ArticleNucleic acids research2012
Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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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.
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Who cites it
33 citing papers in PubMed, 60 citations in OpenAlex.
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- Improved DNA binding to a type IV minor pilin increases natural transformation.Nucleic acids research · 2025Article
- Type IV minor pilin ComN predicted the USS-receptor in Pasteurellaceae.Frontiers in microbiology · 2025Article
- Genomic profiling of cefotaxime-resistantFrontiers in microbiology · 2025Article
- DNA modifications impact natural transformation of Acinetobacter baumannii.Nucleic acids research · 2023Article
- Cell-to-cell natural transformation in Bacillus subtilis facilitates large scale of genomic exchanges and the transfer of long continuous DNA regions.Nucleic acids research · 2023Article
- Genetic Adaptation and Acquisition of Macrolide Resistance in Haemophilus spp. during Persistent Respiratory Tract Colonization in Chronic Obstructive Pulmonary Disease (COPD) Patients Receiving Long-Term Azithromycin Treatment.Microbiology spectrum · 2023Article
- Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Quinolone Resistance Is Transferred Horizontally via Uptake Signal Sequence Recognition in Haemophilus influenzae.Antimicrobial agents and chemotherapy · 2022Article
- The molecular diversity of transcriptional factor TfoX is a determinant in natural transformation inFrontiers in microbiology · 2022Article
- Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus.The ISME journal · 2021Article
- A novel AST2 mutation generated upon whole-genome transformation of Saccharomyces cerevisiae confers high tolerance to 5-Hydroxymethylfurfural (HMF) and other inhibitors.PLoS genetics · 2021Article
- Article
- Natural Transformation ofFrontiers in microbiology · 2021Article
- Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis.Biochemical Society transactions · 2020Review
- Nucleic Acid Hybrids as Advanced Antibacterial Nanocarriers.Pharmaceutics · 2020Review
- Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae.mSphere · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Some naturally competent bacteria exhibit both a strong preference for DNA fragments containing specific 'uptake sequences' and dramatic overrepresentation of these sequences in their genomes. Uptake sequences are often assumed to directly reflect the specificity of the DNA uptake machinery, but the actual specificity has not been well characterized for any bacterium. We produced a detailed analysis of Haemophilus influenzae's uptake specificity, using Illumina sequencing of degenerate uptake sequences in fragments recovered from competent cells. This identified an uptake motif with the same consensus as the motif overrepresented in the genome, with a 9 bp core (AAGTGCGGT) and two short flanking T-rich tracts. Only four core bases (GCGG) were critical for uptake, suggesting that these make strong specific contacts with the uptake machinery. Other core bases had weaker roles when considered individually, as did the T-tracts, but interaction effects between these were also determinants of uptake. The properties of genomic uptake sequences are also constrained by mutational biases and selective forces acting on USSs with coding and termination functions. Our findings define constraints on gene transfer by natural transformation and suggest how the DNA uptake machinery overcomes the physical constraints imposed by stiff highly charged DNA molecules.
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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.