Investigating protein–protein interfaces in bacterial transcription complexes: a fragmentation approach

Abstract

SummaryTranscription initiation by s 54 -RNA polymerase (RNAP) relies explicitly on a transient interaction with a complex molecular machine belonging to the AAAþ (ATPases associated with various cellular activities) superfamily. Members of the AAAþ superfamily convert chemical energy derived from NTP hydrolysis to a mechanical force used to remodel their target substrate. Recently Bordes and colleagues, (1) using a protein fragmentation approach, identified a unique sequence within s 54 -dependent transcriptional activators that constitutes a s 54 -binding interface. This interface is not static, but subject to nucleotide-dependent movement which may represent a common mechanism for controlling output that has been adopted by other AAAþ proteins. IntroductionDefining the types of strategy and the mechanisms used to control gene expression is important for a full understanding of how the genetic information stored within DNA can be unlocked. Elaborate signal pathways exist to ensure that genes are only expressed when required, thus enabling flexible adaptation in response to changing environmental conditions. At the heart of these pathways lie transcription factors, which regulate the activity of DNA-dependent RNA polymerase (RNAP), the central enzyme in gene expression. Bacterial RNAP is a multisubunit enzyme with subunit composition a 2 bb 0 o; In this 'core' form, the RNAP is catalytically competent but incapable of locating specific DNA target sequences,