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Article: Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes

TitleCytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes
Authors
KeywordsBacterial genomes
C5 methyltransferase
C5-specific methylation
CpG deficiency
GC content
Recognition sites
Issue Date2004
PublisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00239
Citation
Journal Of Molecular Evolution, 2004, v. 58 n. 6, p. 692-700 How to Cite?
AbstractCpG dinucleotide deficiency has been found in viruses, mitochondria, prokaryotes, and eukaryotes. The consensual explanation is that it is due to deamination of methylated cytosines, as established for vertebrate and plants. However, we still do not know whether C5 cytosine methylation is also the major cause of CpG deficiency in bacteria. By combining annotation and experimental data identifying the presence of C5 cytosine methyltransferases with analysis of CpG relative abundance in 67 bacterial species, we found that CpG relative abundance in most bacterial genomes that have cytosine C5 methyltransferases tends to be in the normal range (observed/expected values between 0.82 and 1.21). In contrast, many bacterial species likely to be lacking C5 cytosine methylation showed CpG deficiency. Furthermore, when comparing genomes with one another, TpG and CpA relative abundances were found to be independent from CpG relative abundance. This contrasted with intragenome analyses, where C 3pG1 relative abundance (the subscripts refer to position of a nucleotide in a codon) was found to be generally positively correlated with T3pG1 relative abundances when plotted against GC content in protein coding sequences (CDSs). This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria.
Persistent Identifierhttp://hdl.handle.net/10722/84646
ISSN
2015 Impact Factor: 1.847
2015 SCImago Journal Rankings: 0.952
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorRocha, EPCen_HK
dc.contributor.authorLeung, FCCen_HK
dc.contributor.authorDanchin, Aen_HK
dc.date.accessioned2010-09-06T08:55:28Z-
dc.date.available2010-09-06T08:55:28Z-
dc.date.issued2004en_HK
dc.identifier.citationJournal Of Molecular Evolution, 2004, v. 58 n. 6, p. 692-700en_HK
dc.identifier.issn0022-2844en_HK
dc.identifier.urihttp://hdl.handle.net/10722/84646-
dc.description.abstractCpG dinucleotide deficiency has been found in viruses, mitochondria, prokaryotes, and eukaryotes. The consensual explanation is that it is due to deamination of methylated cytosines, as established for vertebrate and plants. However, we still do not know whether C5 cytosine methylation is also the major cause of CpG deficiency in bacteria. By combining annotation and experimental data identifying the presence of C5 cytosine methyltransferases with analysis of CpG relative abundance in 67 bacterial species, we found that CpG relative abundance in most bacterial genomes that have cytosine C5 methyltransferases tends to be in the normal range (observed/expected values between 0.82 and 1.21). In contrast, many bacterial species likely to be lacking C5 cytosine methylation showed CpG deficiency. Furthermore, when comparing genomes with one another, TpG and CpA relative abundances were found to be independent from CpG relative abundance. This contrasted with intragenome analyses, where C 3pG1 relative abundance (the subscripts refer to position of a nucleotide in a codon) was found to be generally positively correlated with T3pG1 relative abundances when plotted against GC content in protein coding sequences (CDSs). This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria.en_HK
dc.languageengen_HK
dc.publisherSpringer New York LLC. The Journal's web site is located at http://link.springer.de/link/service/journals/00239en_HK
dc.relation.ispartofJournal of Molecular Evolutionen_HK
dc.subjectBacterial genomesen_HK
dc.subjectC5 methyltransferaseen_HK
dc.subjectC5-specific methylationen_HK
dc.subjectCpG deficiencyen_HK
dc.subjectGC contenten_HK
dc.subjectRecognition sitesen_HK
dc.titleCytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0022-2844&volume=58&issue=6&spage=692&epage=700&date=2004&atitle=Cytosine+methylation+is+not+the+major+factor+inducing+CpG+dinucleotide+deficiency+in+bacterial+genomesen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/s00239-004-2591-1en_HK
dc.identifier.pmid15461426-
dc.identifier.scopuseid_2-s2.0-2942656774en_HK
dc.identifier.hkuros95445en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-2942656774&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume58en_HK
dc.identifier.issue6en_HK
dc.identifier.spage692en_HK
dc.identifier.epage700en_HK
dc.identifier.isiWOS:000222089700007-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWang, Y=8710320600en_HK
dc.identifier.scopusauthoridRocha, EPC=7102114167en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK
dc.identifier.scopusauthoridDanchin, A=7103235597en_HK

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