Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.

In recent years, RNA has reemerged as a versatile biological macromolecule capable of performing an astonishing number of biochemical activities. Initially described as the ubiquitous but transient carrier of genetic information in the Central Dogma, RNA has surprised scientists with its capacity to store genetic information, catalyze biochemical reactions, protect telomeres, guide proteins to their targets, help DNA replication and protein synthesis, scaffold ribonucleoprotein complexes, and transmit developmental and epigenetic information through mitotic and even meiotic cell divisions. The latest surprise came during the past decade with advances in deep sequencing technologies, which uncovered the pervasive world of noncoding RNAs (ncRNAs). Functional analysis of ncRNAs has revealed their wide-spread use in several biological pathways including the ones in the nucleus. We now know that nuclear ncRNAs of various sizes facilitate genome stability by inhibiting spurious recombination among repetitive DNA elements, repressing mobilization of transposable elements (TEs), templating or bridging DNA double-strand breaks (DSBs) during repair, and directing developmentally-regulated genome rearrangements in some ciliates. In this paper, we will survey the known mechanisms with which nuclear ncRNAs directly contribute to the maintenance of genome stability and outline the major advances in our understanding of the role of ncRNAs in the nucleus. These studies reveal an unexpected range of mechanisms by which ncRNAs contribute to genome stability and even potentially influence evolution by acting as templates for genome modification.

Summary Quiescence (G0) is a ubiquitous stress response through which cells enter reversible dormancy, acquiring distinct properties including reduced metabolism, resistance to stress and long life. G0 entry involves dramatic changes to chromatin and transcription of cells, but the mechanisms coordinating these processes remain poorly understood. Using the fission yeast, here we track G0-associated chromatin and transcriptional changes temporally and show that as cells enter G0, their survival and global gene expression programs become increasingly dependent on Clr4/SUV39H, the sole histone H3 lysine 9 (H3K9) methyltransferase, and RNA interference (RNAi) proteins. Notably, G0 entry results in RNAi-dependent H3K9 methylation of several euchromatic pockets, prior to which Argonaute1-associated small RNAs from these regions emerge. Overall our data reveal a function for constitutive heterochromatin proteins (the establishment of the global G0 transcriptional program) and suggest that stress-induced alterations in Argonaute-associated sRNAs can target the deployment of transcriptional regulatory proteins to specific sequences.