title: A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.
abstract: Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI) has been shown to be widely prevalent at promoters of genes expressed during the stationary phase of growth in Escherichia coli. However, the extent to which PDI impacts E. coli physiology, and the extent to which PDI occurs in other bacteria is not known. Here we establish a physiological role for PDI in E. coli as a regulatory mechanism that modulates biofilm formation. We further demonstrate using high-throughput sequencing of RNA 5' ends (5' RNA-seq) that PDI occurs in the pathogenic bacterium Vibrio cholerae. A comparative global analysis of PDI in V. cholerae and E. coli reveals that the pattern of PDI is strikingly similar in the two organisms. In particular, PDI is detected in stationary phase, is not detected in exponential phase, and is preferentially apparent at promoters carrying the sequence T-1A+1 or G-1G+1 (where position +1 corresponds to the position of de novo initiation). Our findings demonstrate a physiological role for PDI and suggest PDI may be widespread among Gammaproteobacteria. We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´.
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Sergey Y
authors.initials: SY
authors.lastname: Druzhinin
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Ngat T
authors.initials: NT
authors.lastname: Tran
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Kyle S
authors.initials: KS
authors.lastname: Skalenko
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Seth R
authors.initials: SR
authors.lastname: Goldman
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Jared G
authors.initials: JG
authors.lastname: Knoblauch
authors.affiliation: Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Simon L
authors.initials: SL
authors.lastname: Dove
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Bryce E
authors.initials: BE
authors.lastname: Nickels
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001483:Base Sequence; D018441:Biofilms / Q000254:growth & development*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D020563:Gammaproteobacteria / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017423:Sequence Analysis, RNA; D061785:Transcription Initiation, Genetic / Q000502:physiology*; D014734:Vibrio cholerae / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D001425:Bacterial Outer Membrane Proteins; C560939:BhsA protein, E coli; D029968:Escherichia coli Proteins