Evidence map›Paper›PMID 21948829›Full record

ArticleApplied and environmental microbiology2011

Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes.

Diya Sen, Geraldine A Van der Auwera, Linda M Rogers, Christopher M Thomas, Celeste J Brown, Eva M Top

Open access · bronzeAbstract read
In one paragraph

Article in Applied and environmental microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.

0numbers the graph read from it
0cells of the map it votes in
58citing papers in PubMed
9.6field-weighted citation impact, top 2% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

58 citing papers in PubMed, 94 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Birmingham-group IncP-1Microbial genomics · 2025
    Article
  10. Article
  11. Article
  12. Evolution End Classification ofInternational journal of molecular sciences · 2023
    Article
  13. Article
  14. Article
  15. Article
  16. Why do plasmids manipulate the expression of bacterial phenotypes?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022
    Review
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 4 institutions in 3 countries.

Diya SenDepartment of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies-IBEST, University of Idaho, Moscow, ID 83844-3051, USA.
Geraldine A Van der Auwera
Linda M Rogers
Christopher M Thomas
Celeste J Brown
Eva M Top
Institute of Bioinformatics · INHarvard University · USUniversity of Birmingham · GBUniversity of Idaho · US

Funding

UNDERGRADUATE COLLEGE OUTREACH PROGRAMP20RR016454 · NCRR · UNIVERSITY OF IDAHO · PI CHASE, JENNIFER R · 2001 to 2011
$35.3M
The Evolution of Protein FlexibilityP20RR016448 · NCRR · UNIVERSITY OF IDAHO · PI ROBISON, BARRIE D · 2002 to 2011
$19.3M
NCRR NIH HHS P20 RR016448NCRR NIH HHS P20 RR016454NCRR NIH HHS P20RR016454NCRR NIH HHS P20RR16448
6 · The paper itself

Abstract

Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.

Indexed as

Genes, BacterialHost SpecificityMetagenomeSoilBacteriaDNA, BacterialGenetic VariationINDEL MutationMolecular Sequence DataNorwayPhylogenyPlasmidsRecombination, GeneticSequence Analysis, DNASequence Homology, Amino AcidDNA, BacterialSoil

Identifiers

PMID21948829
PMCPMC3209000
OpenAlexW2136232699

What OpenQuestion holds

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Registered trials

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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.