Coupled transcription-translation in prokaryotes: an old couple with new surprises

M Irastortza-Olaziregi, O Amster-Choder - Frontiers in Microbiology, 2021 - frontiersin.org
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT
occurs when ribosomes associate with and initiate translation of mRNAs whose transcription …

When push comes to shove-RNA polymerase and DNA-bound protein roadblocks

N Hao, AJ Donnelly, IB Dodd, KE Shearwin - Biophysical Reviews, 2023 - Springer
In recent years, transcriptional roadblocking has emerged as a crucial regulatory
mechanism in gene expression, whereby other DNA-bound obstacles can block the …

Improved RNA stability estimation indicates that transcriptional interference is frequent in diverse bacteria

WC Wanney, L Youssar, G Kostova, J Georg - Communications Biology, 2023 - nature.com
We used stochastic simulations and experimental data from E. coli, K. aerogenes,
Synechococcus PCC 7002 and Synechocystis PCC 6803 to provide evidence that …

RoboMoClo: a robotics-assisted modular cloning framework for multiple gene assembly in biofoundry

DH Kang, SC Ko, YB Heo, HJ Lee… - ACS Synthetic …, 2022 - ACS Publications
Efficient and versatile DNA assembly frameworks have had an impact on promoting
synthetic biology to build complex biological systems. To accelerate system development …

Are antisense proteins in prokaryotes functional?

Z Ardern, K Neuhaus, S Scherer - Frontiers in molecular biosciences, 2020 - frontiersin.org
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes.
Across bacterial species hundreds of short open reading frames antisense to annotated …

Analytical kinetic model of native tandem promoters in E. coli

V Chauhan, MNM Bahrudeen, CSD Palma… - PLoS Computational …, 2022 - journals.plos.org
Closely spaced promoters in tandem formation are abundant in bacteria. We investigated
the evolutionary conservation, biological functions, and the RNA and single-cell protein …

Construction of two-input logic gates using transcriptional interference

AE Bordoy, NJ O'Connor, A Chatterjee - ACS Synthetic Biology, 2019 - ACS Publications
Transcriptional interference (TI) has been shown to regulate gene expression at the DNA
level via different molecular mechanisms. The obstacles present on the DNA that a …

Engineering transcriptional interference through RNA polymerase processivity control

NJ O'Connor, AE Bordoy, A Chatterjee - ACS Synthetic Biology, 2021 - ACS Publications
Antisense transcription is widespread in all kingdoms of life and has been shown to
influence gene expression through transcriptional interference (TI), a phenomenon in which …

RNA polymerase pausing at a protein roadblock can enhance transcriptional interference by promoter occlusion

N Hao, MT Crooks, AC Palmer, IB Dodd… - FEBS …, 2019 - Wiley Online Library
Convergent promoters exert transcriptional interference (TI) by several mechanisms
including promoter occlusion, where elongating RNA polymerases (RNAP s) block access to …

Universal Actuator for Efficient Silencing of Escherichia coli Genes Based on Convergent Transcription Resistant to Rho-Dependent Termination

AA Krylov, VV Shapovalova, EA Miticheva… - ACS Synthetic …, 2020 - ACS Publications
Dynamic control is a distinguished strategy in modern metabolic engineering, in which
inducible convergent transcription is an attractive approach for conditional gene silencing …