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1.
Langmuir ; 40(21): 11106-11115, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38745419

ABSTRACT

Polycyclic aromatic hydrocarbons (PAHs), as persistent environmental pollutants, often reside in nonaqueous-phase liquids (NAPLs). Mycobacterium sp. WY10, boasting highly hydrophobic surfaces, can adsorb to the oil-water interface, stabilizing the Pickering emulsion and directly accessing PAHs for biodegradation. We investigated the impact of Triton X-100 (TX100) on this interfacial uptake of phenanthrene (PHE) by Mycobacteria, using n-tetradecane (TET) and bis-(2-ethylhexyl) phthalate (DEHP) as NAPLs. Interfacial tension, phase behavior, and emulsion stability studies, alongside confocal laser scanning microscopy and electron microscope observations, unveiled the intricate interplay. In surfactant-free systems, Mycobacteria formed stable W/O Pickering emulsions, directly degrading PHE within the NAPLs because of their intimate contact. Introducing low-dose TX100 disrupted this relationship. Preferentially binding to the cells, the surfactant drastically increased the cell hydrophobicity, triggering desorption from the interface and phase separation. Consequently, PAH degradation plummeted due to hindered NAPL access. Higher TX100 concentrations flipped the script, creating surfactant-stabilized O/W emulsions devoid of interfacial cells. Surprisingly, PAH degradation remained efficient. This paradox can be attributed to NAPL emulsification, driven by the surfactant, which enhanced mass transfer and brought the substrate closer to the cells, despite their absence at the interface. This study sheds light on the complex effect of surfactants on Mycobacteria and PAH uptake, revealing an antagonistic effect at low concentrations that ultimately leads to enhanced degradation through emulsification at higher doses. These findings offer valuable insights into optimizing bioremediation strategies in PAH-contaminated environments.


Subject(s)
Biodegradation, Environmental , Mycobacterium , Octoxynol , Phenanthrenes , Surface-Active Agents , Phenanthrenes/chemistry , Phenanthrenes/pharmacology , Phenanthrenes/metabolism , Surface-Active Agents/chemistry , Surface-Active Agents/pharmacology , Mycobacterium/metabolism , Mycobacterium/drug effects , Mycobacterium/chemistry , Octoxynol/chemistry , Emulsions/chemistry , Alkanes/chemistry , Alkanes/metabolism , Hydrophobic and Hydrophilic Interactions
2.
Molecules ; 29(10)2024 May 16.
Article in English | MEDLINE | ID: mdl-38792204

ABSTRACT

Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic pollutants, have long been a focal point of bioremediation research. This study aims to explore the impact and mechanisms of graphene oxide (GO) on the phytoremediation effectiveness of PAHs. The results underscore the significant efficacy of GO in accelerating the degradation of PAHs. Additionally, the introduction of GO altered the diversity and community structure of endophytic bacteria within the roots, particularly those genera with potential for PAH degradation. Through LEfSe analysis and correlation studies, we identified specific symbiotic bacteria, such as Mycobacterium, Microbacterium, Flavobacterium, Sphingomonas, Devosia, Bacillus, and Streptomyces, which coexist and interact under the influence of GO, synergistically degrading PAHs. These bacteria may serve as key biological markers in the PAH degradation process. These findings provide new theoretical and practical foundations for the application of nanomaterials in plant-based remediation of polluted soils and showcase the immense potential of plant-microbe interactions in environmental restoration.


Subject(s)
Bacteria , Biodegradation, Environmental , Graphite , Polycyclic Aromatic Hydrocarbons , Soil Microbiology , Soil Pollutants , Graphite/chemistry , Polycyclic Aromatic Hydrocarbons/metabolism , Soil Pollutants/metabolism , Bacteria/drug effects , Bacteria/metabolism , Endophytes/metabolism , Plant Roots/microbiology , Sphingomonas/metabolism , Plants/microbiology , Plants/metabolism , Mycobacterium/drug effects , Mycobacterium/metabolism , Flavobacterium/drug effects , Flavobacterium/metabolism , Streptomyces/metabolism , Microbacterium/metabolism
3.
Chemosphere ; 359: 142341, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38754485

ABSTRACT

This work comprehensively demonstrates the ability of heterotrophic bacteria, isolated from a chloraminated system, to decay chloramine. This study non-selectively isolated 62 cultures of heterotrophic bacteria from a water sample (0.002 mg-N/L nitrite and 1.42 mg/L total chlorine) collected from a laboratory-scale reactor system; most of the isolates (93.3%) were Mycobacterium sp. Three species of Mycobacterium and one species of Micrococcus were inoculated to a basal inorganic medium with initial concentrations of acetate (from 0 to 24 mg-C/L) and 1.5 mg/L chloramine. Bacterial growth coincided with declines in the concentrations of chloramine, acetate, and ammonium. Detailed experiments with one of the Mycobacterium sp. isolates suggest that the common mechanism of chloramine loss is auto-decomposition likely mediated by chloramine-decaying proteins. The ability of the isolates to grow and decay chloramine underscores the important role of heterotrophic bacteria in the stability of chloramine in water-distribution systems. Existing strategies based on controlling nitrification should be augmented to include minimizing heterotrophic bacteria.


Subject(s)
Bacteria , Chloramines , Heterotrophic Processes , Bacteria/metabolism , Bacteria/isolation & purification , Bacteria/classification , Mycobacterium/metabolism , Mycobacterium/isolation & purification , Mycobacterium/growth & development , Water Pollutants, Chemical/metabolism , Micrococcus/metabolism , Micrococcus/isolation & purification , Nitrification , Water Microbiology
4.
mBio ; 15(5): e0255223, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38567992

ABSTRACT

Since the discovery of extracellular vesicles (EVs) in mycobacterial species 15 years back, we have learned that this phenomenon is conserved in the Mycobacterium genus and has critical roles in bacterial physiology and host-pathogen interactions. Mycobacterium tuberculosis (Mtb), the tuberculosis (TB) causative agent, produces EVs both in vitro and in vivo including a diverse set of biomolecules with demonstrated immunomodulatory effects. Moreover, Mtb EVs (MEVs) have been shown to possess vaccine properties and carry biomarkers with diagnostic capacity. Although information on MEV biogenesis relative to other bacterial species is scarce, recent studies have shed light on how MEVs originate and are released to the extracellular space. In this minireview, we discuss past and new information about the vesiculogenesis phenomenon in Mtb, including biogenesis, MEV cargo, aspects in the context of host-pathogen interactions, and applications that could help to develop effective tools to tackle the disease.


Subject(s)
Extracellular Vesicles , Host-Pathogen Interactions , Mycobacterium tuberculosis , Tuberculosis , Extracellular Vesicles/metabolism , Humans , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/immunology , Mycobacterium tuberculosis/metabolism , Tuberculosis/microbiology , Tuberculosis/diagnosis , Animals , Biomarkers , Mycobacterium/genetics , Mycobacterium/metabolism
5.
Dalton Trans ; 53(15): 6676-6689, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38526845

ABSTRACT

Recently, we have studied the coordination chemistry of the Cu(II)-histidine-rich C-terminal tail (HRCT) complex of the mycobacterial GroEL1 protein. The structure of this domain differs significantly compared to the well-known methionine-glycine-rich GroEL chaperonin - it was predicted that mycobacterial GroEL1 could play a significant role in the metal homeostasis of Mycobacteria, especially copper. However, we found that this particular domain's pattern also repeats in a number of Ni(II)-binding proteins. Here, we present the studies concerning the properties of GroEL1 HRCT as a ligand for Ni(II) ions. For this purpose, we chose eight model peptides: L1 - Ac-DHDHHHGHAH, L2 - Ac-DKPAKAEDHDHHHGHAH, and 6 mutants of the latter in the pH range of 2-11. We examined the stoichiometry, stability, and spectroscopic features of copper complexes. We noticed that similar to the Cu(II)-complex, the presence of a Lys5 residue significantly increases the stability of the system. The impact of His mutations was also examined and carefully studied using NMR spectroscopy. His9 and His13 are the crucial residues for Ni(II) binding, whereas His12 has minimal relevance in complex formation.


Subject(s)
Histidine , Mycobacterium , Histidine/chemistry , Copper/chemistry , Binding Sites , Magnetic Resonance Spectroscopy , Mutation , Mycobacterium/metabolism
6.
Microbiol Res ; 282: 127664, 2024 May.
Article in English | MEDLINE | ID: mdl-38422860

ABSTRACT

Drug-resistant tuberculosis (TB) outbreak has emerged as a global public health crisis. Therefore, new and innovative therapeutic options like host-directed therapies (HDTs) through novel modulators are urgently required to overcome the challenges associated with TB. In the present study, we have investigated the anti-mycobacterial effect of 4-(Benzyloxy)phenol. Cell-viability assay asserted that 50 µM of 4-(Benzyloxy)phenol was not cytotoxic to phorbol 12-myristate 13-acetate (PMA) differentiated THP-1 (dTHP-1) cells. It was observed that 4-(Benzyloxy)phenol activates p53 expression by hindering its association with KDM1A. Increased ROS, intracellular Ca2+ and phagosome-lysosome fusion, were also observed upon 4-(Benzyloxy)phenol treatment. 4-(Benzyloxy)phenol mediated killing of intracellular mycobacteria was abrogated in the presence of specific inhibitors of ROS, Ca2+ and phagosome-lysosome fusion like NAC, BAPTA-AM, and W7, respectively. We further demonstrate that 4-(Benzyloxy)phenol mediated enhanced ROS production is mediated by acetylation of p53. Blocking of p53 acetylation by Pifithrin-α (PFT- α) enhanced intracellular mycobacterial growth by blocking the mycobactericidal effect of 4-(Benzyloxy)phenol. Altogether, the results showed that 4-(Benzyloxy)phenol executed its anti-mycobacterial effect by modulating p53-mediated ROS production to regulate phagosome-lysosome fusion through Ca2+ production.


Subject(s)
Mycobacterium , Tumor Suppressor Protein p53 , Humans , Reactive Oxygen Species/metabolism , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/pharmacology , Macrophages , Phenol , THP-1 Cells , Phagosomes/metabolism , Phagosomes/microbiology , Lysosomes/metabolism , Mycobacterium/metabolism , Phenols/pharmacology , Phenols/metabolism
7.
J Biol Chem ; 300(3): 105768, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38367664

ABSTRACT

Galactan polymer is a prominent component of the mycobacterial cell wall core. Its biogenesis starts at the cytoplasmic side of the plasma membrane by a build-up of the linker disaccharide [rhamnosyl (Rha) - N-acetyl-glucosaminyl (GlcNAc) phosphate] on the decaprenyl-phosphate carrier. This decaprenyl-P-P-GlcNAc-Rha intermediate is extended by two bifunctional galactosyl transferases, GlfT1 and GlfT2, and then it is translocated to the periplasmic space by an ABC transporter Wzm-Wzt. The cell wall core synthesis is finalized by the action of an array of arabinosyl transferases, mycolyl transferases, and ligases that catalyze an attachment of the arabinogalactan polymer to peptidoglycan through the linker region. Based on visualization of the GlfT2 enzyme fused with fluorescent tags it was proposed that galactan polymerization takes place in a specific compartment of the mycobacterial cell envelope, the intracellular membrane domain, representing pure plasma membrane free of cell wall components (previously denoted as the "PMf" domain), which localizes to the polar region of mycobacteria. In this work, we examined the activity of the galactan-producing cellular machine in the cell-wall containing cell envelope fraction and in the cell wall-free plasma membrane fraction prepared from Mycobacterium smegmatis by the enzyme assays using radioactively labeled substrate UDP-[14C]-galactose as a tracer. We found that despite a high abundance of GlfT2 in both of these fractions as confirmed by their thorough proteomic analyses, galactan is produced only in the reaction mixtures containing the cell wall components. Our findings open the discussion about the distribution of GlfT2 and the regulation of its activity in mycobacteria.


Subject(s)
Galactans , Mycobacterium , Galactans/biosynthesis , Polymers/metabolism , Proteomics , Transferases/metabolism , Mycobacterium/metabolism
8.
Cell Chem Biol ; 31(4): 669-682.e7, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38266648

ABSTRACT

Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. The conserved whiB7 stress response reduces the effectiveness of antibiotic therapy by activating several intrinsic antibiotic resistance mechanisms. Despite our comprehensive biochemical understanding of WhiB7, the complex set of signals that induce whiB7 expression remain less clear. We employed a reporter-based, genome-wide CRISPRi epistasis screen to identify a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 expression. We show that whiB7 expression is determined by the amino acid composition of the 5' regulatory uORF, thereby allowing whiB7 to sense amino acid starvation. Although deprivation of many amino acids can induce whiB7, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. These findings describe a metabolic function for whiB7 and help explain its evolutionary conservation across mycobacterial species occupying diverse ecological niches.


Subject(s)
Mycobacterium tuberculosis , Mycobacterium , Transcription Factors/metabolism , Alanine/genetics , Alanine/metabolism , Gene Expression Regulation, Bacterial , Mycobacterium/genetics , Mycobacterium/metabolism , Drug Resistance, Microbial , Mycobacterium tuberculosis/metabolism , Bacterial Proteins/metabolism
9.
Int J Biol Macromol ; 260(Pt 2): 129583, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38242409

ABSTRACT

Cell wall synthesis and cell division are two closely linked pathways in a bacterial cell which distinctly influence the growth and survival of a bacterium. This requires an appreciable coordination between the two processes, more so, in case of mycobacteria with an intricate multi-layered cell wall structure. In this study, we investigated a conserved gene cluster using CRISPR-Cas12 based gene silencing technology to show that knockdown of most of the genes in this cluster leads to growth defects. Investigating conserved genes is important as they likely perform vital cellular functions and the functional insights on such genes can be extended to other mycobacterial species. We characterised one of the genes in the locus, MSMEG_0311. The repression of this gene not only imparts severe growth defect but also changes colony morphology. We demonstrate that the protein preferentially localises to the polar region and investigate its influence on the polar growth of the bacillus. A combination of permeability and drug susceptibility assay strongly suggests a cell wall associated function of this gene which is also corroborated by transcriptomic analysis of the knockdown where a number of cell wall associated genes, particularly iniA and sigF regulon get altered. Considering the gene is highly conserved across mycobacterial species and appears to be essential for growth, it may serve as a potential drug target.


Subject(s)
Mycobacterium tuberculosis , Mycobacterium , Mycobacterium smegmatis/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Mycobacterium/genetics , Mycobacterium/metabolism , Cell Wall/genetics , Cell Wall/metabolism , Cell Division , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/metabolism
10.
Int J Antimicrob Agents ; 63(2): 107089, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38218322

ABSTRACT

OBJECTIVES: Aminoglycoside resistance in bacteria is typically conferred by specific drug-modifying enzymes. Infrequently, such resistance is achieved through 16S ribosomal RNA methyltransferases, such as NpmA and KamB encoded by Escherichia coli and Streptoalloteichus tenebrarius, respectively. These enzymes are not widespread and have not been described in Nocardia species to date. METHODS: We report the genomic mining of 18 Nocardia wallacei isolates that were found to be specifically and substantially resistant to amikacin. RESULTS: We identified a gene coding for a protein with very distant homology to NpmA and KamB. However, 3-D modeling revealed that the tertiary structure of these three proteins was highly similar. Cloning and expressing this gene in two susceptible bacteria Nocardia asteroides, and Mycobacterium smegmatis (another Actinobacterium) led to high-level, pan-aminoglycoside resistance in both cases. We named this gene warA (Wallacei Amikacin Resistance A). CONCLUSIONS: This is the first description and experimental characterization of a gene of this family in Nocardia, and the first demonstration that such activity could lead to pan-aminoglycoside resistance in Mycobacteria as well. The discovery of this novel gene has important biotechnology and clinical implications.


Subject(s)
Mycobacterium , Nocardia , Aminoglycosides/metabolism , Amikacin/pharmacology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/metabolism , Nocardia/genetics , Nocardia/metabolism , Escherichia coli/genetics , Mycobacterium/genetics , Mycobacterium/metabolism , RNA, Ribosomal, 16S/genetics , Drug Resistance, Bacterial/genetics
11.
Nucleic Acids Res ; 52(2): 816-830, 2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38048321

ABSTRACT

Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like protein in dormant mycobacteria, induces dormancy phenotypes, e.g. chromosome compaction and growth suppression. For these functions, the polycationic intrinsically disordered region (IDR) is essential. However, the disordered property of IDR stands in the way of clarifying the molecular mechanism. Here we clarified the molecular and structural mechanism of DNA compaction by MDP1. Using high-speed atomic force microscopy, we observed that monomeric MDP1 bundles two adjacent DNA duplexes side-by-side via IDR. Combined with coarse-grained molecular dynamics simulation, we revealed the novel dynamic DNA cross-linking model of MDP1 in which a stretched IDR cross-links two DNA duplexes like double-sided tape. IDR is able to hijack HU function, resulting in the induction of strong mycobacterial growth arrest. This IDR-mediated reversible DNA cross-linking is a reasonable model for MDP1 suppression of the genomic function in the resuscitable non-replicating dormant mycobacteria.


Subject(s)
DNA Packaging , Intrinsically Disordered Proteins , Mycobacterium , DNA/metabolism , Histones , Intrinsically Disordered Proteins/metabolism , Mycobacterium/metabolism
12.
J Biol Chem ; 300(1): 105539, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38072054

ABSTRACT

L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5'-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present the crystallographic structure of the ergothioneine-biosynthesis C-S lyase EgtE from Mycobacterium smegmatis (MsEgtE) represents the first published structure of ergothioneine-biosynthesis C-S lyases in bacteria and shows the effects of active site residues on the enzymatic reaction. The MsEgtE and the previously reported ergothioneine-biosynthesis C-S lyase Egt2 from Neurospora crassa (NcEgt2) fold similarly. However, discrepancies arise in terms of substrate recognition, as observed through sequence and structure comparison of MsEgtE and NcEgt2. The structural-based sequence alignment of the ergothioneine-biosynthesis C-S lyase from fungi and bacteria shows clear distinctions among the recognized substrate residues, but Arg348 is critical and an extremely conserved residue for substrate recognition. The α14 helix is exclusively found in the bacteria EgtE, which represent the most significant difference between bacteria EgtE and fungi Egt2, possibly resulting from the convergent evolution of bacteria and fungi.


Subject(s)
Ergothioneine , Lyases , Mycobacterium , Ergothioneine/chemistry , Ergothioneine/metabolism , Fungi/metabolism , Lyases/chemistry , Lyases/metabolism , Mycobacterium/metabolism , Mycobacterium smegmatis/chemistry , Mycobacterium smegmatis/enzymology , Models, Molecular , Protein Structure, Quaternary , Protein Structure, Tertiary
13.
Commun Biol ; 6(1): 1222, 2023 12 02.
Article in English | MEDLINE | ID: mdl-38042942

ABSTRACT

The WYL domain is a nucleotide-sensing module that controls the activity of transcription factors involved in the regulation of DNA damage response and phage defense mechanisms in bacteria. In this study, we investigated a WYL domain-containing transcription factor in Mycobacterium smegmatis that we termed stress-involved WYL domain-containing regulator (SiwR). We found that SiwR controls adjacent genes that belong to the DinB/YfiT-like putative metalloenzymes superfamily by upregulating their expression in response to various genotoxic stress conditions, including upon exposure to H2O2 or the natural antibiotic zeocin. We show that SiwR binds different forms of single-stranded DNA (ssDNA) with high affinity, primarily through its characteristic WYL domain. In combination with complementation studies of a M. smegmatis siwR deletion strain, our findings support a role of the WYL domains as signal-sensing activity switches of WYL domain-containing transcription factors (WYL TFs). Our study provides evidence that WYL TFs are involved in the adaptation of bacteria to changing environments and encountered stress conditions.


Subject(s)
Hydrogen Peroxide , Mycobacterium , Hydrogen Peroxide/pharmacology , Bacterial Proteins/metabolism , Transcription Factors/genetics , Mycobacterium/genetics , Mycobacterium/metabolism , DNA, Single-Stranded , DNA Damage
14.
Sheng Wu Gong Cheng Xue Bao ; 39(11): 4550-4562, 2023 Nov 25.
Article in Chinese | MEDLINE | ID: mdl-38013183

ABSTRACT

Mycobacterium neoaurum has the ability to produce steroidal intermediates known as 22-hydroxy-23, 24-bisnorchol-4-en-3-one (BA) upon the knockout of the genes for either the hydroxyacyl-CoA dehydrogenase (Hsd4A) or acyl-CoA thiolase (FadA5). In a previous study, we discovered a novel metabolite in the fermentation products when the fadA5 gene was deleted. This research aims to elucidate the metabolic pathway of this metabolite through structural identification, homologous sequence analysis of the fadA5 gene, phylogenetic tree analysis of M. neoaurum HGMS2, and gene knockout. Our findings revealed that the metabolite is a C23 metabolic intermediate, named 24-norchol-4-ene-3, 22-dione (designated as 3-OPD). It is formed when a thioesterase (TE) catalyzes the formation of a ß-ketonic acid by removing CoA from the side chain of 3, 22-dioxo-25, 26-bisnorchol-4-ene-24-oyl CoA (22-O-BNC-CoA), followed by spontaneously undergoing decarboxylation. These results have the potential to contribute to the development of novel steroid intermediates.


Subject(s)
Mycobacterium , Mycobacterium/genetics , Mycobacterium/metabolism , Phylogeny , Steroids/metabolism , Metabolic Networks and Pathways , Sterols/metabolism
15.
Nat Commun ; 14(1): 6694, 2023 10 23.
Article in English | MEDLINE | ID: mdl-37872138

ABSTRACT

We report on the existence of two phosphatidic acid biosynthetic pathways in mycobacteria, a classical one wherein the acylation of the sn-1 position of glycerol-3-phosphate (G3P) precedes that of sn-2 and another wherein acylations proceed in the reverse order. Two unique acyltransferases, PlsM and PlsB2, participate in both pathways and hold the key to the unusual positional distribution of acyl chains typifying mycobacterial glycerolipids wherein unsaturated substituents principally esterify position sn-1 and palmitoyl principally occupies position sn-2. While PlsM selectively transfers a palmitoyl chain to the sn-2 position of G3P and sn-1-lysophosphatidic acid (LPA), PlsB2 preferentially transfers a stearoyl or oleoyl chain to the sn-1 position of G3P and an oleyl chain to sn-2-LPA. PlsM is the first example of an sn-2 G3P acyltransferase outside the plant kingdom and PlsB2 the first example of a 2-acyl-G3P acyltransferase. Both enzymes are unique in their ability to catalyze acyl transfer to both G3P and LPA.


Subject(s)
Acyltransferases , Mycobacterium , Acyltransferases/genetics , Acyltransferases/metabolism , Glycerol-3-Phosphate O-Acyltransferase/genetics , Glycerol-3-Phosphate O-Acyltransferase/metabolism , Acylation , Mycobacterium/genetics , Mycobacterium/metabolism
16.
Int J Biol Macromol ; 253(Pt 3): 126876, 2023 Dec 31.
Article in English | MEDLINE | ID: mdl-37709237

ABSTRACT

Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation.


Subject(s)
Mycobacterium , RNA, Ribosomal, 23S , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/chemistry , RNA, Ribosomal, 23S/metabolism , Cryoelectron Microscopy , Ribosomes/metabolism , Mycobacterium/genetics , Mycobacterium/metabolism , Protein Structure, Secondary , Nucleic Acid Conformation
17.
Cell Host Microbe ; 31(9): 1469-1480.e4, 2023 09 13.
Article in English | MEDLINE | ID: mdl-37567169

ABSTRACT

In eukaryotic cells, serine/threonine protein kinases (StpKs) play important roles in limiting viral infections. StpKs are commonly activated upon infections, inhibiting the expression of genes central for viral replication. Here, we report that a eukaryotic-like StpK7 encoded by MSMEG_1200 in M. smegmatis is required for mycobacteriophage TM4 to escape bacterial defense. stpK7 is located within a gene island, MSMEG_1191-MSMEG_1200, containing multiple anti-phage genes resembling the BREX (bacteriophage exclusion) phage-resistance system. StpK7 negatively regulates the expression of this gene island. Following phage TM4 infection, StpK7 is induced, directly phosphorylating the transcriptional regulator MSMEG_1198 and inhibiting its positive regulatory activity, thus reducing the expression of multiple downstream genes in the BREX-like gene island. Further analysis showed that genes within this anti-phage island critically regulate mycobacterial lipid hemostasis and phage adsorption. Collectively, this work characterizes a regulatory network driven by StpK7, which is utilized by phage TM4 to escape from the host defense against mycobacteria.


Subject(s)
Bacteriophages , Mycobacterium , Bacteriophages/genetics , Bacteriophages/metabolism , Eukaryota , Protein Kinases , Eukaryotic Cells/metabolism , Mycobacterium/metabolism , Protein Serine-Threonine Kinases/genetics , Bacterial Proteins/metabolism
18.
PLoS Pathog ; 19(6): e1011389, 2023 06.
Article in English | MEDLINE | ID: mdl-37262021

ABSTRACT

Mycobacteria are responsible for several human and animal diseases. NOD2 is a pattern recognition receptor that has an important role in mycobacterial recognition. However, the mechanisms by which mutations in NOD2 alter the course of mycobacterial infection remain unclear. Herein, we aimed to review the totality of studies directly addressing the relationship between NOD2 and mycobacteria as a foundation for moving the field forward. NOD2 was linked to mycobacterial infection at 3 levels: (1) genetic, through association with mycobacterial diseases of humans; (2) chemical, through the distinct NOD2 ligand in the mycobacterial cell wall; and (3) immunologic, through heightened NOD2 signaling caused by the unique modification of the NOD2 ligand. The immune response to mycobacteria is shaped by NOD2 signaling, responsible for NF-κB and MAPK activation, and the production of various immune effectors like cytokines and nitric oxide, with some evidence linking this to bacteriologic control. Absence of NOD2 during mycobacterial infection of mice can be detrimental, but the mechanism remains unknown. Conversely, the success of immunization with mycobacteria has been linked to NOD2 signaling and NOD2 has been targeted as an avenue of immunotherapy for diseases even beyond mycobacteria. The mycobacteria-NOD2 interaction remains an important area of study, which may shed light on immune mechanisms in disease.


Subject(s)
Mycobacterium Infections , Mycobacterium , Humans , Animals , Mice , Ligands , Signal Transduction/physiology , NF-kappa B/metabolism , Cytokines/metabolism , Mycobacterium/metabolism , Nod2 Signaling Adaptor Protein/genetics
19.
Small Methods ; 7(9): e2300183, 2023 09.
Article in English | MEDLINE | ID: mdl-37291735

ABSTRACT

ESX-3 is a secretion pathway which is essential for mycobactin-mediated iron acquisition under iron-limited conditions. Although present in all Mycobacterium sp., ESX-3 remains to be elucidated in Mycobacterium abscessus. In the study reported here, impaired ESX-3 seriously restricts the growth of M. abscesses under iron-limited conditions; growth is salvaged by functional ESX-3 or iron supplementation. Notably, impaired ESX-3 does not kill M. abscesses when environmental iron is insufficient but induces persistence to bedaquiline, a diarylquinoline class antibiotic used to treat multidrug-resistant mycobacteria. One potential mechanism contributing to persistence is the iron deficiency due to impaired ESX-3 suppressing succinate dehydrogenase activity, which dysregulates the tricarboxylic acid cycle and inactivates bedaquiline. Experiments conducted here also demonstrate that the regulator, MtrA, can bind ESX-3 and promote the survival of M. abscessus. As such, this study suggests that a novel pathway involving MtrA, ESX-3, iron metabolism, and the TCA cycle contributes to bedaquiline persistence in M. abscesses growing under iron-limited conditions.


Subject(s)
Iron Metabolism Disorders , Mycobacterium abscessus , Mycobacterium , Humans , Mycobacterium abscessus/metabolism , Diarylquinolines/pharmacology , Diarylquinolines/metabolism , Abscess , Mycobacterium/metabolism , Iron/pharmacology
20.
Microbes Infect ; 25(7): 105144, 2023.
Article in English | MEDLINE | ID: mdl-37120009

ABSTRACT

Exploiting the heterologous effects of vaccines is a feasible strategy to combat different pathogens. These effects have been explained by enhanced immune responses of innate immune cells. Mycobacterium paragordonae is a rare nontuberculosis mycobacterium that has temperature-sensitive properties. Although natural killer (NK) cells exhibit heterologous immunity features, the cellular crosstalk between NK cells and dendritic cells (DCs) during live mycobacterial infection has remained elusive. We show that live but not dead M. paragordonae enhances heterologous immunity against unrelated pathogens in NK cells by IFN-ß of DCs in both mouse models and primary human immune cells. C-di-GMP from live M. paragordonae acted as a viability-associated pathogen-associated molecular pattern (Vita-PAMP), leading to STING-dependent type I IFN production in DCs via the IRE1α/XBP1s pathway. Also, increased cytosolic 2'3'-cGAMP by cGAS can induce type I IFN response in DCs by live M. paragordonae infection. We found that DC-derived IFN-ß plays a pivotal role in NK cell activation by live M. paragordonae infection, showing NK cell-mediated nonspecific protective effects against Candida albicans infection in a mouse model. Our findings indicate that the heterologous effect of live M. paragordonae vaccination is mediated by NK cells based on the crosstalk between DCs and NK cells.


Subject(s)
Interferon Type I , Mycobacterium , Mice , Animals , Humans , Interferon Type I/metabolism , Protein Serine-Threonine Kinases/metabolism , Immunity, Heterologous , Endoribonucleases/metabolism , Mycobacterium/metabolism , Killer Cells, Natural , Dendritic Cells
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