ArticleCommunications biology2021
Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 23 citations in OpenAlex.
- Dissecting host stress responses for predictable heterologous gene expression in E. coli.Nucleic acids research · 2026Article
- Approaches for accelerating microbial gene function discovery using artificial intelligence.Nature microbiology · 2026Review
- Distribution and evolution of the LysR-type transcriptional regulators of the Salmonella genus.PloS one · 2026Article
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.Nature communications · 2024Article
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- Emergence and genomic insights of non-pandemic O1Microbiology spectrum · 2023Article
- A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic acids research · 2023Article
- Model-driven experimental design workflow expands understanding of regulatory role of Nac inNAR genomics and bioinformatics · 2023Article
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.bioRxiv : the preprint server for biology · 2023Article
- A roadmap for the functional annotation of protein families: a community perspective.Database : the journal of biological databases and curation · 2022Article
- A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli.Scientific reports · 2022Article
- Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators.Nucleic acids research · 2022Article
- Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal ThermoacidophileFrontiers in microbiology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
Abstract
Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, the analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively.
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.