ArticleBMC genomics2018
Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Discovery of diketopiperazine alkaloids from an endophytic Kitasatospora sp. by heterologous expression.The Journal of antibiotics · 2026Article
- Analysis of the genome of a Pseudomonas monsensis isolate that produces the antifungal dipeptide maculosin.Access microbiology · 2026Article
- Not to be overlooked: dipeptides and their role in plant stress resilience.Journal of experimental botany · 2025Review
- Characterization of the cyclic dipeptide cyclo(His-Pro) in Arabidopsis.Plant physiology · 2025Article
- Crystal Structure and Mutagenesis of an XYP Subfamily Cyclodipeptide Synthase Reveal Key Determinants of Enzyme Activity and Substrate Specificity.Biochemistry · 2024Article
- Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase.Nature communications · 2023Article
- Natural and engineered cyclodipeptides: Biosynthesis, chemical diversity, and engineering strategies for diversification and high-yield bioproduction.Engineering microbiology · 2023Review
- Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria.Chembiochem : a European journal of chemical biology · 2023Article
- Active site remodelling of a cyclodipeptide synthase redefines substrate scope.Communications chemistry · 2022Article
- Lentzeacins A-E, New Bacterial-Derived 2,5- and 2,6-Disubstituted Pyrazines from a BGC-Rich Soil BacteriumMolecules (Basel, Switzerland) · 2021Article
- Deciphering a Cyclodipeptide Synthase Pathway Encoding Prenylated Indole Alkaloids in Streptomyces leeuwenhoekii.Applied and environmental microbiology · 2021Article
- Modifications of diketopiperazines assembled by cyclodipeptide synthases with cytochrome PApplied microbiology and biotechnology · 2021Review
- Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid inMolecules (Basel, Switzerland) · 2020Review
- Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.Nature communications · 2020Article
- In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli.Microbial cell factories · 2020Article
- Expanding the Structural Diversity of Drimentines by Exploring the Promiscuity of Two N-methyltransferases.iScience · 2020Article
- Bioactive Potential of Extracts ofMolecules (Basel, Switzerland) · 2020Article
- Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry.Biomolecules · 2019Review
- Genome mining of cyclodipeptide synthases unravels unusual tRNA-dependent diketopiperazine-terpene biosynthetic machinery.Nature communications · 2018Article
- A Comprehensive Overview of the Cyclodipeptide Synthase Family Enriched with the Characterization of 32 New Enzymes.Frontiers in microbiology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmong naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery.
resultsWe developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures. We leveraged this tool to conduct a global analysis of tRNA-derived cyclodipeptide biosynthesis in 93,107 prokaryotic genomes, and compared predicted cyclodipeptides to known cyclodipeptide synthase products and all known chemically characterized cyclodipeptides. By integrating predicted chemical structures and gene cluster architectures, we created a unified map of known and unknown genetically encoded cyclodipeptides.
conclusionsOur analysis suggests that sizeable regions of the chemical space encoded within sequenced prokaryotic genomes remain unexplored. Our map of the landscape of genetically encoded cyclodipeptides provides candidates for targeted discovery of novel compounds. The integration of our pipeline into a user-friendly web application provides a resource for further discovery of cyclodipeptides in newly sequenced prokaryotic genomes.
Indexed as
Identifiers
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.