION OF CELLULAR RNA-CONTENT [J].
BENTHIN, S ;
NIELSEN, J ;
VILLADSEN, J .
BIOTECHNOLOGY TECHNIQUES, 1991, 5 (01) :39-42
[8]   A revised annotation and comparative analysis of Helicobacter pylori genomes [J].
Boneca, IG ;
de Reuse, H ;
Epinat, JC ;
Pupin, M ;
Labigne, A ;
Moszer, I .
NUCLEIC ACIDS RESEARCH, 2003, 31 (06) :1704-1714
[9]   Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism [J].
Borodina, I ;
Krabben, P ;
Nielsen, J .
GENOME RESEARCH, 2005, 15 (06) :820-829
[10]   The European Bioinformatics Institute's data resources: towards systems biology [J].
Brooksbank, C ;
Cameron, G ;
Thornton, J .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D46-D53