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Control of directionality in integrase-mediated recombination: Examination of recombination directionality factors (RDFs) including Xis and Cox proteins

Lewis, JA and Hatfull, GF (2001) Control of directionality in integrase-mediated recombination: Examination of recombination directionality factors (RDFs) including Xis and Cox proteins. Nucleic Acids Research, 29 (11). 2205 - 2216. ISSN 0305-1048

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Similarity between the DNA substrates and products of integrase-mediated site-specific recombination reactions results in a single recombinase enzyme being able to catalyze both the integration and excision reactions. The control of directionality in these reactions is achieved through a class of small accessory factors that favor one reaction while interfering with the other. These proteins, which we will refer to collectively as recombination directionality factors (RDFs), play architectural roles in reactions catalyzed by their cognate recombinases and have been identified in conjunction with both tyrosine and serine integrases. Previously identified RDFs are typically small, basic and have diverse amino acid sequences. A subset of RDFs, the cox genes, also function as transcriptional regulators. We present here a compilation of all the known RDF proteins as well as those identified through database mining that we predict to be involved in conferring recombination directionality. Analysis of this group of proteins shows that they can be grouped into distinct subgroups based on their sequence similarities and that they are likely to have arisen from several independent evolutionary lineages. This compilation will prove useful in recognizing new proteins that confer directionality upon site-specific recombination reactions encoded by plasmids, transposons, phages and prophages.


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Lewis, JA
Hatfull, GFgfh@pitt.eduGFH
Date: 1 June 2001
Date Type: Publication
Journal or Publication Title: Nucleic Acids Research
Volume: 29
Number: 11
Page Range: 2205 - 2216
DOI or Unique Handle: 10.1093/nar/29.11.2205
Schools and Programs: Dietrich School of Arts and Sciences > Biological Sciences
Refereed: Yes
ISSN: 0305-1048
MeSH Headings: Amino Acid Sequence; Attachment Sites, Microbiological; Bacterial Proteins--metabolism; Bacteriophage P2--genetics; Bacteriophage P2--metabolism; Bacteriophage lambda--genetics; Bacteriophage lambda--metabolism; Binding Sites; DNA Nucleotidyltransferases--genetics; DNA Nucleotidyltransferases--metabolism; DNA-Binding Proteins--genetics; DNA-Binding Proteins--metabolism; Escherichia coli--genetics; Escherichia coli--metabolism; Evolution, Molecular; Integrases--metabolism; Integration Host Factors; Molecular Sequence Data; Phylogeny; Recombination, Genetic; Sequence Alignment; Sequence Homology, Amino Acid; Viral Proteins--genetics; Viral Proteins--metabolism
Other ID: NLM PMC55702
PubMed Central ID: PMC55702
PubMed ID: 11376138
Date Deposited: 19 Nov 2012 16:57
Last Modified: 28 Sep 2022 13:59


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