Impact of genome reduction on bacterial metabolism and its regulation.
To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites, and 13C-glucose experiments provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global analysis of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability, and global gene expression responses are similar, however.
Yus
Eva
E
Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, Avenida Dr. Aiguader 88, 08003 Barcelona, Spain.
Maier
Tobias
T
Michalodimitrakis
Konstantinos
K
van Noort
Vera
V
Yamada
Takuji
T
Chen
Wei-Hua
WH
Wodke
Judith A H
JA
Güell
Marc
M
Martínez
Sira
S
Bourgeois
Ronan
R
Kühner
Sebastian
S
Raineri
Emanuele
E
Letunic
Ivica
I
Kalinina
Olga V
OV
Rode
Michaela
M
Herrmann
Richard
R
Gutiérrez-Gallego
Ricardo
R
Russell
Robert B
RB
Gavin
Anne-Claude
AC
Bork
Peer
P
Serrano
Luis
L
D000255:Adenosine Triphosphate / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D003470:Culture Media; D004734:Energy Metabolism; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006019:Glycolysis; D053858:Metabolic Networks and Pathways; D009177:Mycoplasma pneumoniae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology; D014158:Transcription, Genetic; D012407:rRNA Operon
D001426:Bacterial Proteins; D003470:Culture Media; D004798:Enzymes; D012329:RNA, Bacterial; D000255:Adenosine Triphosphate