A predictive model for transcriptional control of physiology in a free living cell.
The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among approximately 80% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments-suggesting a remarkable degree of network completeness. Using this model we have constructed and tested hypotheses critical to this organism's interaction with its changing hypersaline environment. This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments.
Bonneau
Richard
R
Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, NY 10003, USA.
Facciotti
Marc T
MT
Reiss
David J
DJ
Schmid
Amy K
AK
Pan
Min
M
Kaur
Amardeep
A
Thorsson
Vesteinn
V
Shannon
Paul
P
Johnson
Michael H
MH
Bare
J Christopher
JC
Longabaugh
William
W
Vuthoori
Madhavi
M
Whitehead
Kenia
K
Madar
Aviv
A
Suzuki
Lena
L
Mori
Tetsuya
T
Chang
Dong-Eun
DE
Diruggiero
Jocelyne
J
Johnson
Carl H
CH
Hood
Leroy
L
Baliga
Nitin S
NS
D000222:Adaptation, Physiological / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D004777:Environment; D019848:Gene Expression Regulation, Archaeal; D053263:Gene Regulatory Networks; D019617:Halobacterium salinarum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D008957:Models, Genetic; D012333:RNA, Messenger / Q000378:metabolism; D015203:Reproducibility of Results; D012965:Sodium Chloride / Q000378:metabolism*; D049490:Systems Biology; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
D019843:Archaeal Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; D012965:Sodium Chloride