@article {140655, title = {Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria.}, journal = {PLoS Biol}, volume = {22}, year = {2024}, month = {2024 Mar 11}, pages = {e3002540}, abstract = {

DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002540}, author = {Kamat, Aditya and Tran, Ngat T and Sharda, Mohak and Sontakke, Neha and Le, Tung B K and Badrinarayanan, Anjana} } @article {121911, title = {Mechanistic insight into the repair of C8-linked pyrrolobenzodiazepine monomer-mediated DNA damage.}, journal = {RSC Med Chem}, volume = {13}, year = {2022}, month = {2022 Dec 14}, pages = {1621-1633}, abstract = {

Pyrrolobenzodiazepines (PBDs) are naturally occurring DNA binding compounds that possess anti-tumor and anti-bacterial activity. Chemical modifications of PBDs can result in improved DNA binding, sequence specificity and enhanced efficacy. More recently, synthetic PBD monomers have shown promise as payloads for antibody drug conjugates and anti-bacterial agents. The precise mechanism of action of these PBD monomers and their role in causing DNA damage remains to be elucidated. Here we characterized the damage-inducing potential of two C8-linked PBD bi-aryl monomers in and investigated the strategies employed by cells to repair the same. We show that these compounds cause DNA damage and efficiently kill bacteria, in a manner comparable to the extensively used DNA cross-linking agent mitomycin-C (MMC). However, in stark contrast to MMC which employs a mutagenic lesion tolerance pathway, we implicate essential functions for error-free mechanisms in repairing PBD monomer-mediated damage. We find that survival is severely compromised in cells lacking nucleotide excision repair and to a lesser extent, in cells with impaired recombination-based repair. Loss of nucleotide excision repair leads to significant increase in double-strand breaks, underscoring the critical role of this pathway in mediating repair of PBD-induced DNA lesions. Together, our study provides comprehensive insights into how mono-alkylating DNA-targeting therapeutic compounds like PBD monomers challenge cell growth, and identifies the specific mechanisms employed by the cell to counter the same.

}, issn = {2632-8682}, doi = {10.1039/d2md00194b}, author = {Joseph, Asha Mary and Nahar, Kazi and Daw, Saheli and Hasan, Md Mahbub and Lo, Rebecca and Le, Tung B K and Rahman, Khondaker Miraz and Badrinarayanan, Anjana} } @article {17320, title = {Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB.}, journal = {PLoS Genet}, volume = {13}, year = {2017}, month = {2017 May 10}, pages = {e1006783}, abstract = {

In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1006783}, author = {Badrinarayanan, Anjana and Le, Tung B K and Spille, Jan-Hendrik and Cisse, Ibrahim I and Laub, Michael T} }