Identification and classification of bacterial plasmids

INTRODUCTION .................................................................................. 376 HISTORY OF PLASMID CLASSIFICATION ............................................................................376 PLASMID INCOMPATIBILITY .................................................................................. 376 BASIC REPLICONS, AN INTERLUDE .................................................................................. 377 INCOMPATIBILITY (CONTINUED) .................................................................................. 378 REPLICON TYPING................................................................................. 378 Choice and Development of a Bank of rep Probes .....................................................................378 Cloning of sequenced rep probes carrying incompatibility loci involved in copy number control.......379 Cloning of partly sequenced rep probes carrying incompatibility loci probably involved in copy number control ................................................................................. 379 Cloning of rep probes carrying unsequenced incompatibility loci ...............................................380 Analysis of Specificity of rep Probes .................................................................................. 380 Distribution of Replicons Having Similarity to Available rep Probes among Representative Plasmids Belonging to 27 Currently Recognized Incompatibility Groups ..................................381 Replicon typing of plasmids belonging to incompatibility groups with available probes...................381 Problem of IncX plasmids .................................................................................. 386 Replicon typing applied to plasmids belonging to incompatibility groups for which no probes are available ................................................................................. 386 Partition probes .................................................................................. 386 Replicon Typing of Virulence Plasmids Isolated from Bovine Enterotoxigenic E. coli (ETEC) Strains...387 DISCUSSION .................................................................................. 387 APPENDIX I .................................................................................. 387 Technical details of the replicon typing test .............................................................................387 Colony lysis and immobilization of DNA on filters.....................................................................389 Purification and labeling of probes .................................................................................. 389 Hybridization of the immobilized DNA with the labeled probes....................................................389 Nick-translational labeling of probe DNA with biotin and colorimetric detection of hybridization ........389 APPENDIX II ................................................................................. 389 Construction of a bank of hybrid plasmids carrying probes for replicons .......................................389 repFIA: inclrep functions ................................................................................. 389 repFIB: inc functions ................................................................................. 390 repFIC: inclrep functions .................................................................................. 390 repFIIA: inclrep functions .................................................................................. 390 rep9: inclrep functions .................................................................................. 390 repll: inclrep functions.................................................................................. 390 repB/O: inclrep functions .................................................................................. 390 repK: inc functions .................................................................................. 390 repHIl: inc functions .................................................................................. 390 repHI2: inc functions .................................................................................. 390 repL/M: inclrep functions.................................................................................. 390 repN: inc functions ................................................................................. 390 repP: inclrep functions ................................................................................. 391 repQ: inclrep functions .................................................................................. 391 repT: inclrep functions .................................................................................. 391 repU: inc functions .................................................................................. 391 repW: inclrep functions .................................................................................. 391 repX: inclrep functions .................................................................................. 391 repY: inclrep functions .................................................................................. 391 ACKNOWLEDGMENTS .................................................................................. 391 LITERATURE CITED .................................................................................. 391