We are analyzing https://link.springer.com/article/10.1186/1759-8753-3-6.

Title:
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes | Mobile DNA
Description:
Background Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes. Results A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of α- and β-proteobacteria. Conclusions The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer.
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Keywords {🔍}

pubmed, proteins, famint, article, tbssrs, plasmid, google, scholar, families, cas, tbssr, protein, plasmids, table, elements, bacterial, rit, family, sitespecific, central, sequence, encoded, mobile, dna, genes, sequences, types, related, copies, annotation, recombinases, clusters, genomes, mge, aclame, set, conserved, predicted, multiple, recombination, phage, transposons, data, enzymes, genetic, prophage, additional, file, analysis, type,

Topics {✒️}

tyrosine-based site-specific recombinases tyrosine-based site-specific recombinase cre-loxp site-specific recombination article download pdf mobile genetic element view=genome&id=mge shufflon-specific dna recombinase open access article plasmid di-multi-mers de-novo assembly tools site-specific transposon tn554 conserved aspartate-glutamate-aspartate potential catalytic motif long n-terminal extension intra-cluster clustering coefficient α-proteobacterium novosphingobium aromaticivorans pilv-specific cell aggregates gipsi lima-mendez replicative transposition 4-chlorobiphenyl-catabolic transposon tn4371 antonie van leeuwenhoek putative catalytic sites author information authors large serine recombinases bacterial hosts based catalyzing integration/excision reactions /perl/aclame/genomes/prot_view dna breaking-rejoining enzymes site-specific recombination mobile genetic elements full size image integrate inci1 plasmids colib-p9 privacy choices/manage cookies c-terminal end c-terminal segments search tyrosine recombinases sherratt dj catalytic motif integrated conjugative elements open reading frames constant n-terminal catalyze integration/excision reactions mercury resistance genes multiple sequence comparison aureus tn554-related transposons insertion site supports mobile dna ii biomed central

Questions {❓}

Casjens S: Prophages and bacterial genomics: what have we learned so far?
Plasmid resolvases?

Schema {🗺️}

WebPage:
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         headline:Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
         description:Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes. A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of α- and β-proteobacteria. The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer.
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            Catalytic Motif
            Integrate Conjugative Element
            Replicative Transposition
            Plasmid Protein
            Human Genetics
            Animal Genetics and Genomics
            Plant Genetics and Genomics
            Developmental Biology
            Microbiology
            Microbial Genetics and Genomics
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      headline:Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
      description:Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes. A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of α- and β-proteobacteria. The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer.
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         Catalytic Motif
         Integrate Conjugative Element
         Replicative Transposition
         Plasmid Protein
         Human Genetics
         Animal Genetics and Genomics
         Plant Genetics and Genomics
         Developmental Biology
         Microbiology
         Microbial Genetics and Genomics
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      name:Research Group of Bioinformatics and (Eco-)systems Biology, Microbiology Unit (MICR), Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
      name:Unit of Microbiology (MIC), Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200 Mol, Belgium
      name:Laboratoire Bioinformatique des Génomes et Réseaux (BiGRe), Université Libre de Bruxelles, Bvd du Triomphe, Bruxelles, Belgium

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