R loops: from transcription byproducts to threats to genome stability

A Aguilera, T García-Muse - Molecular cell, 2012 - cell.com
RNA: DNA hybrid structures known as R loops were thought to be rare byproducts of
transcription. In the last decade, however, accumulating evidence has pointed to a new view …

Somatic mitochondrial DNA mutations in mammalian aging

NG Larsson - Annual review of biochemistry, 2010 - annualreviews.org
Mitochondrial dysfunction is heavily implicated in the multifactorial aging process. Aging
humans have increased levels of somatic mtDNA mutations that tend to undergo clonal …

A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery

LM Wee, AB Tong, AJ Florez Ariza… - Cell, 2023 - cell.com
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called
coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well …

Functionally uncoupled transcription–translation in Bacillus subtilis

GE Johnson, JB Lalanne, ML Peters, GW Li - Nature, 2020 - nature.com
Tight coupling of transcription and translation is considered a defining feature of bacterial
gene expression,. The pioneering ribosome can both physically associate and kinetically …

Real-time kinetics of gene activity in individual bacteria

I Golding, J Paulsson, SM Zawilski, EC Cox - Cell, 2005 - cell.com
Protein levels have been shown to vary substantially between individual cells in clonal
populations. In prokaryotes, the contribution to such fluctuations from the inherent …

The contribution of co-transcriptional RNA: DNA hybrid structures to DNA damage and genome instability

S Hamperl, KA Cimprich - DNA repair, 2014 - Elsevier
Accurate DNA replication and DNA repair are crucial for the maintenance of genome
stability, and it is generally accepted that failure of these processes is a major source of DNA …

Proteome organization in a genome-reduced bacterium

S Kühner, V van Noort, MJ Betts, A Leo-Macias… - Science, 2009 - science.org
The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating
organisms. To study the basic principles of bacterial proteome organization, we used …

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

C Colijn, A Brandes, J Zucker, DS Lun… - PLoS computational …, 2009 - journals.plos.org
Metabolism is central to cell physiology, and metabolic disturbances play a role in numerous
disease states. Despite its importance, the ability to study metabolism at a global scale using …

Transcription as a source of genome instability

N Kim, S Jinks-Robertson - Nature Reviews Genetics, 2012 - nature.com
Alterations in genome sequence and structure contribute to somatic disease, affect the
fitness of subsequent generations and drive evolutionary processes. The crucial roles of …

Toward an orthogonal central dogma

CC Liu, MC Jewett, JW Chin, CA Voigt - Nature chemical biology, 2018 - nature.com
The central dogma processes of DNA replication, transcription, and translation are
responsible for the maintenance and expression of every gene in an organism. An …