TY - JOUR
T1 - A first global analysis of plasmid encoded proteins in the ACLAME database
AU - Leplae, Raphaël
AU - Lima-Mendez, Gipsi
AU - Toussaint, Ariane
PY - 2006/11
Y1 - 2006/11
N2 - Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed analysis of the plasmid sequence information, as illustrated by a network representation of the relationships between plasmids.
AB - Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed analysis of the plasmid sequence information, as illustrated by a network representation of the relationships between plasmids.
KW - ACLAME
KW - Global analysis
KW - Network
KW - Plasmid
KW - Protein family
UR - http://www.scopus.com/inward/record.url?scp=33750055232&partnerID=8YFLogxK
U2 - 10.1111/j.1574-6976.2006.00044.x
DO - 10.1111/j.1574-6976.2006.00044.x
M3 - Review article
C2 - 17064288
AN - SCOPUS:33750055232
SN - 0168-6445
VL - 30
SP - 980
EP - 994
JO - FEMS microbiology reviews
JF - FEMS microbiology reviews
IS - 6
ER -