A simple method for genome-wide screening for advantageous insertions of mobile DNAs in Escherichia coli

被引:18
作者
Edwards, RJ [1 ]
Sockett, RE [1 ]
Brookfield, JFY [1 ]
机构
[1] Univ Nottingham, Genet Inst, Queens Med Ctr, Nottingham NG7 2UH, England
关键词
D O I
10.1016/S0960-9822(02)00837-0
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Laboratory evolution in Escherichia coli has revealed that fitness typically increases in experimental populations [1, 2]. These changes are sometimes associated with changes in insertion sequence positions, some of which may themselves cause advantageous phenotypes [3, 4]. We have a novel and general method for identifying genes in Escherichia coli, whose knockout by mobile DNA insertions is beneficial in experimental evolution. Insertion sites in favored clones can be identified by reference to genomic information. We have implemented the method using modified Tn10 transposons bearing kanamycin and chloramphenicol resistance cassettes. Results are consistent across replicated experiments, demonstrating that the insertions are themselves creating selective advantages, rather than hitch-hiking with favorable base substitutions. The successful clones have subsequently been confirmed to have a fitness advantage relative to the progenitor strain. In experiments in shaking culture, we find that advantageous insertions usually fall in operons required in the pathways creating flagella. The method allows a rapid genome-wide screening for advantageous insertions in arbitrary environmental conditions. It allows investigation of the extent to which transient mutations generating environment-dependent selective advantages may help to explain the persistence of mobile DNAs in primarily clonal organisms, such as E. coli.
引用
收藏
页码:863 / 867
页数:5
相关论文
共 10 条
[1]   The complete genome sequence of Escherichia coli K-12 [J].
Blattner, FR ;
Plunkett, G ;
Bloch, CA ;
Perna, NT ;
Burland, V ;
Riley, M ;
ColladoVides, J ;
Glasner, JD ;
Rode, CK ;
Mayhew, GF ;
Gregor, J ;
Davis, NW ;
Kirkpatrick, HA ;
Goeden, MA ;
Rose, DJ ;
Mau, B ;
Shao, Y .
SCIENCE, 1997, 277 (5331) :1453-+
[2]   Distribution of fitness effects caused by random insertion mutations in Escherichia coli [J].
Elena, SF ;
Ekunwe, L ;
Hajela, N ;
Oden, SA ;
Lenski, RE .
GENETICA, 1998, 102-3 (0) :349-358
[3]  
HICKEY DA, 1982, GENETICS, V101, P519
[4]  
KLECKNER N, 1991, METHOD ENZYMOL, V204, P139
[5]   LONG-TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA-COLI .1. ADAPTATION AND DIVERGENCE DURING 2,000 GENERATIONS [J].
LENSKI, RE ;
ROSE, MR ;
SIMPSON, SC ;
TADLER, SC .
AMERICAN NATURALIST, 1991, 138 (06) :1315-1341
[6]  
MCNAB RM, 1987, FLAGELLA ESCHERICHIA, P70
[7]   Genomic evolution during a 10,000-generation experiment with bacteria [J].
Papadopoulos, D ;
Schneider, D ;
Meier-Eiss, J ;
Arber, W ;
Lenski, RE ;
Blot, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (07) :3807-3812
[8]  
Sambrook J., 1989, MOL CLONING
[9]  
Schneider D, 2000, GENETICS, V156, P477
[10]   EXPERIMENTAL TESTS OF THE ROLES OF ADAPTATION, CHANCE, AND HISTORY IN EVOLUTION [J].
TRAVISANO, M ;
MONGOLD, JA ;
BENNETT, AF ;
LENSKI, RE .
SCIENCE, 1995, 267 (5194) :87-90