Different structures of selected and unselected araB‐lacZ fusions

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Abstract
Summary: Formation of araB‐lacZ coding‐sequence fusions is a key adaptive mutation system. Eighty‐four independent araB‐lacZ fusions were sequenced. All fusions carried rearranged MuR linker sequences between the araB and lacZ domains indicating that they arose from the standard intermediate of the well‐characterized Mu DNA rearrangement process, the strand transfer complex (STC). Five non‐standard araB‐lacZ fusions isolated after indirect sib selection had novel structures containing back‐to‐back inverted MuR linkers. The observation that different isolation procedures gave rise to standard and non‐standard fusions indicates that cellular physiology can influence late steps in the multi‐step biochemical sequence leading to araB‐lacZ fusions. Each araB‐lacZ fusion contained two novel DNA junctions. The MuR‐lacZ junctions showed‘hot‐spotting’according to established rules for Mu target selection. The araB‐MuR and MuR‐MuR junctions all involved exchanges at regions of short sequence homology. More extensive homology between MuR and araB sequences indicates potential STC isomerization into a resolvable four‐way structure analogous to a Holliday junction. These results highlight the molecular complexity of araB‐lacZ fusion formation, which may be thought of as a multi‐step cell biological process rather than a unitary biochemical reaction.