OUP accepted manuscript

Bradley, Noah P.; Washburn, Lauren A; Christov, Plamen P.; Watanabe, Coran M. H.; Eichman, Brandt F.

doi:10.1093/nar/gkaa346

Cited by 9 publications

(1 citation statement)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Significant improvements have been made to the curation of DNA repair enzymes, with a particular focus on the addition of reactions that accurately reflect the catalytic activities of these important proteins. Eleven new reactions were created as part of this process, including those for two newly described enzymes: the genome maintenance protein encoded by yedK ( Mohni et al, 2019 ; Thompson et al, 2019 ; Wang et al, 2019 ) and an interstrand DNA crosslink repair glycosylase encoded by ycaQ ( Bradley et al, 2020 ). Figure 2 shows the new reactions assigned to YedK and YcaQ.…”

Section: Resultsmentioning

confidence: 99%

The EcoCyc Database in 2021

et al. 2021

View full text Add to dashboard Cite

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

show abstract

Section: Resultsmentioning

confidence: 99%

The EcoCyc Database in 2021

et al. 2021

View full text Add to dashboard Cite

show abstract

Overcoming stochastic variations in culture variables to quantify and compare growth curve data

Sausen

Bochman

2021

BioEssays

View full text Add to dashboard Cite

The comparison of growth, whether it is between different strains or under different growth conditions, is a classic microbiological technique that can provide genetic, epigenetic, cell biological, and chemical biological information depending on how the assay is used. When employing solid growth media, this technique is limited by being largely qualitative and low throughput. Collecting data in the form of growth curves, especially automated data collection in multi-well plates, circumvents these issues. However, the growth curves themselves are subject to stochastic variation in several variables, most notably the length of the lag phase, the doubling rate, and the maximum expansion of the culture. Thus, growth curves are indicative of trends but cannot always be conveniently averaged and statistically compared. Here, we summarize a simple method to compile growth curve data into a quantitative format that is amenable to statistical comparisons and easy to graph and display. K E Y W O R D Sgrowth curve, microbe, Saccharomyces cerevisiae (e.g., the calculation of mutant fitness in synthetic genetic array [SGA]) analyses [8] ), but it is cumbersome, time consuming, and difficult to perform with spot dilution assays relative to SGA analyses.

show abstract

Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA

Tripathi

Bruner

2021

Biochemistry

View full text Add to dashboard Cite

The natural product colibactin, along with its associated biosynthetic gene cluster, is an example system for the role microbially derived small molecules play in the human microbiome. This is particularly relevant in the human gut, where host microbiota is involved in various disorders, including colorectal cancer pathogenesis. Bacteria harboring the colibactin gene cluster induce alkylation of nucleobases in host DNA, forming interstrand cross-links both in vivo and in vitro. These lesions can lead to deleterious double-strand breaks and have been identified as the primary mechanism of colibactin-induced cytotoxicity. The gene product ClbS is one of several mechanisms utilized by the producing bacteria to maintain genome integrity. ClbS catalyzes hydrolytic inactivation of colibactin and has been shown to bind DNA, incurring self-resistance. Presented is the molecular basis for ClbS bound to a DNA oligonucleotide. The structure shows the interaction of the protein with the ends of a DNA duplex with terminal nucleotides flipped to the enzyme active site. The structure suggests an additional function for ClbS, the binding to damaged DNA followed by repair. Additionally, our study provides general insight into the function of the widely distributed and largely uncharacterized DUF1706 protein family.

show abstract

OUP accepted manuscript

Cited by 9 publications

References 74 publications

The EcoCyc Database in 2021

The EcoCyc Database in 2021

Overcoming stochastic variations in culture variables to quantify and compare growth curve data

Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA

Contact Info

Product

Resources

About