title: Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator.
abstract: An experimental system was designed to measure in vivo termination efficiency (TE) of the Rho-independent terminator and position-function relations were quantified for the terminator tR2 in Escherichia coli The terminator function was almost completely repressed when tR2 was located several base pairs downstream from the gene, and TE gradually increased to maximum values with the increasing distance between the gene and terminator. This TE-distance relation reflected a stochastic coupling of the ribosome and RNA polymerase (RNAP). Terminators located in the first 100 bp of the coding region can function efficiently. However, functional repression was observed when the terminator was located in the latter part of the coding region, and the degree of repression was determined by transcriptional and translational dynamics. These results may help to elucidate mechanisms of Rho-independent termination and reveal genomic locations of terminators and functions of the sequence that precedes terminators. These observations may have important applications in synthetic biology.
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: State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China National Center for Nanoscience and Technology, Beijing 100190, China jbli@iccas.ac.cn.
authors.forename: Junbai
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China shihl@itp.ac.cn.
authors.forename: Hualin
authors.initials: H
authors.lastname: Shi
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009876:Operon; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012234:Rho Factor / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism; D013728:Terminator Regions, Genetic; D061806:Transcription Termination, Genetic; D014169:Transformation, Bacterial
chemical_list: D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D012234:Rho Factor; D012321:DNA-Directed RNA Polymerases