RETRACTED: Reactome array: forging a link between metabolome and genome.
We describe a sensitive metabolite array for genome sequence-independent functional analysis of metabolic phenotypes and networks, the reactomes, of cell populations and communities. The array includes 1676 dye-linked substrate compounds collectively representing central metabolic pathways of all forms of life. Application of cell extracts to the array leads to specific binding of enzymes to cognate substrates, transformation to products, and concomitant activation of the dye signals. Proof of principle was shown by reconstruction of the metabolic maps of model bacteria. Utility of the array for unsequenced organisms was demonstrated by reconstruction of the global metabolisms of three microbial communities derived from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater. Enzymes of interest are captured on nanoparticles coated with cognate metabolites, sequenced, and their functions unequivocally established.
Beloqui
Ana
A
CSIC, Institute of Catalysis, 28049 Madrid, Spain.
Guazzaroni
María-Eugenia
ME
Pazos
Florencio
F
Vieites
José M
JM
Godoy
Marta
M
Golyshina
Olga V
OV
Chernikova
Tatyana N
TN
Waliczek
Agnes
A
Silva-Rocha
Rafael
R
Al-Ramahi
Yamal
Y
La Cono
Violetta
V
Mendez
Carmen
C
Salas
José A
JA
Solano
Roberto
R
Yakimov
Michail M
MM
Timmis
Kenneth N
KN
Golyshin
Peter N
PN
Ferrer
Manuel
M
D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism; D019295:Computational Biology; D017753:Ecosystem; D004798:Enzymes / Q000378:metabolism*; D004800:Enzymes, Immobilized; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D045482:Hot Springs / Q000382:microbiology; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D046228:Microarray Analysis / Q000379:methods*; D053758:Nanoparticles; D016958:Pseudomonas putida / Q000235:genetics / Q000378:metabolism; D012623:Seawater / Q000382:microbiology; D048372:Streptomyces coelicolor / Q000235:genetics / Q000378:metabolism; D014871:Water Microbiology
D001426:Bacterial Proteins; D004798:Enzymes; D004800:Enzymes, Immobilized