ArticleThe Journal of biological chemistry2013
Insights into the mechanism of initial transcription in Escherichia coli RNA polymerase.
Article in The Journal of biological chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Process and analytical strategies for the safe production of mRNA vaccines and therapeutics.Molecular biology reports · 2026Review
- Article
- An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts.Nature biotechnology · 2023Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Diverse and unified mechanisms of transcription initiation in bacteria.Nature reviews. Microbiology · 2021Review
- Structure, mechanism, and regulation of mitochondrial DNA transcription initiation.The Journal of biological chemistry · 2020Review
- Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences.Biomolecules · 2020Article
- The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation.Nucleic acids research · 2020Article
- Article
- Structural basis for transcription initiation by bacterial ECF σ factors.Nature communications · 2019Article
- The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase.Nucleic acids research · 2019Article
- Locking the nontemplate DNA to control transcription.Molecular microbiology · 2018Article
- DNA template sequence control of bacterial RNA polymerase escape from the promoter.Nucleic acids research · 2018Article
- Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.Nature communications · 2018Article
- Different types of pausing modes during transcription initiation.Transcription · 2017Article
- Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence.Protein science : a publication of the Protein Society · 2017Review
- Mechanism of transcription initiation and promoter escape byProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.Frontiers in molecular biosciences · 2016Review
- Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.Molecular cell · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
It has long been known that during initial transcription of the first 8-10 bases of RNA, complexes are relatively unstable, leading to the release of short abortive RNA transcripts. An early "stressed intermediate" model led to a more specific mechanistic model proposing "scrunching" stress as the basis for the instability. Recent studies in the single subunit T7 RNA polymerase have argued against scrunching as the energetic driving force and instead argue for a model in which pushing of the RNA-DNA hybrid against a protein element associated with promoter binding, while likely driving promoter release, reciprocally leads to instability of the hybrid. In this study, we test these models in the structurally unrelated multisubunit bacterial RNA polymerase. Via the targeted introduction of mismatches and nicks in the DNA, we demonstrate that neither downstream bubble collapse nor compaction/scrunching of either the single-stranded template or nontemplate strands is a major force driving abortive instability (although collapse from the downstream end of the bubble does contribute significantly to the instability of artificially halted complexes). In contrast, pushing of the hybrid against a mobile protein element (σ3.2 in the bacterial enzyme) results in substantially increased abortive instability and is likely the primary energetic contributor to abortive cycling. The results suggest that abortive instability is a by-product of the mechanistic need to couple the energy of nucleotide addition (RNA chain growth) to driving the timed release of promoter contacts during initial transcription.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.