title: Kinetics of transcription initiation directed by multiple cis-regulatory elements on the glnAp2 promoter.
abstract: Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three low-affinity sequences (sites III-V), to which the transcriptional activator NtrC binds. By structure reconstruction, we analyze all possible organization architectures of the transcription apparatus (TA). The main regulatory mode involves two NtrC hexamers: one at enhancer II transiently associates with site V such that the other at enhancer I can rapidly approach and catalyze the σ54-RNA polymerase holoenzyme. We build a kinetic model characterizing essential steps of the TA operation; with the known kinetics of the holoenzyme interacting with DNA, this model enables the kinetics beyond technical detection to be determined by fitting the input-output function of the wild-type promoter. The model further quantitatively reproduces transcriptional activities of various mutated promoters. These results reveal different roles played by two enhancers and interpret why the low-affinity elements conditionally enhance or repress transcription. This work presents an integrated dynamic picture of regulated transcription initiation and suggests an evolutionarily conserved characteristic guaranteeing reliable transcriptional response to regulatory signals.
authors.affiliation: National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China.
authors.forename: Yaolai
authors.initials: Y
authors.lastname: Wang
authors.affiliation: National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China fliu@nju.edu.cn.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
authors.forename: Feng
authors.identifier: 0000-0001-9560-8518
authors.initials: F
authors.lastname: Liu
authors.affiliation: National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China wangwei@nju.edu.cn.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D003198:Computer Simulation; D019277:Entropy; D015964:Gene Expression Regulation, Bacterial; D005974:Glutamate-Ammonia Ligase / Q000235:genetics*; D007700:Kinetics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D061785:Transcription Initiation, Genetic; D015533:Transcriptional Activation
chemical_list: D012333:RNA, Messenger; C081173:glutamine synthetase I; D005974:Glutamate-Ammonia Ligase