title: A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli.
abstract: Living cells reorganize their gene expression through regulatory machineries in response to external perturbations. The contribution of the regulation to the noise in gene expression is of great interest. In this study, we evaluate the contribution of both native and foreign regulations to the extrinsic noise in gene expression. We analyzed the gene expression data of a mini-library containing 70 genetic constructs of 136 clones into which the gfp gene had been chromosomally incorporated under the control of either native or foreign regulation. We found that the substitution of native by foreign regulation, i.e., the insertion of the Ptetpromoter, triggered a decrease in the extrinsic noise, which was independent of the protein abundance. The reanalyses of varied genomic data sets verified that the noisy gene expression mediated by native regulations is a common feature, regardless of the diversity in the genetic approaches used. Disturbing native regulations by a synthetic promoter reduced the extrinsic noise in gene expression in Escherichia coli. It indicated that the extrinsic noise in gene expression caused by the native regulation could be further repressed. These results suggest a tendency of released regulation leading to reduced noise and a linkage between noise and plasticity in the regulation of gene expression.
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan. Electronic address: ying.beiwen.gf@u.tsukuba.ac.jp.
authors.forename: Bei-Wen
authors.initials: BW
authors.lastname: Ying
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Shigeto
authors.initials: S
authors.lastname: Seno
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsuda
authors.affiliation: Institute of Biology and Information Science, East China Normal University, 3663 Zhong Shan Road (N), Shanghai 200062, China. Electronic address: yomo@sei.cc.ecnu.cn.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics* / Q000378:metabolism; D016254:Mutagenesis, Insertional; D011401:Promoter Regions, Genetic; D015202:Protein Engineering; D059629:Signal-To-Noise Ratio; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D049452:Green Fluorescent Proteins
keywords: Extrinsic noise; Gene expression; Gene regulation; Genomics; Synthetic promoter; Transcriptome