ArticleJournal of bacteriology2012
Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579.
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 19 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
19 citing papers in PubMed, 27 citations in OpenAlex.
- Structural analysis of the BisI family of modification dependent restriction endonucleases.Nucleic acids research · 2024Article
- Deciphering microbial gene function using natural language processing.Nature communications · 2022Article
- Article
- Article
- Article
- Type II Restriction of Bacteriophage DNA With 5hmdU-Derived Base Modifications.Frontiers in microbiology · 2019Article
- CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases.Nucleic acids research · 2017Article
- Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements.Journal of bacteriology · 2017Article
- Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference.Scientific reports · 2015Article
- Biochemical functional predictions for protein structures of unknown or uncertain function.Computational and structural biotechnology journal · 2015Review
- Article
- DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.Nucleic acids research · 2014Article
- Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity.BMC genomics · 2014Article
- Objective: biochemical function.Frontiers in genetics · 2014Article
- Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing.Biology direct · 2013Article
- Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease.Nucleic acids research · 2013Article
- The COMBREX project: design, methodology, and initial results.PLoS biology · 2013Article
- The methylomes of six bacteria.Nucleic acids research · 2012Article
- A mimicking-of-DNA-methylation-patterns pipeline for overcoming the restriction barrier of bacteria.PLoS genetics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genomes of two Bacillus cereus strains (ATCC 10987 and ATCC 14579) have been sequenced. Here, we report the specificities of type II/III restriction (R) and modification (M) enzymes. Found in the ATCC 10987 strain, BceSI is a restriction endonuclease (REase) with the recognition and cut site CGAAG 24-25/27-28. BceSII is an isoschizomer of AvaII (G/GWCC). BceSIII cleaves at ACGGC 12/14. The BceSIII C terminus resembles the catalytic domains of AlwI, MlyI, and Nt.BstNBI. BceSIV is composed of two subunits and cleaves on both sides of GCWGC. BceSIV activity is strongly stimulated by the addition of cofactor ATP or GTP. The large subunit (R1) of BceSIV contains conserved motifs of NTPases and DNA helicases. The R1 subunit has no endonuclease activity by itself; it strongly stimulates REase activity when in complex with the R2 subunit. BceSIV was demonstrated to hydrolyze GTP and ATP in vitro. BceSIV is similar to CglI (GCSGC), and homologs of R1 are found in 11 sequenced bacterial genomes, where they are paired with specificity subunits. In addition, homologs of the BceSIV R1-R2 fusion are found in many sequenced microbial genomes. An orphan methylase, M.BceSV, was found to modify GCNGC, GGCC, CCGG, GGNNCC, and GCGC sites. A ParB-methylase fusion protein appears to nick DNA nonspecifically. The ATCC 14579 genome encodes an active enzyme Bce14579I (GCWGC). BceSIV and Bce14579I belong to the phospholipase D (PLD) family of endonucleases that are widely distributed among Bacteria and Archaea. A survey of type II and III restriction-modification (R-M) system genes is presented from sequenced B. cereus, Bacillus anthracis, and Bacillus thuringiensis strains.
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.