Intracellular pathogens such as Mycobacterium tuberculosis have evolved strategies for coping with the pressures encountered inside host cells. The ability to coordinate global gene expression in response to environmental and internal cues is one key to their success. Prolonged survival and replication within macrophages, a key virulence trait of M. tuberculosis, requires dynamic adaptation to diverse and changing conditions within its phagosomal niche. However, the physiological adaptations during the different phases of this infection process remain poorly understood. To address this knowledge gap, we have developed a multi-tiered approach to define the temporal patterns of gene expression in M. tuberculosis in a macrophage infection model that extends from infection, through intracellular adaptation, to the establishment of a productive infection. Using a clock plasmid to measure intracellular replication and death rates over a 14-day infection and electron microscopy to define bacterial integrity, we observed an initial period of rapid replication coupled with a high death rate. This was followed by period of slowed growth and enhanced intracellular survival, leading finally to an extended period of net growth. The transcriptional profiles of M. tuberculosis reflect these physiological transitions as the bacterium adapts to conditions within its host cell. Finally, analysis with a Transcriptional Regulatory Network model revealed linked genetic networks whereby M. tuberculosis coordinates global gene expression during intracellular survival. The integration of molecular and cellular biology together with transcriptional profiling and systems analysis offers unique insights into the host-driven responses of intracellular pathogens such as M. tuberculosis. The impact of Mycobacterium tuberculosis on global health is undeniable, with ∼2 million deaths and ∼9 million new cases of tuberculosis each year. A key to the success of M. tuberculosis as a persistent, intracellular pathogen is its ability to survive for extended periods within professional phagocytes. Sustained growth within macrophage phagosomes requires avoiding or resisting antimicrobial mechanisms and adapting to replicate in a stressful, nutrient-restricted environment. Our understanding of the survival strategies, metabolism, and physiology of M. tuberculosis during intracellular growth remains incomplete. We employed multi-disciplinary approaches to gain new insights into adaptive responses that M. tuberculosis mobilizes to secure a productive infection. We simultaneously quantified replication and death rates, used electron microscopy to evaluate bacterial integrity, and determined the temporal changes in bacterial gene expression during a 14-day infection. By overlaying this temporal transcriptome dataset onto an extended Transcriptional Regulatory Network model, we identified regulatory pathways, stress responses, and metabolic adaptations activated during key physiological transitions over the 14 days of infection.

Signals modulating the production of Mycobacterium tuberculosis (Mtb) virulence factors essential for establishing long-term persistent infection are unknown. The WhiB3 redox regulator is known to regulate the production of Mtb virulence factors, however the mechanisms of this modulation are unknown. To advance our understanding of the mechanisms involved in WhiB3 regulation, we performed Mtb in vitro, intraphagosomal and infected host expression analyses. Our Mtb expression analyses in conjunction with extracellular flux analyses demonstrated that WhiB3 maintains bioenergetic homeostasis in response to available carbon sources found in vivo to establish Mtb infection. Our infected host expression analysis indicated that WhiB3 is involved in regulation of the host cell cycle. Detailed cell-cycle analysis revealed that Mtb infection inhibited the macrophage G₁/S transition, and polyketides under WhiB3 control arrested the macrophages in the G₀-G₁ phase. Notably, infection with the Mtb whiB3 mutant or polyketide mutants had little effect on the macrophage cell cycle and emulated the uninfected cells. This suggests that polyketides regulated by Mtb WhiB3 are responsible for the cell cycle arrest observed in macrophages infected with the wild type Mtb. Thus, our findings demonstrate that Mtb WhiB3 maintains bioenergetic homeostasis to produce polyketide and lipid cyclomodulins that target the host cell cycle. This is a new mechanism whereby Mtb modulates the immune system by altering the host cell cycle to promote long-term persistence. This new knowledge could serve as the foundation for new host-directed therapeutic discovery efforts that target the host cell cycle. Mycobacterium tuberculosis (Mtb) is responsible for the estimated 1.8 million people with tuberculosis. One of the reasons for the success of this pathogen is its ability to modulate the immune system and establish a persistent infection. The manner whereby the mycobacterium senses the environment and modulates the host immune system is poorly understood. In this study, we used transcriptional analyses of both Mtb and the infected macrophage to ascertain mechanisms whereby Mtb adapts to and resides in macrophages. We found that WhiB3, a redox sensor in Mtb that controls virulence lipid production, is also involved in modulating the mycobacterium’s energy metabolic pathways in response to available carbon sources. As redox homeostasis regulates the virulent lipid production in Mtb, and the oxido-reductive homeostasis is tightly coupled with bioenergetic homeostasis, the virulent lipid production will be dependent on bioenergetic homeostasis. From the host’s perspective, transcriptional analysis revealed that Mtb regulates the macrophage’s cell cycle and comprehensive cell cycle analysis indicated that Mtb arrested the macrophages’ cell cycle. We discovered that polyketides under Mtb WhiB3 control were responsible for this cell cycle arrest that will potentially modulate the immune response to this intracellular pathogen. These studies reveal a novel strategy of targeting the host cell cycle for chemotherapeutic intervention.

The dormant phenotype acquired by Mycobacterium tuberculosis (Mtb) during infection poses a major challenge in disease treatment since these bacilli are tolerant to front-line drugs. Therefore, it is imperative to find novel compounds that effectively kill dormant bacteria. By screening 4,400 marine natural product samples against dual-fluorescent Mtb under both replicating and non-replicating conditions we have identified compounds that are selectively active against dormant Mtb. This validates our strategy of screening all compounds in both assays as opposed to using the dormancy model as a secondary screen. Bioassay guided deconvolution enabled the identification of unique pharmacophores active in each screening model. To confirm the activity of samples against dormant Mtb we used a luciferase reporter assay and CFU enumeration. The structures of five purified active compounds were defined by NMR and mass spectrometry. We identified two lipid compounds with potent activity towards dormant and actively growing Mtb. One of these was commercially obtained and showed similar activity against Mtb in both screening models. Furthermore, puupehenone-like molecules were purified with potent and selective activity against dormant Mtb. In conclusion, we have identified and characterized antimycobacterial compounds from marine organisms with novel activity profiles which appear to target Mtb pathways conditionally essential for dormancy survival.

Mycobacterium abscessus (Mab) is a non-tuberculous mycobacterium that causes pulmonary and non-pulmonary infections. Mab is resistant to many chemotherapeutic agents and the current treatment options show poor clinical outcomes. Thus, there is a dire need to find new antimicrobials effective at killing Mab. Screening drug libraries to identify potential antimicrobials has been impeded by the lack of validated HTS assays for Mab. In this study, we developed two 384-well high-throughput screening assays using fluorescent and bioluminescent reporter strains of Mab for drug discovery. Optimization of inoculum size, incubation time and the volume-per-well based on Z-factor and signal intensity yielded two complementary, robust tools for Mab drug discovery with Z-factor > 0.8. The MIC of known drugs, amikacin and clarithromycin, as determined by bioluminescence was in agreement with the published MIC values. A proof-of-concept screen of 2,093 natural product-inspired compounds was conducted using the 384-well bioluminescent assay to identify novel scaffolds active against Mab. Five active “hit” compounds identified in this pilot screen were confirmed and characterized by a CFU assay and MIC determination. Overall, we developed and validated a 384-well screen that offers simple, sensitive and fast screening of compounds for activity against this emerging pathogen. To our knowledge, this is the first reporter–based high-throughput screening study aimed at Mab drug discovery.

Mycobacterium abscessus (Mab), an emerging opportunistic pathogen, predominantly infects individuals with underlying pulmonary diseases such as cystic fibrosis (CF). Current treatment outcomes for Mab infections are poor due to Mab’s inherent antibiotic resistance and unique host interactions that promote phenotypic tolerance and hinder drug access. The hypoxic, mucus-laden airways in the CF lung and antimicrobial phagosome within macrophages represent hostile niches Mab must overcome via alterations in gene expression for survival. Regulatory mechanisms important for the adaptation and long-term persistence of Mab within the host are poorly understood, warranting further genetic and transcriptomics study of this emerging pathogen. DosRS_Mab, a two-component signaling system (TCS), is one proposed mechanism utilized to subvert host defenses and counteract environmental stress such as hypoxia. The homologous TCS of Mycobacterium tuberculosis (Mtb), DosRS_Mtb, is known to induce a ~50 gene regulon in response to hypoxia, carbon monoxide (CO) and nitric oxide (NO) in vitro and in vivo. Previously, a small DosR_Mab regulon was predicted using bioinformatics based on DosR_Mtb motifs however, the role and regulon of DosRS_Mab in Mab pathogenesis have yet to be characterized in depth. To address this knowledge gap, our lab generated a Mab dosRS knockout strain (Mab_ΔdosRS) to investigate differential gene expression, and phenotype in an in vitro hypoxia model of dormancy. qRT-PCR and lux reporter assays demonstrate Mab_dosR and 6 predicted downstream genes are induced in hypoxia. In addition, RNAseq revealed induction of a much larger hypoxia response comprised of >1000 genes, including 127 differentially expressed genes in a dosRS mutant strain. Deletion of DosRS_Mab led to attenuated growth under low oxygen conditions, a shift in morphotype from smooth to rough, and down-regulation of 216 genes. This study provides the first look at the global transcriptomic response of Mab to low oxygen conditions encountered in the airways of CF patients and within macrophage phagosomes. Our data also demonstrate the importance of DosRS_Mab for adaptation of Mab to hypoxia, highlighting a distinct regulon (compared to Mtb) that is significantly larger than previously described, including both genes conserved across mycobacteria as well as Mab-specific genes.

A deep-water sponge of the genus Spongosorites has yielded a bis-indole alkaloid which we have named dragmacidin G. Dragmacidin G was first reported by us in the patent literature and has recently been reported by Hitora et al. from a sponge of the genus Lipastrotheya. Dragmacidin G is the first in this series of compounds to have a pyrazine ring linking the two indole rings. It also has a rare N-(2-mercaptoethyl)-guanidine side chain. Dragmacidin G shows a broad spectrum of biological activity including inhibition of methicillin-resistant Staphylococcus aureus, Mycobacterium tuberculosis, Plasmodium falciparum, and a panel of pancreatic cancer cell lines.