Evidence map›Paper›PMID 22685277›Full record

ArticleJournal of bacteriology2012

Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element.

Yoshiyuki Ohtsubo, Yoko Ishibashi, Hideaki Naganawa, Satoshi Hirokawa, Satomi Atobe, Yuji Nagata, Masataka Tsuda

Open access · bronzeAbstract read
In one paragraph

Article in Journal of bacteriology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
3.7field-weighted citation impact, top 7% 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

17 citing papers in PubMed, 44 citations in OpenAlex.

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  14. Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.Proceedings of the National Academy of Sciences of the United States of America · 2015
    Article
  15. Article
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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

7 authors at 1 institution in 1 country.

Yoshiyuki OhtsuboDepartment of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan. yohtsubo@ige.tohoku.ac.jp
Yoko Ishibashi
Hideaki Naganawa
Satoshi Hirokawa
Satomi Atobe
Yuji Nagata
Masataka Tsuda
Tohoku University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

A polychlorinated biphenyl (PCB)/biphenyl degradation gene cluster in Acidovorax sp. strain KKS102, which is very similar to that in Tn4371 from Cupriavidus oxalaticus A5, was transferred to several proteobacterial strains by conjugation. The mobilized DNA fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), DNA transfer (dtr), integrase (int), and replication-partition proteins (rep-parAB). In the transconjugants, transferred DNA was integrated at ATTGCATCAG or similar sequences. The circular-form integrative and conjugative element (ICE) was detected by PCR, and quantitative PCR analyses revealed that, in KKS102 cells, the ratio of the circular form to the integrated form was very low (approximately 10(-5)). The circular form was not detected in a mutant of the int gene, which was located at the extreme left and transcribed in the inward direction, and the level of int transcriptional activity was much higher in the circular form than in the integrated form. These findings clearly demonstrated that the genes for PCB/biphenyl degradation in KKS102 cells are located on an ICE, which was named ICE(KKS102)4677. Comparisons of similar ICE-like elements collected from the public database suggested that those of beta- and gammaproteobacteria were distinguishable from other ICE-like elements, including those in alphaproteobacteria, with respect to the gene composition and gene organization.

Indexed as

Conjugation, GeneticGene Transfer, HorizontalInterspersed Repetitive SequencesBiotransformationComamonadaceaeMetabolic Networks and PathwaysMultigene FamilyPolychlorinated BiphenylsReal-Time Polymerase Chain ReactionSequence HomologyPolychlorinated Biphenyls

Identifiers

PMID22685277
PMCPMC3416211
OpenAlexW2104241082

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.