Mycobacterium abscessus DosRS two-component system controls a species-specific regulon required for adaptation to hypoxia

Pathogenicity and virulence of Mycobacterium abscessus

Non-tuberculous mycobacteria (NTM), such as Mycobacterium abscessus (Mab) are an increasing cause of human disease. While the majority of immunocompetent hosts control Mab infections, the robust survival of Mab within the environment has shaped survival in human cells to help drive persistence and cause inflammatory damage in susceptible individuals. With high intrinsic resistance to antibiotics, there is an important need to fully understand how Mab causes infection, define protective host pathways that control disease, and develop new strategies to treat those at high risk. This review will examine the existing literature related to host-Mab interactions with a focus on virulence, the host response, and therapy development. The goal is to highlight key gaps in our understanding and describe novel approaches to encourage new research avenues that better define the pathogenesis and host response against this increasingly important human pathogen.

Synthesis and anti-mycobacterial activity of novel medium-chain β-lactone derivatives: a multi-target strategy to combat Mycobacterium abscessus

The constant emergence of drug-resistant mycobacteria, together with the lack of new antibiotics entering the market, has become a global public health problem that threatens the effective treatment of infectious diseases. The development of single molecules targeting different proteins should significantly reduce the emergence of resistant strains, and therefore represent a promising strategy to overcome such an issue. In this challenging context, a new series of 30 lipophilic compounds based on the β-lactone-core has been synthesized by varying the nature of the substituents on the lactone ring. The evaluation of their antibacterial activity against M. tuberculosis and M. abscessus, two major pathogenic mycobacteria, highlighted potential candidates. The VM038, VM040 and VM045 were active only against M. tuberculosis, while VM025, VM026 and VM043 inhibited the growth of both M. tuberculosis and the S and R variants of M. abscessus. Competitive click chemistry activity-based protein profiling revealed several potential M. abscessus target enzymes of VM043, the best extracellular growth inhibitor. Finally, when tested against intracellular bacteria, although VM043 was found inactive, VM025 & VM026 proved to be potent and promising inhibitors of intramacrophagic M. abscessus growth with minimal inhibitory concentrations (MIC50Raw) comparable to the standard antibiotic imipenem. Overall, these results strengthen the added value of our VM β-lactone derivatives not only in the fight against pathogenic mycobacteria, leading to the arrest of M. abscessus and/or M. tuberculosis growth through multitarget enzyme inhibition, but also as efficient probes to identify novel potential therapeutic targets using chemoproteomics approaches.

A Simple In Vitro Method to Determine Bactericidal Activity Against Mycobacterium abscessus Under Hypoxic Conditions

Background/Objectives: Non-replicating persisters (NRPs) of Mycobacterium abscessus are a bacterial subpopulation that can survive in the host under unfavorable conditions, such as hypoxia or nutrient starvation. The eradication of these bacteria is difficult, which is one reason for the long treatment duration and treatment failure. The drug discovery process should therefore contain methods to screen activity against NRPs. Methods: A hypoxic environment is used to generate NRPs of M. abscessus that are termed low-oxygen persisters (LOPs). For this, an oxidation process is used to transition a replicating culture of M. abscessus distributed in microtiter plates within a sealable box into LOPs. Colony counting, automated object counting, bactericidal activity determination of known agents, and confocal laser scanning microscopy are used to study the obtained culture. Results: The obtained culture shows typical attributes of non-replicating cells, such as significantly reduced replication, the reversibility of the LOP state under aerobic conditions, delayed regrowth on solid medium, altered morphological patterns on a single-cell level, and phenotypical resistance against a variety of clinically relevant antimycobacterial compounds. The study reveals metronidazole and niclosamide as bactericidal against M. abscessus LOPs. These compounds can be used as LOP verification compounds within the described model. Conclusions: Our model is easily implemented and quickly identifies compounds that are inactive under hypoxic conditions. It can therefore accelerate the identification of clinically effective antimycobacterial drug substances, and can be a helpful tool during the drug development process.

The DosR regulon of Mycobacterium avium and adaptation to hypoxia

Like other tuberculous and nontuberculous mycobacterial pathogens of human lung such as Mycobacterium tuberculosis and M. abscessus, M. avium is likely exposed to a variety of stressors during infection, including hypoxic conditions inside activated macrophages and in the avascular necrotic regions of granulomas. How M. avium survives hypoxic stress to establish a chronic infection is currently not well understood. Using RNA-sequencing, we here show that M. avium grown under progressive microaerophilic conditions activates more than 4-fold a subset of 16 genes, the expression of 13 of which is dependent on the two-component system regulator DosRS. A subset of M. avium DosR regulon genes was confirmed to also be activated upon exposure to nitric oxide. Although a second sensor kinase besides DosS has been proposed to function with the transcriptional regulator DosR in M. avium, we show that this other kinase cannot compensate for a deficiency in DosS. Loss of dosRS expression in M. avium led to a significant reduction in viability under hypoxia that was more marked at acidic than at neutral pH. Unlike the situation in M. abscessus, however, loss of DosRS did not significantly impact the ability of M. avium to establish a drug tolerant state in vitro or form biofilms under host relevant conditions. Collectively, these results are suggestive of a lesser impact of DosRS on the ability of M. avium to develop antibiotic tolerance compared to other nontuberculous mycobacteria. The M. avium dosRS mutant further showed no signs of virulence attenuation in murine macrophages and in chronically infected immunocompetent BALB/c mice.

Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis

The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.

Distinct gene expression patterns of mono-isoniazid resistant Mycobacterium tuberculosis uncover divergent responses to isoniazid in host-mimicked condition

Isoniazid stands as a frontline antibiotic utilized in the treatment of tuberculosis (TB), predominantly impacting the mycolic acid component within the cell wall of Mycobacterium tuberculosis (Mtb). It also affects the formation of lipoarabinomannan (LAM), an essential glycolipid in the cell envelope of Mtb. Despite the effectiveness of antibiotics for TB treatment, drug tolerance development in mycobacteria frequently stems from their adaptation to the hostile environment within the host, leading to treatment failure. Herein, we investigate mycobacterial adaptation to the isoniazid exposure in the host-mimicked conditions by focusing on the stress response genes (virS, icl1, whiB3, tgs1) and LAM-related genes (lprG, p55, lmeA, mptA, embC). Mtb H37Rv and mono-isoniazid resistant (INH-R) strains were cultivated in the host-mimicked multi-stress condition (MS) with or without isoniazid and the relative expressions of these gene candidates were measured using real-time PCR. In the INH-R strain, treatment with isoniazid in multi-stress conditions caused significant upregulation of tgs1, and LAM precursor-lipomannan (LM) synthesis and its transport genes (lprG, p55, lmeA, embC). In the case of H37Rv, all LAM-related genes and tgs1 were downregulated whereas other stress response genes were upregulated, remarkably in icl1 and whiB3. These findings highlight differences in gene expression patterns between drug-sensitive and resistant strains in multi-stress environments with drug pressure. Notably, stress response genes, particularly tgs1, may play a crucial role in regulating LAM production in the INH-R strain in response to isoniazid exposure. This study enhances our understanding of the mechanisms underlying drug resistance, offering valuable insights that could contribute to the development of new strategies for treating and eliminating TB.

Atypical Mycobacterium abscessus BlaRI Ortholog Mediates Regulation of Energy Metabolism but Not β-Lactam Resistance

Mycobacterium abscessus (Mab) is highly drug resistant, and understanding regulation of antibiotic resistance is critical to future antibiotic development. Regulatory mechanisms controlling Mab's β-lactamase (BlaMab) that mediates β-lactam resistance remain unknown. S. aureus encodes a prototypical protease-mediated two-component system BlaRI regulating the β-lactamase BlaZ. BlaR binds extracellular β-lactams, activating an intracellular peptidase domain which cleaves BlaI to derepress blaZ. Mycobacterium tuberculosis (Mtb) encodes homologs of BlaRI (which we will denote as BlaIR to reflect the inverted gene order in mycobacteria) that regulate not only the Mtb β-lactamase, blaC, but also additional genes related to respiration. We identified orthologs of blaIRMtb in Mab and hypothesized that they regulate blaMab. Surprisingly, neither deletion of blaIRMab nor overexpression of only blaIMab altered blaMab expression or β-lactam susceptibility. However, BlaIMab did bind to conserved motifs upstream of several Mab genes involved in respiration, yielding a putative regulon that partially overlapped with BlaIMtb. Prompted by evidence that respiration inhibitors including clofazimine induce the BlaI regulon in Mtb, we found that clofazimine triggers induction of blaIRMab and its downstream regulon. Highlighting an important role for BlaIRMab in adapting to disruptions in energy metabolism, constitutive repression of the BlaIMab regulon rendered Mab highly susceptible to clofazimine. In addition to our unexpected findings that BlaIRMab does not regulate β-lactam resistance, this study highlights the novel role of mycobacterial BlaRI-type regulators in regulating electron transport and respiration.

Amoebae as training grounds for microbial pathogens

Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.

Orphan response regulator NnaR is critical for nitrate and nitrite assimilation in Mycobacterium abscessus

Mycobacterium abscessus (Mab) is an opportunistic pathogen afflicting individuals with underlying lung disease such as Cystic Fibrosis (CF) or immunodeficiencies. Current treatment strategies for Mab infections are limited by its inherent antibiotic resistance and limited drug access to Mab in its in vivo niches resulting in poor cure rates of 30-50%. Mab's ability to survive within macrophages, granulomas and the mucus laden airways of the CF lung requires adaptation via transcriptional remodeling to counteract stresses like hypoxia, increased levels of nitrate, nitrite, and reactive nitrogen intermediates. Mycobacterium tuberculosis (Mtb) is known to coordinate hypoxic adaptation via induction of respiratory nitrate assimilation through the nitrate reductase narGHJI. Mab, on the other hand, does not encode a respiratory nitrate reductase. In addition, our recent study of the transcriptional responses of Mab to hypoxia revealed marked down-regulation of a locus containing putative nitrate assimilation genes, including the orphan response regulator nnaR (nitrate/nitrite assimilation regulator). These putative nitrate assimilation genes, narK3 (nitrate/nitrite transporter), nirBD (nitrite reductase), nnaR, and sirB (ferrochelatase) are arranged contiguously while nasN (assimilatory nitrate reductase identified in this work) is encoded in a different locus. Absence of a respiratory nitrate reductase in Mab and down-regulation of nitrogen metabolism genes in hypoxia suggest interplay between hypoxia adaptation and nitrate assimilation are distinct from what was previously documented in Mtb. The mechanisms used by Mab to fine-tune the transcriptional regulation of nitrogen metabolism in the context of stresses e.g. hypoxia, particularly the role of NnaR, remain poorly understood. To evaluate the role of NnaR in nitrate metabolism we constructed a Mab nnaR knockout strain (MabΔnnaR ) and complement (MabΔnnaR+C ) to investigate transcriptional regulation and phenotypes. qRT-PCR revealed NnaR is necessary for regulating nitrate and nitrite reductases along with a putative nitrate transporter. Loss of NnaR compromised the ability of Mab to assimilate nitrate or nitrite as sole nitrogen sources highlighting its necessity. This work provides the first insights into the role of Mab NnaR setting a foundation for future work investigating NnaR's contribution to pathogenesis.

Regulation of heme biosynthesis via the coproporphyrin dependent pathway in bacteria

Heme biosynthesis in the Gram-positive bacteria occurs mostly via a pathway that is distinct from that of eukaryotes and Gram-negative bacteria in the three terminal heme synthesis steps. In many of these bacteria heme is a necessary cofactor that fulfills roles in respiration, gas sensing, and detoxification of reactive oxygen species. These varying roles for heme, the requirement of iron and glutamate, as glutamyl tRNA, for synthesis, and the sharing of intermediates with the synthesis of other porphyrin derivatives necessitates the need for many points of regulation in response to nutrient availability and metabolic state. In this review we examine the regulation of heme biosynthesis in these bacteria via heme, iron, and oxygen species. We also discuss our perspective on emerging roles of protein-protein interactions and post-translational modifications in regulating heme biosynthesis.

Clinically relevant mutations in the PhoR sensor kinase of host-adapted Mycobacterium abscessus isolates impact response to acidic pH and virulence

IMPORTANCE

Difficult-to-treat pulmonary infections caused by nontuberculous mycobacteria of the Mycobacterium abscessus group have been steadily increasing in the USA and globally. Owing to the relatively recent recognition of M. abscessus as a human pathogen, basic and translational research to address critical gaps in diagnosis, treatment, and prevention of diseases caused by this microorganism has been lagging behind that of the better-known mycobacterial pathogen, Mycobacterium tuberculosis. To begin unraveling the molecular mechanisms of pathogenicity of M. abscessus, we here focus on the study of a two-component regulator known as PhoPR which we found to be under strong evolutionary pressure during human lung infection. We show that PhoPR is activated at acidic pH and serves to regulate a defined set of genes involved in host adaptation. Accordingly, clinical isolates from chronically infected human lungs tend to hyperactivate this regulator enabling M. abscessus to escape macrophage killing.