title: Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.
abstract: In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.
authors.affiliation: Molecular Signaling Lab, Computational Systems Biology Research Group, Signal Processing Department, Tampere University of Technology, PO Box 553, 33101, Tampere, Finland.
authors.forename: Adrien
authors.initials: A
authors.lastname: Sala
authors.forename: Muhammad
authors.initials: M
authors.lastname: Shoaib
authors.forename: Olga
authors.initials: O
authors.lastname: Anufrieva
authors.forename: Gnanavel
authors.initials: G
authors.lastname: Mutharasu
authors.forename: Rawnak
authors.initials: R
authors.lastname: Jahan Hoque
authors.forename: Olli
authors.initials: O
authors.lastname: Yli-Harja
authors.forename: Meenakshisundaram
authors.initials: M
authors.lastname: Kandhavelu
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D056968:Lac Repressors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008274:Magnesium / Q000378:metabolism; D008962:Models, Theoretical; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D056968:Lac Repressors; C539064:LacI protein, E coli; D012321:DNA-Directed RNA Polymerases; D008274:Magnesium