A first global analysis of plasmid encoded proteins in the ACLAME database

被引:35
作者
Leplae, Raphael [1 ]
Lima-Mendez, Gipsi [1 ]
Toussaint, Ariane [1 ]
机构
[1] Univ Libre Bruxelles, SCMBB, B-1050 Brussels, Belgium
关键词
plasmid; protein family; global analysis; ACLAME; network;
D O I
10.1111/j.1574-6976.2006.00044.x
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
引用
收藏
页码:980 / 994
页数:15
相关论文
共 51 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]   Birth and death of orphan genes in Rickettsia [J].
Amiri, H ;
Davids, W ;
Andersson, SGE .
MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (10) :1575-1587
[3]   GenBank [J].
Benson, DA ;
Karsch-Mizrachi, I ;
Lipman, DJ ;
Ostell, J ;
Wheeler, DL .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D34-D38
[4]   Agrobacterium VirB10, an ATP energy sensor required for type IV secretion [J].
Cascales, E ;
Christie, PJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (49) :17228-17233
[5]   A bacterial genome in flux:: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi [J].
Casjens, S ;
Palmer, N ;
van Vugt, R ;
Huang, WM ;
Stevenson, B ;
Rosa, P ;
Lathigra, R ;
Sutton, G ;
Peterson, J ;
Dodson, RJ ;
Haft, D ;
Hickey, E ;
Gwinn, M ;
White, O ;
Fraser, CM .
MOLECULAR MICROBIOLOGY, 2000, 35 (03) :490-516
[6]   The pKO2 linear plasmid prophage of Klebsiella oxytoca [J].
Casjens, SR ;
Gilcrease, EB ;
Huang, WM ;
Bunny, KL ;
Pedulla, ML ;
Ford, ME ;
Houtz, JA ;
Hatfull, GF ;
Hendrix, RW .
JOURNAL OF BACTERIOLOGY, 2004, 186 (06) :1818-1832
[7]  
CHANDLER M, 2003, INSERTION SEQUENCES, P305
[8]   A MULTIDRUG-RESISTANCE REGULATORY CHROMOSOMAL LOCUS IS WIDESPREAD AMONG ENTERIC BACTERIA [J].
COHEN, SP ;
YAN, W ;
LEVY, SB .
JOURNAL OF INFECTIOUS DISEASES, 1993, 168 (02) :484-488
[9]   Assembly and function of type III secretory systems [J].
Cornelis, GR ;
Van Gijsegem, F .
ANNUAL REVIEW OF MICROBIOLOGY, 2000, 54 :735-774
[10]   The protelomerase of temperate Escherichia coli phage N15 has cleaving-joining activity [J].
Deneke, J ;
Ziegelin, G ;
Lurz, R ;
Lanka, E .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (14) :7721-7726