Evolution of diverse strategies for promoter regulation

V Brázda, M Bartas, RP Bowater - Trends in Genetics, 2021 - cell.com
DNA is fundamentally important for all cellular organisms due to its role as a store of
hereditary genetic information. The precise and accurate regulation of gene transcription …

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

F Ponath, C Tawk, Y Zhu, L Barquist, F Faber… - Nature …, 2021 - nature.com
Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently
garnered renewed attention for its association with several different human cancers. The …

Deep Profiling of the Proteome Dynamics of Pseudomonas aeruginosa Reference Strain PAO1 under Different Growth Conditions

M Hou, J Huang, T Jia, Y Guan, F Yang… - Journal of Proteome …, 2023 - ACS Publications
As one of the most common bacterial pathogens causing nosocomial infections,
Pseudomonas aeruginosa is highly adaptable to survive under various conditions. Here, we …

Functional expansion of a TCA cycle operon mRNA by a 3′ end-derived small RNA

M Miyakoshi, G Matera, K Maki, Y Sone… - Nucleic Acids …, 2019 - academic.oup.com
Global RNA profiling studies in bacteria have predicted the existence of many of small
noncoding RNAs (sRNAs) that are processed off mRNA 3′ ends to regulate other mRNAs …

Compendium-wide analysis of Pseudomonas aeruginosa core and accessory genes reveals transcriptional patterns across strains PAO1 and PA14

AJ Lee, G Doing, SL Neff, T Reiter, DA Hogan… - …, 2023 - Am Soc Microbiol
Pseudomonas aeruginosa is an opportunistic pathogen that causes difficult-to-treat
infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have …

[HTML][HTML] Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum

S Duboux, M Golliard, JA Muller, G Bergonzelli… - Scientific reports, 2021 - nature.com
Abstract The Serine Protease Inhibitor (serpin) protein has been suggested to play a key
role in the interaction of bifidobacteria with the host. By inhibiting intestinal serine proteases …

The functional determinants in the organization of bacterial genomes

Z Liu, J Feng, B Yu, Q Ma, B Liu - Briefings in Bioinformatics, 2021 - academic.oup.com
Bacterial genomes are now recognized as interacting intimately with cellular processes.
Uncovering organizational mechanisms of bacterial genomes has been a primary focus of …

SLING: a tool to search for linked genes in bacterial datasets

G Horesh, A Harms, C Fino, L Parts… - Nucleic acids …, 2018 - academic.oup.com
Gene arrays and operons that encode functionally linked proteins form the most basic unit of
transcriptional regulation in bacteria. Rules that govern the order and orientation of genes in …

[HTML][HTML] OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

R Krishnakumar, AM Ruffing - PLoS computational biology, 2022 - journals.plos.org
Operon prediction in prokaryotes is critical not only for understanding the regulation of
endogenous gene expression, but also for exogenous targeting of genes using newly …

Systematic analysis of the underlying genomic architecture for transcriptional–translational coupling in prokaryotes

R Bharti, D Siebert, B Blombach… - NAR Genomics and …, 2022 - academic.oup.com
Transcriptional-translational coupling is accepted to be a fundamental mechanism of gene
expression in prokaryotes and therefore has been analyzed in detail. However, the …