title: Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale.
abstract: Genes expressing circadian RNA rhythms are enriched for metabolic pathways, but the adaptive significance of cyclic gene expression remains unclear. We estimated the genome-wide synthetic and degradative cost of transcription and translation in three organisms and found that the cost of cycling genes is strikingly higher compared to non-cycling genes. Cycling genes are expressed at high levels and constitute the most costly proteins to synthesize in the genome. We demonstrate that metabolic cycling is accelerated in yeast grown under higher nutrient flux and the number of cycling genes increases ∼40%, which are achieved by increasing the amplitude and not the mean level of gene expression. These results suggest that rhythmic gene expression optimizes the metabolic cost of global gene expression and that highly expressed genes have been selected to be downregulated in a cyclic manner for energy conservation.
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Guang-Zhong
authors.initials: GZ
authors.lastname: Wang
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Hickey
authors.affiliation: Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Hung-Chung
authors.initials: HC
authors.lastname: Huang
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Prachi
authors.initials: P
authors.lastname: Nakashe
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Nobuya
authors.initials: N
authors.lastname: Koike
authors.affiliation: Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Tu
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: joseph.takahashi@utsouthwestern.edu.
authors.forename: Joseph S
authors.initials: JS
authors.lastname: Takahashi
authors.affiliation: Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: genevieve.konopka@utsouthwestern.edu.
authors.forename: Genevieve
authors.initials: G
authors.lastname: Konopka
mesh_terms: D000818:Animals; D002940:Circadian Rhythm / Q000502:physiology; D004330:Drosophila / Q000378:metabolism; D004734:Energy Metabolism / Q000235:genetics*; D053263:Gene Regulatory Networks; D016678:Genome; D005947:Glucose / Q000378:metabolism; D008099:Liver / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D051379:Mice; D020543:Proteome / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D020543:Proteome; D012333:RNA, Messenger; D005947:Glucose