Evidence map›Paper›PMID 28911108›Full record

ArticleNucleic acids research2017

The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.

Piotr M Skowron, Brian P Anton, Edyta Czajkowska, Joanna Zebrowska, Ewa Sulecka, Daria Krefft, Joanna Jezewska-Frackowiak, Olga Zolnierkiewicz, Malgorzata Witkowska, Richard D Morgan and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.2field-weighted citation impact, top 50% 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

3 citing papers in PubMed, 6 citations in OpenAlex.

  1. Review
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  3. 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

14 authors at 2 institutions in 2 countries.

Piotr M SkowronDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Brian P AntonNew England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Edyta CzajkowskaDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Joanna ZebrowskaDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Ewa SuleckaDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Daria KrefftDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Joanna Jezewska-FrackowiakDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Olga ZolnierkiewiczDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Malgorzata WitkowskaDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
Richard D MorganNew England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Geoffrey G WilsonNew England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Alexey FomenkovNew England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Richard J RobertsNew England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Agnieszka Zylicz-StachulaDepartment of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
University of Gdańsk · PLNew England Biolabs (United States) · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Two restriction-modification systems have been previously discovered in Thermus aquaticus YT-1. TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves within the symmetric sequence 5'-TCGA-3'. TaqII, in contrast, is a 1105-aa Type IIC restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally reported to recognize two different asymmetric sequences: 5'-GACCGA-3' and 5'-CACCCA-3'. We previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli, and showed that TaqII recognizes the 5'-GACCGA-3' sequence only. Here, we report the discovery, isolation, and characterization of TaqIII, the third R-M system from T. aquaticus YT-1. TaqIII is a 1101-aa Type IIC/IIL enzyme and recognizes the 5'-CACCCA-3' sequence previously attributed to TaqII. The cleavage site is 11/9 nucleotides downstream of the A residue. The enzyme exhibits striking biochemical similarity to TaqII. The 93% identity between their aa sequences suggests that they have a common evolutionary origin. The genes are located on two separate plasmids, and are probably paralogs or pseudoparalogs. Putative positions and aa that specify DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family enzymes were predicted.

Indexed as

Nucleotide MotifsAmino Acid SequenceBacterial ProteinsCloning, MolecularDeoxyribonucleases, Type II Site-SpecificDNA CleavageEscherichia coliGene ExpressionIsoenzymesMolecular WeightPlasmidsRecombinant ProteinsSequence AlignmentSequence Homology, Amino AcidSubstrate SpecificityThermusBacterial ProteinsDeoxyribonucleases, Type II Site-Specificendodeoxyribonuclease TaqIIIsoenzymesRecombinant Proteins

Identifiers

PMID28911108
PMCPMC5587805
OpenAlexW2736013894

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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.