title: Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation.
abstract: Genes are organized into operons in procaryote, and these genes in one operon generally have related functions. However, genes in the same operon are usually not equally expressed, and the ratio needs to be fine-tuned for specific functions. We examine the difference of gene expression noise and correlation when tuning the expression level at the transcriptional or translational level in a bicistronic operon driven by a constitutive or a two-state promoter. We get analytic results for the noise and correlation of gene expression levels, which is confirmed by our stochastic simulations. Both the noise and the correlation of gene expressions in an operon with a two-state promoter are higher than in an operon with a constitutive promoter. Premature termination of mRNA induced by transcription terminator in the intergenic region or changing translation rates can tune the protein ratio at the transcriptional level or at the translational level. We find that gene expression correlation between promoter-proximal and promoter-distal genes at the protein level decreases as termination increases. In contrast, changing translation rates in the normal range almost does not alter the correlation. This explains why the translation rate is a key factor of modulating gene expressions in an operon. Our results can be useful to understand the relationship between the operon structure and the biological function of a gene network, and also may help in synthetic biology design.
authors.affiliation: State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Li
authors.affiliation: Department of Physics and Biophysics & Complex System Center, Jilin University, Changchun 130012, China.
authors.forename: Liufang
authors.initials: L
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: shihl@itp.ac.cn.
authors.forename: Hualin
authors.initials: H
authors.lastname: Shi
mesh_terms: D003198:Computer Simulation; D015964:Gene Expression Regulation, Bacterial; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D009876:Operon / Q000235:genetics; D011387:Prokaryotic Cells / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes; D000097573:Red Fluorescent Protein
chemical_list: D049452:Green Fluorescent Proteins; D008164:Luminescent Proteins; D012333:RNA, Messenger; D000097573:Red Fluorescent Protein
keywords: Gene expression correlation; Operon structure; Polar effect; The two-state promoter; Transcription terminator