A comprehensive review of m6A/m6Am RNA methyltransferase structures

S Oerum, V Meynier, M Catala, C Tisné - Nucleic acids research, 2021‏ - academic.oup.com
Gene expression is regulated at many levels including co-or post-transcriptionally, where
chemical modifications are added to RNA on riboses and bases. Expression control via RNA …

A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulphate-reducing prokaryotes

R Rabus, SS Venceslau, L Wöhlbrand… - Advances in microbial …, 2015‏ - Elsevier
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing
prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have …

Mutant phenotypes for thousands of bacterial genes of unknown function

MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018‏ - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

A Heinken, DA Ravcheev, F Baldini, L Heirendt… - Microbiome, 2019‏ - Springer
Background The human gut microbiome performs important functions in human health and
disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of …

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

H Liu, AL Shiver, MN Price, HK Carlson, VV Trotter… - Cell reports, 2021‏ - cell.com
Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of
the constituent bacteria, as the functions of most of their genes are unknown. Here, we …

gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions

L Cheng, C Qi, H Zhuang, T Fu… - Nucleic acids research, 2020‏ - academic.oup.com
Abstract gutMDisorder (http://bio-annotation. cn/gutMDisorder), a manually curated
database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in …

Glycolytic strategy as a tradeoff between energy yield and protein cost

A Flamholz, E Noor, A Bar-Even… - Proceedings of the …, 2013‏ - pnas.org
Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

J Blom, J Kreis, S Spänig, T Juhre… - Nucleic acids …, 2016‏ - academic.oup.com
The rapidly increasing availability of microbial genome sequences has led to a growing
demand for bioinformatics software tools that support the functional analysis based on the …

Engineering dynamic pathway regulation using stress-response promoters

RH Dahl, F Zhang, J Alonso-Gutierrez, E Baidoo… - Nature …, 2013‏ - nature.com
Heterologous pathways used in metabolic engineering may produce intermediates toxic to
the cell. Dynamic control of pathway enzymes could prevent the accumulation of these …

RegPrecise 3.0–a resource for genome-scale exploration of transcriptional regulation in bacteria

PS Novichkov, AE Kazakov, DA Ravcheev, SA Leyn… - BMC genomics, 2013‏ - Springer
Background Genome-scale prediction of gene regulation and reconstruction of
transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern …