This chapter presents an analysis of the organization and distribution of the IS200/IS605 family of insertion sequences (IS). Members of this family are widespread in both bacteria and archaea. They are unusual because they use obligatory single-strand DNA intermediates, which distinguishes them from classical IS. We summarize studies of the experimental model systems IS608 (from Helicobacter pylori) and ISDra2 (from Deinococcus radiodurans) and present biochemical, genetic, and structural data that describe their transposition pathway and the way in which their transposase (an HuH rather than a DDE enzyme) catalyzes this process. The transposition of IS200/IS605 family members can be described as a "Peel-and-Paste" mechanism. We also address the probable domestication of IS200/IS605 family transposases as enzymes involved in multiplication of repeated extragenic palindromes and as potential homing endonucleases in intron-IS chimeras.

Xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. To adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ECF) factors. The alternative sigma factor E , encoded by rpoE, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. Here, we combine different approaches to investigate the role and mechanism of E -dependent activation in X. campestris pv. campestris. We show that the rpoE gene is organized as a single transcription unit with the anti-gene rseA and the protease gene mucD and that rpoE transcription is autoregulated. rseA and mucD transcription is also controlled by a highly conserved E -dependent promoter within the E gene sequence. The E -mediated stress response is required for stationary-phase survival, resistance to cadmium, and adaptation to membrane-perturbing stresses (elevated temperature and ethanol). Using microarray technology, we started to define the E regulon of X. campestris pv. campestris. These genes encode proteins belonging to different classes, including periplasmic or membrane proteins, biosynthetic enzymes, classical heat shock proteins, and the heat stress factor H . The consensus sequence for the predicted E -regulated promoter elements is GGAACTN 15-17 GTCNNA. Determination of the rpoH transcription start site revealed that rpoH was directly regulated by E under both normal and heat stress conditions. Finally, E activity is regulated by the putative regulated intramembrane proteolysis (RIP) proteases RseP and DegS, as previously described in many other bacteria. However, our data suggest that RseP and DegS are not only dedicated to RseA cleavage and that the proteolytic cascade of RseA could involve other proteases.Bacteria often encounter diverse and rapidly changing environments. To overcome harmful situations, they must be capable of sensing external changes and transmitting this information across biological membranes into the cell, which results in the appropriate redirection of gene expression to prevent or repair cellular damages caused by stress. Extracytoplasmic function (ECF) factors provide one common means of bacterial signal transduction to regulate gene expression in response to various extracellular changes (65). ECF factors represent the largest and most diverse subfamily of 70 proteins. They generally recognize a Ϫ35 box with a clear bias toward a GAAC in their target promoters, while the Ϫ10 region tends to be highly variable between ECF subfamily members (65). One of the best-studied ECF factors is the key regulator of the extracytoplasmic stress response factor E from Escherichia coli, encoded by the rpoE gene (56). ECF proteins were recently divided into 43 major phylogenetically distinct groups named ECF01 to ECF43 (65). RpoE-like ECF factors are part of one predominant subgroup found in most b...