Identifying targets of antibacterial compounds remains a challenging step in antibiotic development. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures, identified from directional biases in insertions, revealed known molecular targets and resistance mechanisms for the majority of these. Because single gene upregulation does not always confer resistance, we used a complementary machine learning approach to predict mechanism from inactivation mutant fitness profiles. This approach suggested the cell wall precursor Lipid II as the molecular target of the lysocins, a mechanism we have confirmed. We conclude that docking to membrane-anchored Lipid II precedes the selective bacteriolysis that distinguishes these lytic natural products, showing the utility of our approach for nominating antibiotic mechanism of action.

Bacteria are protected by a polymer of peptidoglycan that serves as an exoskeleton 1. In Staphylococcus aureus, the peptidoglycan assembly enzymes relocate during the cell cycle from the periphery, where they are active during growth, to the division site where they build the partition between daughter cells 2-4. But how peptidoglycan synthesis is regulated throughout the cell cycle is poorly understood 5,6. Here we used a transposon screen to identify a membrane protein complex that spatially regulates S. aureus peptidoglycan synthesis.

Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. We treated the libraries with daptomycin to assess whether the strain-dependent differences impact pathways important for survival. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, consistently promote survival under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains.

CHD1 is a conserved chromatin remodeling enzyme required for development and linked to prostate cancer in adults, yet its role in human cells is poorly understood. Here, we show that targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR), resulting in hypersensitivity to ionizing radiation as well as PARP and PTEN inhibition. CHD1 knockout cells show reduced H2AX phosphorylation (γH2AX) and foci formation as well as impairments in CtIP recruitment to the damaged sites. Chromatin immunoprecipitation following a single DSB shows that the reduced levels of γH2AX accumulation at DSBs in CHD1-KO cells are due to both a global reduction in H2AX incorporation and poor retention of H2AX at the DSBs. We also identified a unique N-terminal region of CHD1 that inhibits the DNA binding, ATPase, and chromatin assembly and remodeling activities of CHD1. CHD1 lacking the N terminus was more active in rescuing the defects in γH2AX formation and CtIP recruitment in CHD1-KO cells than full-length CHD1, suggesting the N terminus is a negative regulator in cells. Our data point to a role for CHD1 in the DSB repair process and identify a novel regulatory region of the protein.

13Bacteria are protected by a polymer of peptidoglycan that serves as an exoskeleton. In 14 Staphylococcus aureus, the enzymes that assemble peptidoglycan move during the cell cycle from 15 the periphery, where they are active during growth, to the division site where they build the 16 partition between daughter cells. But how peptidoglycan synthesis is regulated throughout the cell 17 cycle is not understood. Here we identify a membrane protein complex that spatially regulates S. 18 aureus peptidoglycan synthesis. This complex consists of an amidase that removes peptide chains 19 from uncrosslinked peptidoglycan and a partner protein that controls its activity. Typical amidases 20 act after cell division to hydrolyze peptidoglycan between daughter cells so they can separate. 21 130 peptidoglycan that is not, or at least not extensively, crosslinked. 131Slowing peptidoglycan synthesis rescues lytH deletion defects 132 We next investigated how LytH could regulate cell division. The division defects resulting 133 from lytH deletion implied LytH is important for FtsZ assembly. We found using a functional 134 FtsZ-sGFP fusion 5 that FtsZ is frequently mislocalized in ∆lytH cells ( Fig. 4a and Supplementary 135 157 misplaced septa or peripheral puncta ( Fig. 5a and Supplementary Fig. 14). By measuring the ratio 158

Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of gene essentiality across multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, become consistently essential under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains.Author summaryAntibiotic-resistant Staphylococcus aureus kills thousands of people every year in the United States alone. To stay ahead of the looming threat of multidrug-resistant infections, we must continue to develop new antibiotics and find ways of making our current repertoire of antibiotics more effective, including by finding pairs of compounds that perform best when administered together. In the age of next-generation sequencing, we can now use transposon sequencing to find potential targets for new antibiotics on a genome-wide scale, identified as either essential genes or genes that become essential in the presence of an antibiotic. In this work, we created a compendium of genes that are essential across a range of S. aureus strains, as well as those that are essential in the presence of the antibiotic daptomycin. The results will be a resource for researchers working to develop the next generation of antibiotic therapies.

Antibiotic resistance in bacterial pathogens is an ongoing public health concern. The arylomycins are a class of natural product antibiotics that target the type I signal peptidase, which carries out the terminal step in protein secretion.

The anticancer prodrug laromustine induces cytotoxic DNA damage and has had clinical success against acute myelogenous leukemia and glioblastoma multiforme. The causative DNA damage is principally a G-C interstrand crosslink preceded by 2-chloroethylation of guanine O6 by a subspecies of laromustine generated in situ upon base-catalyzed activation. Another cogenerated electrophile, methylisocyanate, contributes synergistically with the DNA alkylating activity towards cytotoxicity. Given this synergism, DNA repair enzymes are considered likely targets of methylisocyanate, which can carbamoylate amines and sulfhydryls. The inhibition of O6-alkylguanine-DNA alkyltransferase (AGT) and DNA polymerase beta by laroumustine's carbamoylating activity, observed in vitro, may contribute to cytotoxicity. To further investigate the relationship between laromustine and DNA repair, drug-induced changes in the transcription of 88 DNA repair genes were measured in cultured human promyelocytic (HL-60) cells using quantitative real-time reverse transcriptase PCR. Cells were treated with laromustine or vehicle for six hours before harvesting mRNA for analysis. The expression of a subset of the tested genes emerged as significantly different in cells treated with laromustine as compared to control cells. Included among those genes with significantly increased expression were: NTHL1 (17 fold), PARP1 (8 fold), and AGT (5 fold). Included among those genes with significantly decreased expression were: PARP2 (-5 fold) and MSH6 (-74 fold). Increased expression of NTHL1, which encodes for an N-glycosylase that can remove damaged guanine bases, may reduce the effectiveness of laromustine's alkylation of guanine O6. A strong negative correlation between the level of AGT activity in patient samples and the efficacy of laromustine has already been established. Some of the gene products identified in this study, such as NTHL1, may emerge as possible cotherapeutic targets or markers for clinical screening. Citation Format: Kristen N. Robinson, Kathryn A. Coe, Justin E. Owumi, Kevin P. Rice. Changes in expression of DNA repair genes in human leukemia cells treated with laromustine. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5498. doi:10.1158/1538-7445.AM2014-5498