Small RNAs in bacteria and archaea: who they are, what they do, and how they do it

EGH Wagner, P Romby - Advances in genetics, 2015 - Elsevier
Small RNAs are ubiquitously present regulators in all kingdoms of life. Most bacterial and
archaeal small RNAs (sRNAs) act by antisense mechanisms on multiple target mRNAs …

Differential RNA-seq: the approach behind and the biological insight gained

CM Sharma, J Vogel - Current opinion in microbiology, 2014 - Elsevier
Highlights•RNA-seq has become the method of choice for bacterial transcriptomics.•
Differential RNA-seq (dRNA-seq) distinguishes primary and processed transcripts.•dRNA …

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

C Kröger, SC Dillon, ADS Cameron… - Proceedings of the …, 2012 - pnas.org
More than 50 y of research have provided great insight into the physiology, metabolism, and
molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but …

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

A Lomsadze, K Gemayel, S Tang… - Genome …, 2018 - genome.cshlp.org
In a conventional view of the prokaryotic genome organization, promoters precede operons
and ribosome binding sites (RBSs) with Shine-Dalgarno consensus precede genes …

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

G Dugar, A Herbig, KU Förstner, N Heidrich… - PLoS …, 2013 - journals.plos.org
Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans.
Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic …

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

JA Leigh, SV Albers, H Atomi… - FEMS microbiology …, 2011 - academic.oup.com
The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our
knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies …

Genome-wide antisense transcription drives mRNA processing in bacteria

I Lasa, A Toledo-Arana, A Dobin, M Villanueva… - Proceedings of the …, 2011 - pnas.org
RNA deep sequencing technologies are revealing unexpected levels of complexity in
bacterial transcriptomes with the discovery of abundant noncoding RNAs, antisense RNAs …

Long-term effect of biochar amendment on the biodegradation of petroleum hydrocarbons in soil microbial fuel cells

X Li, Y Li, X Zhang, X Zhao, Y Sun, L Weng… - Science of the Total …, 2019 - Elsevier
Biochar is extensively applied in amendment of contaminated soils. However, the effect of
biochar on the biodegradation of petroleum hydrocarbons and electricity generation in soil …

[HTML][HTML] Understanding and application of Bacillus nitrogen regulation: a synthetic biology perspective

H He, Y Li, L Zhang, Z Ding, G Shi - Journal of Advanced Research, 2023 - Elsevier
Background Nitrogen sources play an essential role in maintaining the physiological and
biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism …

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase

P Zhelyazkova, CM Sharma, KU Förstner, K Liere… - The Plant …, 2012 - academic.oup.com
Gene expression in plastids of higher plants is dependent on two different transcription
machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear …