title: A predictive model for transcriptional control of physiology in a free living cell.
abstract: 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.
authors.affiliation: 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.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.forename: Marc T
authors.initials: MT
authors.lastname: Facciotti
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: Amy K
authors.initials: AK
authors.lastname: Schmid
authors.forename: Min
authors.initials: M
authors.lastname: Pan
authors.forename: Amardeep
authors.initials: A
authors.lastname: Kaur
authors.forename: Vesteinn
authors.initials: V
authors.lastname: Thorsson
authors.forename: Paul
authors.initials: P
authors.lastname: Shannon
authors.forename: Michael H
authors.initials: MH
authors.lastname: Johnson
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Bare
authors.forename: William
authors.initials: W
authors.lastname: Longabaugh
authors.forename: Madhavi
authors.initials: M
authors.lastname: Vuthoori
authors.forename: Kenia
authors.initials: K
authors.lastname: Whitehead
authors.forename: Aviv
authors.initials: A
authors.lastname: Madar
authors.forename: Lena
authors.initials: L
authors.lastname: Suzuki
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Mori
authors.forename: Dong-Eun
authors.initials: DE
authors.lastname: Chang
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Diruggiero
authors.forename: Carl H
authors.initials: CH
authors.lastname: Johnson
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: 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
chemical_list: D019843:Archaeal Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; D012965:Sodium Chloride