Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
Tóm tắt
Từ khóa
Tài liệu tham khảo
AM Feist, 2009, Reconstruction of biochemical networks in microorganisms., Nat Rev Microbiol, 7, 129, 10.1038/nrmicro1949
NC Duarte, 2007, Global reconstruction of the human metabolic network based on genomic and bibliomic data., Proc Natl Acad Sci U S A, 104, 1777, 10.1073/pnas.0610772104
NC Duarte, 2004, Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model., Genome Res, 14, 1298, 10.1101/gr.2250904
L Kuepfer, 2005, Metabolic functions of duplicate genes in Saccharomyces cerevisiae., Genome Res, 15, 1421, 10.1101/gr.3992505
AK Chavali, 2008, Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major., Mol Syst Biol, 4, 177, 10.1038/msb.2008.15
AM Feist, 2007, A genome-scale metabolic reconstruction for <italic>Escherichia coli</italic> K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information., Mol Syst Biol, 3, 121, 10.1038/msb4100155
I Thiele, 2005, An expanded metabolic reconstruction of Helicobacter pylori (<italic>i</italic>IT341 GSM/GPR): an <italic>in silico</italic> genome-scale characterization of single and double deletion mutants., J Bacteriol, 187, 5818, 10.1128/JB.187.16.5818-5830.2005
MA Oberhardt, 2008, Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1., J Bacteriol, 190, 2790, 10.1128/JB.01583-07
J Nogales, 2008, A genome-scale metabolic reconstruction of <italic>Pseudomonas putida</italic> KT2440: <italic>i</italic>JN746 as a cell factory., BMC Syst Biol, 2, 79, 10.1186/1752-0509-2-79
J Puchalka, 2008, Genome-scale reconstruction and analysis of the <italic>Pseudomonas putida</italic> KT2440 metabolic network facilitates applications in biotechnology., PLoS Comput Biol, 4, e1000210, 10.1371/journal.pcbi.1000210
I Thiele, 2007, Bringing genomes to life: the use of genome-scale <italic>in silico</italic> models., 14
JL Reed, 2006, Systems approach to refining genome annotation., Proc Natl Acad Sci U S A, 103, 17480, 10.1073/pnas.0603364103
I Thiele, 2005, Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet., J Biol Chem, 280, 11683, 10.1074/jbc.M409072200
SS Fong, 2004, Metabolic gene-deletion strains of <italic>Escherichia coli</italic> evolve to computationally predicted growth phenotypes., Nat Genet, 36, 1056, 10.1038/ng1432
E Almaas, 2004, Global organization of metabolic fluxes in the bacterium <italic>Escherichia coli</italic>., Nature, 427, 839, 10.1038/nature02289
JH Park, 2007, Metabolic engineering of <italic>Escherichia coli</italic> for the production of <sc>l</sc>-valine based on transcriptome analysis and in silico gene knockout simulation., Proc Natl Acad Sci U S A, 104, 7797, 10.1073/pnas.0702609104
ND Price, 2003, Genome-scale microbial in silico models: the constraints-based approach., Trends Biotechnol, 21, 162, 10.1016/S0167-7799(03)00030-1
JA Papin, 2005, Reconstruction of cellular signalling networks and analysis of their properties., Nat Rev Mol Cell Biol, 6, 99, 10.1038/nrm1570
F Li, Functional assessment of the TLR receptor network., PLoS Comput Biol
MS Dasika, 2006, A computational framework for the topological analysis and targeted disruption of signal transduction networks., Biophys J, 91, 382, 10.1529/biophysj.105.069724
EP Gianchandani, 2006, Matrix formalism to describe functional states of transcriptional regulatory systems., PLoS Comput Biol, 2, e101, 10.1371/journal.pcbi.0020101
TE Allen, 2003, Sequenced-based analysis of metabolic demands for protein synthesis in prokaryotes., J Theor Biol, 220, 1, 10.1006/jtbi.2003.3087
AD Tadmor, 2008, A coarse-grained biophysical model of <italic>E. coli</italic> and its application to perturbation of the rRNA operon copy number., PLoS Comput Biol, 4, e1000038, 10.1371/journal.pcbi.1000038
PF Suthers, 2007, Rapid responses of ribosomal RNA synthesis to nutrient shifts., Biotechnol Bioeng, 97, 1230, 10.1002/bit.21318
A Mehra, 2003, Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations., Biotechnol Bioeng, 84, 822, 10.1002/bit.10860
A Mehra, 2006, An algorithmic framework for genome-wide modeling and analysis of translation networks., Biophys J, 90, 1136, 10.1529/biophysj.105.062521
H Zouridis, 2007, A model for protein translation: polysome self-organization leads to maximum protein synthesis rates., Biophys J, 92, 717, 10.1529/biophysj.106.087825
N Jamshidi, 2008, Formulating genome-scale kinetic models in the post-genome era., Mol Syst Biol, 4, 171, 10.1038/msb.2008.8
FH Crick, 1958, On protein synthesis., Symp Soc Exp Biol, 12, 138
M Riley, 2006, <italic>Escherichia coli</italic> K-12: a cooperatively developed annotation snapshot—2005., Nucleic Acids Res, 34, 1, 10.1093/nar/gkj405
E Deuerling, 2003, Trigger factor and DnaK possess overlapping substrate pools and binding specificities., Mol Microbiol, 47, 1317, 10.1046/j.1365-2958.2003.03370.x
MJ Kerner, 2005, Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli., Cell, 122, 209, 10.1016/j.cell.2005.05.028
M Kanehisa, 2004, The KEGG resource for deciphering the genome., Nucleic Acids Res, 32, D277, 10.1093/nar/gkh063
PD Karp, 2004, The <italic>E. coli</italic> EcoCyc Database: no longer just a metabolic pathway database., ASM News, 70, 25
ME Smulson, 1967, The biosynthesis of the 7-deazaadenine ribonucleoside, tubercidin, by Streptomyces tubercidicus., J Biol Chem, 242, 2872, 10.1016/S0021-9258(18)99586-4
RJ Suhadolnik, 1970, Biosynthesis of the pyrrolopyrimidine nucleoside antibiotic, toyocamycin. VII. Origin of the pyrrole carbons and the cyano carbon., J Biol Chem, 245, 4365, 10.1016/S0021-9258(19)63804-4
SA Becker, 2006, Metabolite coupling in genome-scale metabolic networks., BMC Bioinformatics, 7, 111, 10.1186/1471-2105-7-111
ND Price, 2004, Genome-scale models of microbial cells: evaluating the consequences of constraints., Nat Rev Microbiol, 2, 886, 10.1038/nrmicro1023
M Nomura, 1999, Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles., J Bacteriol, 181, 6857, 10.1128/JB.181.22.6857-6864.1999
1996, <italic>Escherichia coli</italic> and <italic>Salmonella</italic>: cellular and molecular biology. 2nd edition
M Nomura, 1984, Regulation of the synthesis of ribosomes and ribosomal components., Annu Rev Biochem, 53, 75, 10.1146/annurev.bi.53.070184.000451
JS Edwards, 1997, Significant redundancy and robustness exist in the central metabolic pathways; 12–15 October 1997
M Nomura, 1977, Genetics of bacterial ribosomes., Annu Rev Genet, 11, 297, 10.1146/annurev.ge.11.120177.001501
C Condon, 1993, Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies., EMBO J, 12, 4305, 10.1002/j.1460-2075.1993.tb06115.x
BS Stevenson, 2004, Life history implications of rRNA gene copy number in Escherichia coli., Appl Environ Microbiol, 70, 6670, 10.1128/AEM.70.11.6670-6677.2004
T Asai, 1999, Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons., J Bacteriol, 181, 3803, 10.1128/JB.181.12.3803-3809.1999
C Condon, 1995, rRNA operon multiplicity in <italic>Escherichia coli</italic> and the physiological implications of rrn inactivation., J Bacteriol, 177, 4152, 10.1128/jb.177.14.4152-4156.1995
JS Edwards, 2000, The <italic>Escherichia coli</italic> MG1655 <italic>in silico</italic> metabolic genotype: its definition, characteristics, and capabilities., Proc Natl Acad Sci U S A, 97, 5528, 10.1073/pnas.97.10.5528
J Forster, 2003, Large-scale evaluation of <italic>in silico</italic> gene knockouts in <italic>Saccharomyces cerevisiae</italic>., Omics, 7, 193, 10.1089/153623103322246584
MW Covert, 2004, Integrating high-throughput and computational data elucidates bacterial networks., Nature, 429, 92, 10.1038/nature02456
FC Neidhardt, 1990, Physiology of the Bacterial Cell: A Molecular Approach
T Gaal, 1997, Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria., Science, 278, 2092, 10.1126/science.278.5346.2092
J Voulgaris, 1999, Increased rrn gene dosage causes intermittent transcription of rRNA in <italic>Escherichia coli</italic>., J Bacteriol, 181, 4170, 10.1128/JB.181.14.4170-4175.1999
JA Bernstein, 2002, Global analysis of mRNA decay and abundance in <italic>Escherichia coli</italic> at single-gene resolution using two-color fluorescent DNA microarrays., Proc Natl Acad Sci U S A, 99, 9697, 10.1073/pnas.112318199
AP Burgard, 2004, Flux coupling analysis of genome-scale metabolic network reconstructions., Genome Res, 14, 301, 10.1101/gr.1926504
G Butland, 2005, Interaction network containing conserved and essential protein complexes in <italic>Escherichia coli</italic>., Nature, 433, 531, 10.1038/nature03239
M Arifuzzaman, 2006, Large-scale identification of protein-protein interaction of <italic>Escherichia coli</italic> K-12., Genome Res, 16, 686, 10.1101/gr.4527806
HS Cummings, 1994, Translation initiation factor IF1 is essential for cell viability in <italic>Escherichia coli</italic>., J Bacteriol, 176, 198, 10.1128/jb.176.1.198-205.1994
MW Covert, 2008, Integrating metabolic, transcriptional regulatory and signal transduction models in <italic>Escherichia coli</italic>., Bioinformatics, 24, 2044, 10.1093/bioinformatics/btn352
J Min Lee, 2008, Dynamic analysis of integrated signaling, metabolic, and regulatory networks., PLoS Comput Biol, 4, e1000086, 10.1371/journal.pcbi.1000086
AM Feist, 2008, The growing scope of applications of genome-scale metabolic reconstructions using <italic>Escherichia coli</italic>., Nat Biotechnol, 26, 659, 10.1038/nbt1401
C Holden, 2002, Alliance launched to model <italic>E. coli</italic>., Science, 297, 1459, 10.1126/science.297.5586.1459a
FR Blattner, 1997, The complete genome sequence of <italic>Escherichia coli</italic> K-12., Science, 277, 1453, 10.1126/science.277.5331.1453
JS Edwards, 2002, Metabolic modeling of microbes: the flux-balance approach., Environ Microbiol, 4, 133, 10.1046/j.1462-2920.2002.00282.x
A Varma, 1994, Metabolic flux balancing: basic concepts, scientific and practical use., Nat Biotechnol, 12, 994, 10.1038/nbt1094-994
R Mahadevan, 2003, The effects of alternate optimal solutions in constraint-based genome-scale metabolic models., Metab Eng, 5, 264, 10.1016/j.ymben.2003.09.002
CB Barber, 1996, The Quickhull Algorithm for Convex Hulls., ACM Trans Math Softw, 22, 469, 10.1145/235815.235821
S Sundararaj, 2004, The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli., Nucleic Acids Res, 32, D293, 10.1093/nar/gkh108