5 The role of quorum-sensing in the virulence of Pseudomonas ...

3 Analysis of genomic islands captured using yeast-based
technology: the genomic island capture technique
3 ANALYSIS OF GENOMIC ISLANDS CAPTURED USING YEAST-BASED
TECHNOLOGY: THE GENOMIC ISLAND CAPTURE TECHNIQUE 51
3.1 CAPTURE EXPERIMENTS INVOLVING GENOME SEQUENCED BACTERIAL STRAINS 53
3.1.1 K12 MG1655–SERW 54
3.1.2 K12 MG1655–LEUX 55
3.1.3 PAO1-LYS10 AND PA14-LYS10 56
3.1.4 PA14-LYS47 56
3.2 CAPTURE EXPERIMENTS INVOLVING CLINICAL BACTERIAL STRAINS 58
3.2.1 KR115-LYS10 AND KR159-LYS10 59
3.2.2 E105-SERT 59
3.3 E106-SERW 60
3.3.1 STRUCTURE OF THE E106-SERW 63
3.3.2 ANALYSIS OF E106-SERW CRISPR SYSTEM 67
3.4 E105-LEUX 70
3.4.1 DEFINING E105-LEUX AS A GENOMIC ISLAND (ISLET) 75
3.4.2 THE GENOMIC STRUCTURE OF THE E105-LEUX GENOMIC ISLET 78
3.4.3 EVOLUTION OF THE E105-LEUX GENOMIC ISLET 84
3.5 DISCUSSION 86
3.5.1 GENOMIC ISLAND CAPTURE AS A YEAST-BASED TECHNOLOGY 86
3.5.2 GENOMIC ISLAND CAPTURE AS A GENOMIC ISLAND DISCOVERY TOOL 90
3.6 CONCLUSION AND FURTHER WORK 92
51