ArticleGenome research2012
A vast collection of microbial genes that are toxic to bacteria.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
48 citing papers in PubMed, 79 citations in OpenAlex.
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- Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci.bioRxiv : the preprint server for biology · 2025Article
- Synthetic genomes unveil the effects of synonymous recoding.bioRxiv : the preprint server for biology · 2024Article
- Identification and Characterization of HEPN-MNT Type II TA System from Methanothermobacter thermautotrophicus ΔH.Journal of microbiology (Seoul, Korea) · 2023Article
- Silencing Transcription from an Influenza Reverse Genetics Plasmid inACS synthetic biology · 2023Article
- Phages and their satellites encode hotspots of antiviral systems.Cell host & microbe · 2022Article
- Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.Nucleic acids research · 2022Article
- Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.PLoS computational biology · 2021Article
- Fluoride-Controlled Riboswitch-Based Dampening of Gene Expression for Cloning Potent Promoters.Frontiers in genetics · 2021Article
- An Auto-Regulating Type II Toxin-Antitoxin System Modulates Drug Resistance and Virulence inFrontiers in microbiology · 2021Article
- A ligation and restriction enzyme independent cloning technique: an alternative to conventional methods for cloning hard-to-clone gene segments in the influenza reverse genetics system.Virology journal · 2020Article
- Molecular Dissection of theMicroorganisms · 2020Article
- Genomic integration of unclonable gene expression cassettes in Saccharomyces cerevisiae using rapid cloning-free workflows.MicrobiologyOpen · 2020Article
- In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1.BMC genomics · 2020Article
- Genome-Wide Screening for Identification of Novel Toxin-Antitoxin Systems in Staphylococcus aureus.Applied and environmental microbiology · 2019Article
- Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes, we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes, our assays revealed novel toxins and restriction enzymes, and new classes of small, non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short, toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator DnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.