{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:23:47Z","timestamp":1773660227428,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The Dam methyltransferase (DamMT) activity, broadly distributed in association with restriction endonucleases, as part of the restriction-modification defense systems, has evolved to become intimately associated with essential biological functions in a few organisms. In Escherichia coli, DamMT is involved in multiple aspects of DNA maintenance, replication initiation, daughter chromosome segregation, DNA mismatch repair, gene expression control, etc.<\/jats:p>\n               <jats:p>The participation of DamMT in such a diverse set of functions required that other genes adapted, or emerged through evolution, in response to the DamMT-induced modification of the genomic environment. One example is SeqA, a protein that senses the methylation status of the origin of replication of the chromosome to control the timing of replication initiation.<\/jats:p>\n               <jats:p>Interestingly, seqA is only present in a few DamMT-specifying proteobacteria. This observation led us to hypothesize that other genes, specifying related functions, might also be found in these organisms. To test this hypothesis, we implemented a large-scale comparative genomic screen meant to identify genes specifying DNA methylation sensing domains, probably involved in DNA maintenance functions.<\/jats:p>\n               <jats:p>Results: We carried out a phylogenetic analysis of DamMT, identifying two contrasting behaviors of the protein. Based on this phylogeny, we defined precisely a set of genomes, in which the protein activity is likely to be involved in DNA maintenance functions, the \u2018resident\u2019 dam genomes. We defined a second set of genomes, in which DamMT is not resident. We developped a new tool, \u2018DomainSieve\u2019, in order to screen these two sets for protein domains that are strictly associated with \u2018resident\u2019 dam genomes.<\/jats:p>\n               <jats:p>This approach was rewarding and generated a list of genes, among which some, at least, specify activities with clear linkage to DamMT-dependent DNA methylation and DNA maintenance.<\/jats:p>\n               <jats:p>Availability: DomainSieve is implemented as a web resource and is accessible at<\/jats:p>\n               <jats:p>Contact: \u00a0ferat@cgm.cnrs-gif.fr<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl336","type":"journal-article","created":{"date-parts":[[2006,6,21]],"date-time":"2006-06-21T03:47:02Z","timestamp":1150861622000},"page":"1935-1941","source":"Crossref","is-referenced-by-count":56,"title":["DomainSieve: a protein domain-based screen that led to the identification of <i>dam<\/i>-associated genes with potential link to DNA maintenance"],"prefix":"10.1093","volume":"22","author":[{"given":"Pierre","family":"Br\u00e9zellec","sequence":"first","affiliation":[{"name":"Laboratoire Statistique et G\u00e9nome du CNRS 2 \u00a0 2 \u00a0 \u00a0 Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France"}]},{"given":"Mark","family":"Hoebeke","sequence":"additional","affiliation":[{"name":"Laboratoire Statistique et G\u00e9nome du CNRS 2 \u00a0 2 \u00a0 \u00a0 Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France"}]},{"given":"Marie-Sophie","family":"Hiet","sequence":"additional","affiliation":[{"name":"Centre de G\u00e9n\u00e9tique Mol\u00e9culaire du CNRS 1 \u00a0 1 \u00a0 \u00a0 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France"},{"name":"Laboratoire Statistique et G\u00e9nome du CNRS 2 \u00a0 2 \u00a0 \u00a0 Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France"}]},{"given":"Sophie","family":"Pasek","sequence":"additional","affiliation":[{"name":"Laboratoire Statistique et G\u00e9nome du CNRS 2 \u00a0 2 \u00a0 \u00a0 Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France"}]},{"given":"Jean-Luc","family":"Ferat","sequence":"additional","affiliation":[{"name":"Centre de G\u00e9n\u00e9tique Mol\u00e9culaire du CNRS 1 \u00a0 1 \u00a0 \u00a0 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France"}]}],"member":"286","published-online":{"date-parts":[[2006,6,20]]},"reference":[{"key":"2023012409030105900_b1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012409030105900_b2","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409030105900_b3","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/0092-8674(90)90271-F","article-title":"E.coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork","volume":"62","author":"Campbell","year":"1990","journal-title":"Cell"},{"key":"2023012409030105900_b4","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012409030105900_b5","article-title":"PHYLIP (Phylogeny Inference Package) version 3.6","volume-title":"Department of Genome Sciences, University of Washington","author":"Felsenstein","year":"2004"},{"key":"2023012409030105900_b6","author":"Garrity","year":"2004","journal-title":"Taxonomic outline of the procaryotes, Bergey's Manual of systematic bacteriology"},{"key":"2023012409030105900_b7","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/S1568-7864(03)00024-7","article-title":"Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome","volume":"2","author":"Garibyan","year":"2003","journal-title":"DNA Repair (Amst)"},{"key":"2023012409030105900_b8","doi-asserted-by":"crossref","first-page":"4355","DOI":"10.1073\/pnas.84.13.4355","article-title":"Profile analysis: detection of distantly related proteins","volume":"84","author":"Gribskov","year":"1987","journal-title":"Proc. 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