Cu,Zn superoxide dismutase of Mycobacterium tuberculosis contributes to survival in activated macrophages that are generating an oxidative burst

Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex

Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.

Live Attenuated Vaccines against Tuberculosis: Targeting the Disruption of Genes Encoding the Secretory Proteins of Mycobacteria

Tuberculosis (TB), a chronic infectious disease affecting humans, causes over 1.3 million deaths per year throughout the world. The current preventive vaccine BCG provides protection against childhood TB, but it fails to protect against pulmonary TB. Multiple candidates have been evaluated to either replace or boost the efficacy of the BCG vaccine, including subunit protein, DNA, virus vector-based vaccines, etc., most of which provide only short-term immunity. Several live attenuated vaccines derived from Mycobacterium tuberculosis (Mtb) and BCG have also been developed to induce long-term immunity. Since Mtb mediates its virulence through multiple secreted proteins, these proteins have been targeted to produce attenuated but immunogenic vaccines. In this review, we discuss the characteristics and prospects of live attenuated vaccines generated by targeting the disruption of the genes encoding secretory mycobacterial proteins.

Microbial strategies for copper pollution remediation: Mechanistic insights and recent advances

Environmental contamination is aninsistent concern affecting human health and the ecosystem. Wastewater, containing heavy metals from industrial activities, significantly contributes to escalating water pollution. These metals can bioaccumulate in food chains, posing health risks even at low concentrations. Copper (Cu), an essential micronutrient, becomes toxic at high levels. Activities like mining and fungicide use have led to Copper contamination in soil, water, and sediment beyond safe levels. Copper widely used in industries, demands restraint of heavy metal ion release into wastewater for ecosystem ultrafiltration, membrane filtration, nanofiltration, and reverse osmosis, combat heavy metal pollution, with emphasis on copper.Physical and chemical approaches are efficient, large-scale feasibility may have drawbackssuch as they are costly, result in the production of sludge. In contrast, bioremediation, microbial intervention offers eco-friendly solutions for copper-contaminated soil. Bacteria and fungi facilitate these bioremediation avenues as cost-effective alternatives. This review article emphasizes on physical, chemical, and biological methods for removal of copper from the wastewater as well asdetailing microorganism's mechanisms to mobilize or immobilize copper in wastewater and soil.

Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance

A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop clinical, mostly pulmonary, TB. To dissect mechanisms of susceptibility in immunocompetent individuals, we developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining feature of human TB: development of necrotic lung lesions after infection with virulent Mtb. In this study, we explored the connectivity of the sst1-regulated pathways during prolonged macrophage activation with TNF. We determined that the aberrant response of the sst1-susceptible macrophages to TNF was primarily driven by conflicting Myc and antioxidant response pathways that resulted in a coordinated failure to properly sequester intracellular iron and activate ferroptosis inhibitor enzymes. Consequently, iron-mediated lipid peroxidation fueled IFNβ superinduction and sustained the Type I Interferon (IFN-I) pathway hyperactivity that locked the sst1-susceptible macrophages in a state of unresolving stress and compromised their resistance to Mtb. The accumulation of the aberrantly activated, stressed, macrophages within granuloma microenvironment led to the local failure of anti-tuberculosis immunity and tissue necrosis. Our findings suggest a novel link between metabolic dysregulation in macrophages and susceptibility to TB, offering insights into potential therapeutic targets aimed at modulating macrophage function and improving TB control.

Butyrate induces oxidative burst mediated apoptosis via Glucose-6-Phosphate Dehydrogenase (G6PDH) in macrophages during mycobacterial infection

Microorganisms present in the gut modulate host defence responses against infections in order to maintain immune homeostasis. This host-microbe crosstalk is regulated by gut metabolites. Butyrate is one such small chain fatty acid produced by gut microbes upon fermentation that has the potential to influence immune responses. Here we investigated the role of butyrate in macrophages during mycobacterial infection. Results demonstrate that butyrate significantly suppresses the growth kinetics of mycobacteria in culture medium as well as inhibits mycobacterial survival inside macrophages. Interestingly, butyrate alters the pentose phosphate pathway by inducing higher expression of Glucose-6-Phosphate Dehydrogenase (G6PDH) resulting in a higher oxidative burst via decreased Sod-2 and increased Nox-2 (NADPH oxidase-2) expression. Butyrate-induced G6PDH also mediated a decrease in mitochondrial membrane potential. This in turn lead to an induction of apoptosis as measured by lower expression of the anti-apoptotic protein Bcl-2 and a higher release of Cytochrome C as a result of induction of apoptosis. These results indicate that butyrate alters the metabolic status of macrophages and induces protective immune responses against mycobacterial infection.

Efflux pump Rv1258c activates novel functions of the oxidative stress and via the VII secretion system ESX-3-mediated iron metabolic pathway in Mycobacterium tuberculosis

Oxidative stress and iron metabolism are essential for Mycobacterium tuberculosis (M.tb) survival in host cells. The efflux pump Rv1258c belongs to the major facilitator superfamily (MFS) and can actively pump drugs to promote certain drug resistance in M.tb. In this study, we compared H37RvΔRv1258c with wild-type (WT) M.tb H37Rv. The qRT-PCR results suggested that Rv1258c is potentially involved in the iron metabolic pathway by regulating the expression of ESX-3, which is required for iron uptake. Protein-Protein Affinity Predictor (PPA-Pred2) and the artificial intelligence program AlphaFold 2 were used for prediction and showed that Rv1258c has direct interactions with PPE4 and EccD3 but weak interactions with EccB3. This was further determined via protein-protein interaction analysis of the yeast two-hybrid expression system. By comparing mutant H37RvΔRv1258c strains with WT strains, we discovered that the absence of Rv1258c led to elevated intracellular H+ potential and NAD+/NADH ratios in M.tb, thereby resulting in oxidative stress. We hypothesize that the efflux pump Rv1258c not only has the function of regulating drug resistance in M.tb but also has a novel function in activating oxidative stress and regulating ESX-3-associated iron metabolism in M.tb.

The Benefits of Toxicity: M. smegmatis VapBC TA Module Is Induced by Tetracycline Exposure and Promotes Survival

Toxin-antitoxin (TA) systems are widely present in bacterial genomes. Mycolicibacterium smegmatis, a common model organism for studying Mycobacterium tuberculosis physiology, has eight TA loci, including mazEF and vapBC. This study aims to investigate the physiological significance of these TA systems. Proteomic profiling was conducted on a culture overexpressing the VapC toxin, and the involvement of VapC in M. smegmatis stress responses to heat shock and antibiotic treatment was examined. While deciphering the underlying mechanisms of the altered stress resistance, we assessed the antibiotic susceptibility of vapBC, mazEF, and double vapBC-mazEF deletion mutants. Additionally, the mRNA levels of vapC and mazF were measured following tetracycline supplementation. The results reveal changes in the abundance of metabolic enzymes and stress response proteins associated with VapC overexpression. This activation of the general stress response leads to reduced thermosensitivity in M. smegmatis, but does not affect susceptibility to ciprofloxacin and isoniazid. Under tetracycline treatment, both vapC and mazF expression levels are increased, and the fate of the cell depends on the interaction between the corresponding TA systems.

Exploring the role of the protein tyrosine kinase a (PtkA) in mycobacterial intracellular survival

Mycobacterium tuberculosis (Mtb) continues to define new paradigms of host-pathogen interaction. There are several host proteins known which are regulated by Mtb infection. The proteins which regulate host biological processes like apoptosis, cell processes, stress proteins, metabolic enzymes, etc. are targeted by the pathogens. Mtb proteins interact directly or indirectly with host proteins and play an important role in their persistence and intracellular growth. Mtb is an intracellular pathogen. It remains dormant for years within the host without activating its immune system. Mtb Protein tyrosine kinase (PtkA) regulates host anti-apoptotic protein, metabolic enzymes, and several other proteins that are involved in stress regulation, cell proliferation, protein folding, DNA repair, etc. PtkA regulates other mycobacterial proteins and plays an important role in its growth and survival. Here we summarized the current knowledge of PtkA and reviewed its role in mycobacterial intracellular survival as it regulates several other mycobacterial proteins and host proteins. PtkA regulates PtpA secretion which is essential for mycobacterial virulence and could be used as an attractive drug target.

Host hydrocarbons protect symbiont transmission from a radical host defense

Symbioses with microbes play a pivotal role in the evolutionary success of insects, and can lead to intimate host-symbiont associations. However, how the host maintains a stable symbiosis with its beneficial partners while keeping antagonistic microbes in check remains incompletely understood. Here, we uncover a mechanism by which a host protects its symbiont from the host's own broad-range antimicrobial defense during transmission. Beewolves, a group of solitary digger wasps (Hymenoptera: Crabronidae), provide their brood cells with symbiotic Streptomyces bacteria that are later transferred to the cocoon and protect the offspring from opportunistic pathogens by producing antibiotics. In the brood cell, however, the symbiont-containing secretion is exposed to a toxic burst of nitric oxide (NO) released by the beewolf egg, which effectively kills antagonistic microorganisms. How the symbiont survives this lethal NO burst remained unknown. Here, we report that upon NO exposure in vitro, the symbionts mount a global stress response, but this is insufficient to ensure survival at brood cell-level NO concentrations. Instead, in vivo bioassays demonstrate that the host's antennal gland secretion (AGS) surrounding the symbionts in the brood cell provides an effective diffusion barrier against NO. This physicochemical protection can be reconstituted in vitro by beewolf hydrocarbon extracts and synthetic hydrocarbons, indicating that the host-derived long-chain alkenes and alkanes in the AGS are responsible for shielding the symbionts from NO. Our results reveal how host adaptations can protect a symbiont from host-generated oxidative and nitrosative stress during transmission, thereby efficiently balancing pathogen defense and mutualism maintenance.

Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases"

The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.

Identification and Quantification of S-Sulfenylation Proteome of Mycobacterium tuberculosis under Oxidative Stress

The ability to maintain redox homeostasis is critical for Mycobacterium tuberculosis (Mtb) to survive the redox stress of the host. There are many antioxidant systems in Mtb to ensure its normal replication and survival in the host, and cysteine thiols are one of them. S-sulfenylation is one of the reversible modifications of cysteine thiols to resist oxidative stress. In the study, we investigated the total cysteine thiols modification and S-sulfenylation modification of Mtb proteome under the oxidative stress provided by hydrogen peroxide. To determine and quantify the S-sulfenylation modified proteins, high specific IodoTMT6plex reagents and high resolution mass spectrometry were used to label and quantify the peptides and proteins modified. There are significant differences for the total cysteine modification levels of 279 proteins and S-sulfenylation modification levels of 297 proteins under hydrogen peroxide stress. Functional enrichment analysis indicated that these cysteine-modified proteins were involved in the oxidation-reduction process, fatty acid biosynthetic process, stress response, protein repair, cell wall, etc. In conclusion, our study provides a view of cysteine modifications of the Mtb proteome under oxidative stress, revealing a series of proteins that may play a role in maintaining redox homeostasis. IMPORTANCE With the continuous spread of drug-resistant tuberculosis, there is an urgent need for new antituberculosis drugs with new mechanisms. The ability of Mtb to resist oxidative stress is extremely important for maintaining redox homeostasis and survival in the host. The reversible modifications of cysteine residues have a dual role of protection from irreversible damage to protein functions and regulation, which plays an important role in the redox homeostasis system. Thus, to discover cysteine modification changes in the proteome level under oxidative stress is quintessential to elucidate its antioxidant mechanism. Our results provided a list of proteins involved in the antioxidant process that potentially could be considered targets for drug discovery and vaccine development. Furthermore, it is the first study to determine and quantify the S-sulfenylation-modified proteins in Mtb, which provided better insight into the Mtb response to the host oxidative defense and enable a deeper understanding of Mtb survival strategies.

Adaptation to the intracellular environment of primary human macrophages influences drug susceptibility of Mycobacterium tuberculosis

As a facultative intracellular pathogen, M. tuberculosis (Mtb) is highly adapted to evading antibacterial mechanisms in phagocytic cells. Both the macrophage and pathogen experience transcriptional and metabolic changes from the onset of phagocytosis. To account for this interaction in the assessment of intracellular drug susceptibility, we allowed a 3-day preadaptation phase post-macrophage infection prior to drug treatment. We found that intracellular Mtb in human monocyte-derived macrophages (MDM) presents dramatic alterations in susceptibility to isoniazid, sutezolid, rifampicin and rifapentine when compared to axenic culture. Infected MDM gradually accumulate lipid bodies, adopting a characteristic appearance reminiscent of foamy macrophages in granulomas. Furthermore, TB granulomas in vivo develop hypoxic cores with decreasing oxygen tension gradients across their radii. Accordingly, we evaluated the effects of hypoxia on preadapted intracellular Mtb in our MDM model. We observed that hypoxia induced greater lipid body formation and no additional shifts in drug tolerance, suggesting that the adaptation of intracellular Mtb to baseline host cell conditions under normoxia dominates changes to intracellular drug susceptibility. Using unbound plasma concentrations in patients as surrogates for free drug concentrations in lung interstitial fluid, we estimate that intramacrophage Mtb in granulomas are exposed to bacteriostatic concentrations of most study drugs.

Microplastics in Freshwater Sediments Impact the Role of a Main Bioturbator in Ecosystem Functioning

While microplastic transport, fate, and effects have been a focus of studies globally, the consequences of their presence on ecosystem functioning have not received the same attention. With increasing evidence of the accumulation of microplastics at sediment-water interfaces there is a need to assess their impacts on ecosystem engineers, also known as bioturbators, which have direct and indirect effects on ecosystem health. This study investigated the impact of microplastics on the bioturbator Tubifex tubifex alongside any effects on the biogeochemical processes at the sediment-water interface. Bioturbators were exposed to four sediment microplastic concentrations: 0, 700, 7000, and 70000 particles kg^-1 sediment dry weight. Though no mortality was present, a significant response to oxidative stress was detected in tubificid worms after exposure to medium microplastic concentration (7000 particles kg^-1 sediment dry weight). This was accompanied by a reduction in worm bioturbation activities assessed by their ability to rework sediment and to stimulate exchange water fluxes at the sediment-water interface. Consequently, the contributions of tubificid worms on organic matter mineralization and nutrient fluxes were significantly reduced in the presence of microplastics. This study demonstrated that environmentally realistic microplastic concentrations had an impact on biogeochemical processes at the sediment-water interface by reducing the bioturbation activities of tubificid worms.

Mycobacterium tuberculosis Rv1324 Protein Contributes to Mycobacterial Persistence and Causes Pathological Lung Injury in Mice by Inducing Ferroptosis

Mycobacterium tuberculosis (Mtb) is the pathogenic agent of tuberculosis (TB). Intracellular survival plays a central role in the pathogenesis of Mtb, a process that depends on an array of virulence factors for Mtb to colonize and proliferate within a host. Reactive nitrogen and oxygen species (RNS and ROS) are among the most effective antimycobacterial molecules generated by the host during infection. However, Mtb has evolved a number of proteins and enzymes to detoxify ROS and RNS. Secretory protein Rv1324, as a possible thioredoxin, might also have oxidoreductase activity against ROS and RNS during Mtb infection, and it is a potential virulence factor of Mtb. In this study, we investigated the biochemical properties of Mtb Rv1324 and its role in mycobacterial survival and virulence. The results showed that the Rv1324 protein had antioxidant activity and increased the survival of M. smegmatis that was exposed to ROS and RNS. In addition, Rv1324 enhanced the colonization ability of M. smegmatis in the lungs of mice. Further, mice infected with M. smegmatis harboring Rv1324 exhibited pathological injury and inflammation in the lung, which was mediated by ferroptosis. In summary, this study advances our understanding of the mechanisms of mycobacterial survival and pathogenesis, and it reveals a novel target for TB treatment. IMPORTANCE The intracellular survival of M. tuberculosis (Mtb) plays a crucial role in its pathogenesis, which depends on various Mtb oxidoreductases that are resistant to reactive oxygen and nitrogen species (ROS and RNS) that are generated by the host during Mtb infection. Secretory protein Rv1324 is a potential virulence factor of Mtb and is a possible thioredoxin that has oxidoreductase activity against ROS and RNS during Mtb infection. We investigated the biochemical properties of Mtb Rv1324 and its role in mycobacterial survival and virulence. It was confirmed that the Rv1324 protein had antioxidant activity and an increased mycobacterial resistance to ROS and RNS. In addition, Rv1324 enhanced mycobacterial persistence and induced pathological injury and inflammation in the lungs of mice by activating ferroptosis. This study advances our understanding of the mechanisms of mycobacterial survival and pathogenesis, and it reveals a novel target for TB treatment.

Single and combined toxicity assessment of primary or UV-aged microplastics and adsorbed organic pollutants on microalga Chlorella pyrenoidosa

Microplastics (MPs), an emerging pollutant, have been increasingly raising concern due to the potential impacts on aquatic organisms. Moreover, the environmental aged MPs always exhibit different environmental behavior and interaction effect with organic pollutants from virgin MPs. In this work, the single and combined toxicity impact on Chlorella pyrenoidosa, a symbiont representative, has been investigated between MPs (e.g., polyamide microplastic (PA6), 75 μm) and organic pollutants (e.g., sulfamethoxazole (SMX) and dicamba (DCB)). Growth inhibition, chlorophyll accumulation, superoxide dismutase (SOD), malondialdehyde (MDA), and catalase (CAT) were investigated with the primary or UV-aged PA6. Above 0.5 g/L PA6 (primary or UV-aged) inhibited cell growth and chlorophyll accumulation after 96 h cultivation as compared with the control. Besides, the inhibition impacts have enhanced as the UV-aging time extending in the single PA6 systems. The algae growth inhibition rate after 96 h cultivation in both the system i.e., single (PA6: 6.9%) and combined (PA6-SMX: 14.2%, PA6-DCB: 14.9%) was slightly lower than that of exposing in organic pollutants alone (SMX: 23.9%, DCB: 25.0%), while the chl. b concentration in 60 days UV-aged PA6 combined with SMX (1.19 mg/L) or DCB (1.40 mg/L) systems were higher than in single SMX (1.04 mg/L) or DCB (1.33 mg/L) system. In addition, there were several differences of the cellular oxidative stress in the combined system of SMX and DCB. Specially, it was not noticeable of three enzymatic activities for SMX exposing in the presence of primary or UV-aged PA6. While SOD, CAT, and MDA activities was obviously increasing after exposing in PA6 and DCB combined system, indicating the significant synergistic effect on algae cells damage. This research verified the remarkable combined toxicity between UV-aged MPs and organic pollutants on microalgae.

Targeted Mutagenesis of Mycobacterium Strains by Homologous Recombination

Targeted mutagenesis by homologous recombination (TMHR) is an efficient allelic exchange mutagenesis for bacterial genome engineering in synthetic biology. Unlike other allelic exchange methods, TMHR does not require a heterologous recombinase to insert or excise a selectable marker from the genome. In contrast, positive and negative selection is achieved solely by suicide vector-encoded functional and host cell proteins. Here we describe a concise protocol to knock out and knock in a 3-ketosteroid-1,2-dehydrogenase gene (kstd) in Mycobacterium neoaurum HGMS2 using TMHR approach. The homology arms flanking the kstd gene are amplified by PCR in vitro and then subcloned into a common homologous recombination vector. The vector is then electroporated into the HGMS2 competent cells. The replacement of the kstd gene by homologous recombination produces antibiotic-resistant single-crossover recombination via the first allelic exchange. Double-crossover markerless mutants are directly separated using sucrose-mediated counterselection. These two steps can generate seamless mutations down to a single DNA base pair. The whole process takes less than 2 weeks.

Ingestion and impacts of water-borne polypropylene microplastics on Daphnia similis

Polypropylene microplastics are the leading contaminant in aquatic environments, although research on their toxicity remains scarce. The proposed research focuses on the harmful consequences of acute exposure to polypropylene microplastics in Daphnia similis. This work converts widely available polypropylene bags into microplastics using xylene. FTIR findings demonstrated the lack of xylene residue in the produced polypropylene microplastic particles, which were spherical and ranged in size from 11.86 to 44.62 µm (FE-SEM). The results indicate that acute exposure to polypropylene microplastics causes immobility in D. similis. Ingestion of microplastics enhances the generation of reactive oxygen species (ROS), as shown by biochemical studies. Due to the production of free radicals in D. similis, the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) and a non-antioxidant enzyme of reduced glutathione (GSH) and also oxidative stress effects in lipid (lipid peroxidation - LPO), protein (carbonyl protein - CP) were increased. Additionally, the amount of the neurotransmitter enzyme acetylcholinesterase (AChE) activity was decreased. These findings indicate that the accumulation of polypropylene microplastics in the bodies of filter-feeding organisms should aggravate toxicity in the freshwater environment.

Individual and combined toxicity of microplastics and diuron differs between freshwater and marine diatoms

Microplastics are considered as the emerging pollutants, which not only directly affect aquatic organisms, but also causes combined pollution by adsorbing other pollutants. Diuron, as one of the most widely used herbicides, is frequently monitored in the aquatic environment for its adverse effects on aquatic organisms. However, little is known about the combined toxicity of microplastics and diuron to aquatic organisms, especially diatoms. In this study, freshwater diatom (Cyclotella meneghiniana) and marine diatom (Skeletonema costatum) were selected to study the individual and combined toxicity of microplastics (polystyrene, 0.6- 1.0 μm) and diuron. Experimental concentrations of microplastics and diuron were set at 50 mg/L and 100 μg/L, respectively, which have been shown to significantly inhibit the growth of aquatic organisms. Results suggested that both single microplastics and single diuron significantly inhibited the growth of the two diatoms, while significant SOD and MDA increase were only found in single diuron exposure. For diatoms exposed to individual microplastics, the microplastic particles adsorbed inside Cyclotella sp. and those aggregated around Skeletonema sp. were the major factor inhibiting the growth of diatom, respectively. According to the independent action model, the combined toxicity for both diatoms were all antagonistic. The adsorption behavior of microplastics to diuron alleviated the intracellular damage to diatoms caused by diuron, and the oxidative stress induced by diuron mitigated the physical damage to diatoms caused by microplastics. Collectively, our findings suggest that the co-existence of microplastics and diuron may affect their respective toxicity to diatoms. The mechanism of this "cross-phenomenon" between microplastics and diuron and their combined toxicity to different aquatic organisms need to be further studied.

Short-Term Exposure to MPs and DEHP Disrupted Gill Functions in Marine Bivalves

The synergistic impact of microplastics (MPs) and organic pollutants remains poorly understood in the marine environment. This study aimed to assess the toxicity of polypropylene microplastics (PS) and/or di-(2-ethylhexyl) phthalate (DEHP) on marine clams. Both Ruditapes philippinarum and Tegillarca granosa were exposed to PS and DEHP individually and combined at environmentally relevant concentrations for 48 h. The filtration rate, antioxidant enzymes activity, lipid peroxidation, reactive oxygen species accumulation, and histological alterations were evaluated. Our results show that single or co-exposure to MPs and DEHP significantly decreases the filtration rate in both type of clams, but the latter exhibited stronger inhibition effect. Close examination of accumulation of reactive oxygen species and related biomarkers revealed that combined exposure exerts greater oxidative stress in the cells, which causes more serious histopathological damage in the gills of the bivalves. Our study implies that MPs, in synergy with organic pollutants, can be more harmful for marine organisms.

Polyethylene microplastic exposure and concurrent effect with Aeromonas hydrophila infection on zebrafish

Microplastics are widely distributed in the environment, raising significant concerns owing to their potential negative effects on humans. Zebrafish were used in this study to assess the toxicity of microplastic exposure. Adult zebrafish were exposed to polyethylene (PE) microplastics with smooth clustered sphere shapes and diameters of 75-100 µm for 35 days. Survival rates of the zebrafish were not significantly affected, whereas growth rates were. Analyses on oxidative stress-related enzyme activities showed that glutathione (GSH), glutathione peroxidase (GSH-PX), and glutathione s-transferase (GST) production in the intestines was stimulated when exposed to low concentrations of microplastics (0.1 and 1 mg/L), while superoxide dismutase (SOD), catalase (CAT), GSH, and GSH-PX production was suppressed when exposed to 10 mg/L microplastics. Enzyme activities in the muscles were much less affected. Intestinal injuries and changes in colony structure in the intestines were observed in zebrafish following exposure to microplastics. After 35 days of exposure, concurrent exposure to microplastics and Aeromonas hydrophila did not increase zebrafish mortality compared with those challenged by bacteria alone. This study confirms that intestinal enzyme activities of zebrafish are altered by exposure to PE microplastics but mortality and bacterial infection were not significantly affected under the tested conditions.

Basic Analysis of the Cerebrospinal Fluid: An Important Framework for Laboratory Diagnostics of the Impairment of the Central Nervous System

Laboratory analysis of basic cerebrospinal fluid (CSF) parameters is considered as essential for any CSF evaluation. It can provide rapidly very valuable information about the status of the central nervous system (CNS). Our retrospective study evaluated parameters of basic CSF analysis in cases of either infectious or non-infectious CNS involvement. Neutrophils are effector cells of innate immunity. Predominance of neutrophils was found in 98.2% of patients with purulent inflammation in CNS. Lymphocytes are cellular substrate of adaptive immunity. We found their predominance in 94.8% of patients with multiple sclerosis (MS), 66.7% of patients with tick-borne encephalitis (TBE), 92.2% of patients with neuroborreliosis, 83.3% of patients with inflammatory response with oxidative burst of macrophages in CNS and 75.0% of patients with malignant infiltration of meninges (MIM). The simultaneous assessment of aerobic and anaerobic metabolism in CSF using the coefficient of energy balance (KEB) allows us to specify the type of inflammation in CNS. We found predominantly aerobic metabolism (KEB > 28.0) in 100.0% CSF of patients with normal CSF findings and in 92.8% CSF of patients with MS. Predominant faintly anaerobic metabolism (28.0 > KEB > 20.0) in CSF was found in 71.8% patients with TBE and in 64.7% patients with neuroborreliosis. Strong anaerobic metabolism (KEB < 10.0) was found in the CSF of 99.1% patients with purulent inflammation, 100.0% patients with inflammatory response with oxidative burst of macrophages and in 80.6% patients with MIM. Joint evaluation of basic CSF parameters provides sufficient information about the immune response in the CSF compartment for rapid and reliable diagnosis of CNS involvement.

Deciphering the Proteomic Landscape of Mycobacterium tuberculosis in Response to Acid and Oxidative Stresses

The fundamental to the pathogenicity of Mycobacterium tuberculosis (Mtb) is the modulation in the control mechanisms that play a role in sensing and counteracting the microbicidal milieu encompassing various cellular stresses inside the human host. To understand such changes, we measured the cellular proteome of Mtb subjected to different stresses using a quantitative proteomics approach. We identified defined sets of Mtb proteins that are modulated in response to acid and a sublethal dose of diamide and H₂O₂ treatments. Notably, proteins involved in metabolic, catalytic, and binding functions are primarily affected under these stresses. Moreover, our analysis led to the observations that during acidic stress Mtb enters into energy-saving mode simultaneously modulating the acid tolerance system, whereas under diamide and H₂O₂ stresses, there were prominent changes in the biosynthesis and homeostasis pathways, primarily modifying the resistance mechanism in diamide-treated bacteria while causing metabolic arrest in H₂O₂-treated bacilli. Overall, we delineated the adaptive mechanisms that Mtb may utilize under physiological stresses and possible overlap between the responses to these stress conditions. In addition to offering important protein signatures that can be exploited for future mechanistic studies, our study highlights the importance of proteomics in understanding complex adjustments made by the human pathogen during infection.

Molecular Connectivity between Extracytoplasmic Sigma Factors and PhoP Accounts for Coupled Mycobacterial Stress Response

Mycobacterium tuberculosis encounters numerous stress conditions within the host, but how it is able to mount a coupled stress response remains unknown. Growing evidence suggests that under acidic pH, M. tuberculosis modulates redox homeostasis. In an attempt to dissect the mechanistic details of responses to multiple stress conditions, here we studied the significance of connectivity of extracytoplasmic sigma factors with PhoP. We show that PhoP impacts the mycothiol redox state, and the H37Rv ΔphoP deletion mutant strain displays a significantly higher susceptibility to redox stress than the wild-type bacilli. To probe how the two regulators PhoP and redox-active sigma factor SigH contribute to redox homeostasis, we show that SigH controls expression of redox-active thioredoxin genes, a major mycobacterial antioxidant system, and under redox stress, SigH, but not PhoP, is recruited at the target promoters. Consistent with these results, interaction between PhoP and SigH fails to impact redox-dependent gene expression. This is in striking contrast to our previous results showing PhoP-dependent SigE recruitment within acid-inducible mycobacterial promoters to maintain pH homeostasis. Our subsequent results demonstrate reduced PhoP-SigH interaction in the presence of diamide and enhanced PhoP-SigE interaction under low pH. These contrasting results uncover the underlying mechanism of the mycobacterial adaptive program, coupling low pH with maintenance of redox homeostasis. IMPORTANCE M. tuberculosis encounters reductive stress under acidic pH. To investigate the mechanism of coupled stress response, we show that PhoP plays a major role in mycobacterial redox stress response. We observed a strong correlation of phoP-dependent redox-active expression of thioredoxin genes, a major mycobacterial antioxidant system. Further probing of functioning of regulators revealed that while PhoP controls pH homeostasis via its interaction with SigE, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of thioredoxin genes. These strikingly contrasting results showing enhanced PhoP-SigE interaction under acidic pH and reduced PhoP-SigH interaction under redox conditions uncover the underlying novel mechanism of the mycobacterial adaptive program, coupling low pH with maintenance of redox homeostasis.

NLRP3 inflammasome is involved in the mechanism of the mitigative effect of lycopene on sulfamethoxazole-induced inflammatory damage in grass carp kidneys

Freshwater environmental antibiotic pollution is becoming more severe because of the irregular use of sulfonamide antibiotics. Sulfamethoxazole (SMZ) is a kind of antibiotic that can cause harm to the urinary systems of organisms. However, the toxic impacts of environment-related concentrations of antibiotics in fish have not been thoroughly studied. Lycopene (LYC) has the property of alleviating antibiotic toxicity by diminishing oxidative stress and inflammation. This investigation is intended to examine the instrument of the mitigative part of LYC on SMZ-caused renal inflammatory injury in grass carp. Grass carp were born with SMZ (0. 3 μg L^-1) and LYC (10 mg/kg body weight) for 30 days. Serum was used to measure creatinine (CREA) and urea nitrogen (BUN) contents; what is more, kidneys were used to measure histological structure, oxidative stress indicators, relative expressions of cytokines, and inflammatory factors. We found that SMZ exposure significantly increased oxidative stress, characterized by decreased catalase activity (CAT) and superoxide dismutase (SOD). In addition, inflammation-related factors: interleukin (IL-18, IL-6, and IL-1β), an apoptotic speck-containing protein with a card (ASC), NOD-like receptor protein3 (NLRP3), cysteinyl aspartate specific proteinase-1 (caspase-1), tumor necrosis factor-α (TNF-α), and nuclear factor-activated B cells (NF-κB) expression increased significantly contrasted with those control group. Inflammatory reactions and ultrastructural changes accompany. LYC administration alleviated the changes mentioned above. In conclusion, In conclusion, these results suggest a protective effect of LYC dietary supplements against kidney damage caused by SMZ. LYC is expected to prevent and treat oxidative stress and chronic inflammation caused by antibiotics as a critical component in the fish breeding diet.

Old dogs, new tricks: New insights into the iron/manganese superoxide dismutase family

Superoxide dismutases (SODs) are ancient enzymes of widespread importance present in all domains of life. Many insights have been gained into these important enzymes over the 50 years since their initial description, but recent studies in the context of microbial pathogenesis have resulted in findings that challenge long established dogmas. The repertoire of SODs that bacterial pathogens encode is diverse both in number and in metal dependencies, including copper, copper and zinc, manganese, iron, and cambialistic enzymes. Other bacteria also possess nickel dependent SODs. Compartmentalization of SODs only partially explains their diversity. The need for pathogens to maintain SOD activity across distinct hostile environments encountered during infection, including those limited for essential metals, is also a driver of repertoire diversity. SOD research using pathogenic microbes has also revealed the apparent biochemical ease with which metal specificity can change within the most common family of SODs. Collectively, these studies are revealing the dynamic nature of SOD evolution, both that of individual SOD enzymes that can change their metal specificity to adapt to fluctuating cellular metal availability, and of a cell's repertoire of SOD isozymes that can be differentially expressed to adapt to fluctuating environmental metal availability in a niche.

The H2O2 Concentration-Dependent Kinetics of Gene Expression: Linking the Intensity of Oxidative Stress and Mycobacterial Physiological Adaptation

Defence against oxidative stress is crucial for Mycobacterium tuberculosis to survive and replicate within macrophages. Mycobacteria have evolved multilayer antioxidant systems, including scavenging enzymes, iron homeostasis, repair pathways, and metabolic adaptation, for coping with oxidative stress. How these systems are coordinated to enable the physiological adaptation to different intensities of oxidative stress, however, remains unclear. To address this, we investigated the expression kinetics of the well-characterized antioxidant genes at bacteriostatic H₂O₂ concentrations ranging from 1 mM to 10 mM employing Mycolicibacterium smegmatis as a model. Our results showed that most of the selected genes were expressed in a H₂O₂ concentration-dependent manner, whereas a subset exhibited sustained induction or repression without dose–effect, reflecting H₂O₂ concentration-dependent physiological adaptations. Through analyzing the dynamics of the coordinated gene expression, we demonstrated that the expressions of the H₂O₂ scavenging enzymes, DNA damage response, and Fe–S cluster repair function were strikingly correlated to the intensity of oxidative stress. The sustained induction of mbtB, irtA, and dnaE2 indicated that mycobacteria might deploy increased iron acquisition and error-prone lesion bypass function as fundamental strategies to counteract oxidative damages, which are distinct from the defence tactics of Escherichia coli characterized by shrinking the iron pool and delaying the DNA repair. Moreover, the distinct gene expression kinetics among the tricarboxylic acid cycle, glyoxylate shunt, and methylcitrate cycle suggested that mycobacteria could dynamically redirect its metabolic fluxes according to the intensity of oxidative stress. This work defines the H₂O₂ concentration-dependent gene expression kinetics and provides unique insights into mycobacterial antioxidant defence strategies.

The autophagy-resistant Mycobacterium tuberculosis Beijing strain upregulates KatG to evade starvation-induced autophagic restriction

Mycobacterium tuberculosis utilizes several mechanisms to block phagosome–lysosome fusion to evade host cell restriction. However, induction of host cell autophagy by starvation was shown to overcome this block, resulting in enhanced lysosomal delivery to mycobacterial phagosomes and the killing of the M. tuberculosis reference strain H37Rv. Nevertheless, our previous studies found that strains belonging to the M. tuberculosis Beijing genotype can resist starvation-induced autophagic elimination, though the mycobacterial factors involved remain unclear. In this study, we showed that KatG expression is upregulated in the autophagy-resistant M. tuberculosis Beijing strain (BJN) during autophagy induction by the starvation of host macrophages, while such increase was not observed in the H37Rv. KatG depletion using the CRISPR-dCas9 interference system in the BJN resulted in increased lysosomal delivery to its phagosome and decreased its survival upon autophagy induction by starvation. As KatG functions by catabolizing ROS, we determined the source of ROS contributing to the starvation-induced autophagic elimination of mycobacteria. Using siRNA-mediated knockdown, we found that Superoxide dismutase 2, which generates mitochondrial ROS but not NADPH oxidase 2, is important for the starvation-induced lysosomal delivery to mycobacterial phagosomes. Taken together, these findings showed that KatG is vital for the BJN to evade starvation-induced autophagic restriction.

Mycobacterium avium Subsp. hominissuis Interactions with Macrophage Killing Mechanisms

Non-tuberculosis mycobacteria (NTM) are ubiquitously found throughout the environment. NTM can cause respiratory infections in individuals with underlying lung conditions when inhaled, or systemic infections when ingested by patients with impaired immune systems. Current therapies can be ineffective at treating NTM respiratory infections, even after a long course or with multidrug treatment regimens. NTM, such as Mycobacterium avium subspecies hominissuis (M. avium), is an opportunistic pathogen that shares environments with ubiquitous free-living amoeba and other environmental hosts, possibly their evolutionary hosts. It is highly likely that interactions between M. avium and free-living amoeba have provided selective pressure on the bacteria to acquire survival mechanisms, which are also used against predation by macrophages. In macrophages, M. avium resides inside phagosomes and has been shown to exit it to infect other cells. M. avium’s adaptation to the hostile intra-phagosomal environment is due to many virulence mechanisms. M. avium is able to switch the phenotype of the macrophage to be anti-inflammatory (M2). Here, we have focused on and discussed the bacterial defense mechanisms associated with the intra-phagosome phase of infection. M. avium possesses a plethora of antioxidant enzymes, including the superoxide dismutases, catalase and alkyl hydroperoxide reductase. When these defenses fail or are overtaken by robust oxidative burst, many other enzymes exist to repair damage incurred on M. avium proteins, including thioredoxin/thioredoxin reductase. Finally, M. avium has several oxidant sensors that induce transcription of antioxidant enzymes, oxidation repair enzymes and biofilm- promoting genes. These expressions induce physiological changes that allow M. avium to survive in the face of leukocyte-generated oxidative stress. We will discuss the strategies used by M. avium to infect human macrophages that evolved during its evolution from free-living amoeba. The more insight we gain about M. avium’s mode of pathogenicity, the more targets we can have to direct new anti-virulence therapies toward.

The effects and mechanisms of polystyrene and polymethyl methacrylate with different sizes and concentrations on Gymnodinium aeruginosum

In this study, Gymnodinium aeruginosum was exposed to polystyrene (PS) and polymethyl methacrylate (PMMA) of three particle sizes (0.1 μm, 1.0 μm and 100 μm) and two concentrations (10 mg/L and 75 mg/L) for 96 h. The density of algae cells, the endpoints that reactive oxygen species (ROS), total protein (TP), malondialdehyde (MDA), superoxide dismutase (SOD) and catalase (CAT), scanning and transmission electron microscopy (SEM and TEM) were used to explore the toxicity mechanism to the microalgae. At a concentration of 75 mg/L, the 96 h inhibition ratios (IR) with particle sizes of 0.1 μm, 1.0 μm and 100 μm on G. aeruginosum were 55.9%, 63.7% and 6.0% for PS, respectively, and 3.0%, 4.1% and -0.6% for PMMA, respectively. The most significant changes in ROS, TP, MDA, SOD and CAT were observed at 75 mg/L 1.0 μm of PS when treated for 96 h. When exposed to nanoplastics (NPs) and microplastics (MPs), the algae cells were damaged, and the antioxidant system was activated. Extracellular polymeric substance (EPS) could help to detoxify the algae. In general, PS was more toxic than PMMA. The toxicity of small MNPs (0.1 μm and 1.0 μm) was related to the concentrations, while large MNPs (100 μm) did not.

In silico analyses and design of a chimeric protein containing epitopes of SpaC, PknG, NanH, and SodC proteins for the control of caseous lymphadenitis

Abstract

Caseous lymphadenitis (CLA) is an infectious disease that affects goats and sheep causing drastic impacts on milk and meat production and is caused by Corynebacterium pseudotuberculosis. The disease can be prevented through vaccination but currently, vaccines demonstrate limited efficacy consequently leading to a need for the development of new ones. Here, we described the in silico development of a new chimeric protein constructed with epitopes identified from the sequences of the genes nanH, pknG, spaC, and sodC, previously described as potential vaccinal targets against C. pseudotuberculosis. The chimera was expressed, purified, and its immunogenicity was evaluated using sera of immunized mice. Results indicate the chimeric protein was able to stimulate antibody production. Additionally, analysis using serum from naturally infected goats showed that the protein is recognized by sera from these animals, indicating the possibility for using this chimera in new diagnostic methods.

Key points

• The chimera was expressed with 52 kDa and a yield of 7 mg/L after purification.

• The chimera was recognized by the sera of animals immunized with this formulation.

• Chimera reacted with the serum of goats naturally infected with C. pseudotuberculosis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11619-x.

Azithromycin induces dual effects on microalgae: Roles of photosynthetic damage and oxidative stress

Antibiotics are frequently detected in aquatic ecosystems, posing a potential threat to the freshwater environment. However, the response mechanism of freshwater microalgae to antibiotics remains inadequately understood. Here, the impacts of azithromycin (a broadly used antibiotic) on microalgae Chlorella pyrenoidosa were systematically studied. The results revealed that high concentrations (5-100 μg/L) of azithromycin inhibited algal growth, with a 96-h half maximal effective concentration of 41.6 μg/L. Azithromycin could weaken the photosynthetic activities of algae by promoting heat dissipation, inhibiting the absorption and trapping of light energy, impairing the reaction centre, and blocking electron transfer beyond Q_A. The blockage of the electron transport chain in the photosynthetic process further induced the generation of reactive oxygen species (ROS). The increases in the activities of superoxide dismutase, peroxidase and glutathione played important roles in antioxidant systems but were still not enough to scavenge the excessive ROS, thus resulting in the oxidative damage indicated by the elevated malondialdehyde level. Furthermore, azithromycin reduced the energy reserves (protein, carbohydrate and lipid) and impaired the cellular structure. In contrast, a hormesis effect on algal growth was found when exposed to low concentrations (0.5 and 1 μg/L) of azithromycin. Low concentrations of azithromycin could induce the activities of the PSII reaction centre by upregulating the mRNA expression of psbA. Additionally, increased chlorophyll b and carotenoids could improve the absorption of light energy and decrease oxidative damage, which further contributed to the increase in energy reserves (protein, carbohydrate and lipid). The risk quotients of azithromycin calculated in this study were higher than 1, suggesting that azithromycin could pose considerable ecological risks in real environments. The present work confirmed that azithromycin induced dual effects on microalgae, which provided new insight for understanding the ecological risk of antibiotics.

Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)

The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII2CIV2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII2CIV2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII2CIV2 activity.

Comparison of the effects of continuous and accumulative exposure to nanoplastics on microalga Chlorella pyrenoidosa during chronic toxicity

Most previous studies have focused on the continuous exposure of aquatic organisms to nanoplastics. However, persistent pollutants in natural aquatic surroundings are a threat, and their concentrations are continuously increasing. The discussion and research into the effects of accumulative exposure to these materials are limited. Therefore, this study aimed to compare the effects of continuous and accumulative exposure to polystyrene (PS) nanoplastics (80 nm) on Chlorella pyrenoidosa during chronic toxicity. The results indicated that under conditions of continuous exposure, this alga exhibited self-recovery to defend against the negative effects of PS nanoplastics during 15-21 days of exposure (the 21-d inhibitory rate was 1.41%). However, one unanticipated finding was that during the same period of accumulative exposure, nanoplastics retained a substantial and stable inhibitory effect on the algal growth (the 21-d inhibitory rate was 6.79% in accumulative exposure for twice), indicating the invalid self-recovery of algae. The results of scanning electron microscopy demonstrated that on day 21, the degree of damage to the algal cells under accumulative exposure was more severe than that under continuous exposure. Hence, nanoplastics exerted an irreversibly negative effect on aquatic organisms depending on the pattern, frequency, concentration, and duration of exposure. This project evaluated the practical significance of nanoplastics in aquatic ecosystems.

Spore Germination of the Obligate Biotroph Spongospora subterranea: Transcriptome Analysis Reveals Germination Associated Genes

For soilborne pathogens, germination of the resting or dormant propagule that enables persistence within the soil environment is a key point in pathogenesis. Spongospora subterranea is an obligate soilborne protozoan that infects the roots and tubers of potato causing root and powdery scab disease for which there are currently no effective controls. A better understanding of the molecular basis of resting spore germination of S. subterranea could be important for development of novel disease interventions. However, as an obligate biotroph and soil dwelling organism, the application of new omics techniques for the study of the pre-infection process in S. subterranea has been problematic. Here, RNA sequencing was used to analyse the reprogramming of S. subterranea resting spores during the transition to zoospores in an in-vitro model. More than 63 million mean high-quality reads per sample were generated from the resting and germinating spores. By using a combination of reference-based and de novo transcriptome assembly, 6,664 unigenes were identified. The identified unigenes were subsequently annotated based on known proteins using BLAST search. Of 5,448 annotated genes, 570 genes were identified to be differentially expressed during the germination of S. subterranea resting spores, with most of the significant genes belonging to transcription and translation, amino acids biosynthesis, transport, energy metabolic processes, fatty acid metabolism, stress response and DNA repair. The datasets generated in this study provide a basic knowledge of the physiological processes associated with spore germination and will facilitate functional predictions of novel genes in S. subterranea and other plasmodiophorids. We introduce several candidate genes related to the germination of an obligate biotrophic soilborne pathogen which could be applied to the development of antimicrobial agents for soil inoculum management.

Redox homeostasis in Mycobacterium tuberculosis is modulated by a novel actinomycete-specific transcription factor

Mycobacterium tuberculosis (Mtb) has evolved diverse cellular processes in response to the multiple stresses it encounters within the infected host. We explored available TnSeq datasets to identify transcription factors (TFs) that are essential for Mtb survival inside the host. The analysis identified a single TF, Rv1332 (AosR), conserved across actinomycetes with a so‐far uncharacterized function. AosR mitigates phagocyte‐derived oxidative and nitrosative stress, thus promoting mycobacterial growth in the murine lungs and spleen. Oxidative stress induces formation of a single intrasubunit disulphide bond in AosR, which in turn facilitates AosR interaction with an extracytoplasmic‐function sigma factor, SigH. This leads to the specific upregulation of the CysM‐dependent non‐canonical cysteine biosynthesis pathway through an auxiliary intragenic stress‐responsive promoter, an axis critical in detoxifying host‐derived oxidative and nitrosative radicals. Failure to upregulate AosR‐dependent cysteine biosynthesis during the redox stress causes differential expression of 6% of Mtb genes. Our study shows that the AosR‐SigH pathway is critical for detoxifying host‐derived oxidative and nitrosative radicals to enhance Mtb survival in the hostile intracellular environment.

Evolution of Drug-Resistant Mycobacterium tuberculosis Strains and Their Adaptation to the Human Lung Environment

In the last two decades, multi (MDR), extensively (XDR), extremely (XXDR) and total (TDR) drug-resistant Mycobacterium tuberculosis (M.tb) strains have emerged as a threat to public health worldwide, stressing the need to develop new tuberculosis (TB) prevention and treatment strategies. It is estimated that in the next 35 years, drug-resistant TB will kill around 75 million people and cost the global economy $16.7 trillion. Indeed, the COVID-19 pandemic alone may contribute with the development of 6.3 million new TB cases due to lack of resources and enforced confinement in TB endemic areas. Evolution of drug-resistant M.tb depends on numerous factors, such as bacterial fitness, strain's genetic background and its capacity to adapt to the surrounding environment, as well as host-specific and environmental factors. Whole-genome transcriptomics and genome-wide association studies in recent years have shed some insights into the complexity of M.tb drug resistance and have provided a better understanding of its underlying molecular mechanisms. In this review, we will discuss M.tb phenotypic and genotypic changes driving resistance, including changes in cell envelope components, as well as recently described intrinsic and extrinsic factors promoting resistance emergence and transmission. We will further explore how drug-resistant M.tb adapts differently than drug-susceptible strains to the lung environment at the cellular level, modulating M.tb-host interactions and disease outcome, and novel next generation sequencing (NGS) strategies to study drug-resistant TB.

Chemical- and species-specific toxicity of nonylphenol and octylphenol to microalgae Chlorella pyrenoidosa and Scenedesmus obliquus

As typical endocrine disrupters, nonylphenol (NP) and octylphenol (OP) are emerging pollutants that have attracted wide attention. This study investigated the toxicity effects of NP and OP on microalgae Chlorella pyrenoidosa and Scenedesmus obliquus, particularly on their growth inhibition, photosynthetic pigment, chlorophyll fluorescence, and superoxide dismutase and malondialdehyde levels. Results showed that the 96 h EC₅₀ of NP and OP was 2.89 and 5.21 mg/L on C. pyrenoidosa, respectively, and 1.54 and 8.48 mg/L on S. obliquus, respectively. NP exerted a stronger inhibitory effect on cell growth, photosynthesis, and PSII activity, and it contributed more oxidative stress on C. pyrenoidosa than on S. obliquus. By contrast, OP exerted a stronger inhibitory effect on S. obliquus than on C. pyrenoidosa. Furthermore, the toxicity of OP to the tested microalgae was lower than that of NP. Principal component analysis (PCA) and Pearson's correlation indicate that the accumulation of reactive oxygen species is the dominant mechanism of NP and OP cellular toxicity. The principal components of NP and OP affecting microalgae are distinct in the PCA plot, and different endocrine disrupters have varying chemical-specific influences on algal cells. This study confirmed that the toxicity of NP and OP to microalgae C. pyrenoidosa and S. obliquus is chemical- and species-specific. These findings should be considered when assessing the health risk of environmental pollution.

A novel stress-inducible CmtR-ESX3-Zn2+ regulatory pathway essential for survival of Mycobacterium bovis under oxidative stress

Reactive oxygen species (ROS) are an unavoidable host environmental cue for intracellular pathogens such as Mycobacterium tuberculosis and Mycobacterium bovis; however, the signaling pathway in mycobacteria for sensing and responding to environmental stress remains largely unclear. Here, we characterize a novel CmtR-Zur-ESX3-Zn2+ regulatory pathway in M. bovis that aids mycobacterial survival under oxidative stress. We demonstrate that CmtR functions as a novel redox sensor and that its expression can be significantly induced under H2O2 stress. CmtR can physically interact with the negative regulator Zur and de-represses the expression of the esx-3 operon, which leads to Zn2+ accumulation and promotion of reactive oxygen species detoxication in mycobacterial cells. Zn2+ can also act as an effector molecule of the CmtR regulator, using which the latter can de-repress its own expression for further inducing bacterial antioxidant adaptation. Consistently, CmtR can induce the expression of EsxH, a component of esx-3 operon involved in Zn2+ transportation that has been reported earlier, and inhibit phagosome maturation in macrophages. Lastly, CmtR significantly contributes to bacterial survival in macrophages and in the lungs of infected mice. Our findings reveal the existence of an antioxidant regulatory pathway in mycobacteria and provide novel information on stress-triggered gene regulation and its association with host-pathogen interaction.

The combined toxicity influence of microplastics and nonylphenol on microalgae Chlorella pyrenoidosa

Microplastics and nonylphenol (NP) are considered as emerging pollutant and have attracted wide attention, while their combined toxicity on aquatic organisms is barely researched. Therefore, the combined toxicity influence of NP with three types of microplastics containing polyethylene (PE1000, 13 μm and PE, 150 μm), polyamide (PA1000, 13 μm and PA, 150 μm) polystyrene (PS, 150 μm) on microalgae Chlorella pyrenoidosa was analyzed. Both growth inhibition, chlorophyll fluorescence, superoxide dismutase (SOD), malondialdehyde (MDA), and catalase (CAT) were determined. We found that single microplastics and NP both inhibited algal growth, thereby causing oxidative stress. The order of inhibition effect in single microplastics experiment was PE1000 > PA1000 > PE ≈ PS > PA. The combined toxicity experiment results indicated that the presence of microplastics had positive effect in terms of alleviating NP toxicity to C. pyrenoidosa, and the microplastics adsorption capacity to NP was the dominant contributing factor for this effect. According to the independent action model, the combined toxicity was antagonistic. Because the negative effect of smaller size microplastics on algal growth was aggravated with prolonged exposure time, the optimum effect of microplastics alleviated NP toxicity was PA1000 at 48 h, while this effect was substituted by PA at 96 h during combined toxicity. Thus, the toxicity of smaller size microplastics has a nonnegligible influence on combined toxicity. This study confirms that microplastics significantly affected the toxicity of organic pollutants on microalgae. Further research on the combined toxicity of smaller size microplastics with pollutants in chronic toxicity is needed.

Disappearance of Quorum Sensing in Burkholderia glumae During Experimental Evolution

The plant pathogen Burkholderia glumae uses quorum sensing (QS) that allows bacteria to share information and alter gene expression on the basis of cell density. The wild-type strain of B. glumae produces quorum-sensing signals (autoinducers) to detect their community and upregulate QS-dependent genes across the population for performing social and group behaviors. The model organism B. glumae was selected to investigate adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses by using experimental evolution. The wild-type B. glumae virulent strain showed genotypic changes during regular subculture due to oxygen limitation. The laboratory-evolved clones failed to produce the signaling molecule of C8-HSL/C6-HSL for activation of the quorum-sensing system. Further, the laboratory-evolved clones failed to produce catalase and oxalate for protecting themselves from the toxic environment at stationary phase and phytotoxins (toxoflavin) for infecting rice grain, respectively. The laboratory-evolved clones were completely sequenced and compared with the wild-type. Sequencing analysis of the evolved clones revealed that mutations in QS-responsible genes (iclR), sensor genes (shk, mcp), and signaling genes (luxR) were responsible for quorum-sensing activity failure. The experimental results and sequencing analysis revealed quorum-sensing process failure in the laboratory-evolved clones. In conclusion, the wild-type B. glumae strain was often exposed to oxidative stress during regular subculture and evolved as an avirulent strain (quorum-sensing mutant) by losing the phenotypic and genotypic characteristics.

Mycobacterium tuberculosis exploits host ATM kinase for survival advantage through SecA2 secretome

(Mtb) produces inflections in the host signaling networks to create a favorable milieu for survival. The virulent Mtb strain, Rv caused double strand breaks (DSBs), whereas the non-virulent Ra strain triggered single-stranded DNA generation. The effectors secreted by SecA2 pathway were essential and adequate for the genesis of DSBs. Accumulation of DSBs mediated through Rv activates ATM-Chk2 pathway of DNA damage response (DDR) signaling, resulting in altered cell cycle. Instead of the classical ATM-Chk2 DDR, Mtb gains survival advantage through ATM-Akt signaling cascade. Notably, in vivo infection with Mtb led to sustained DSBs and ATM activation during chronic phase of tuberculosis. Addition of ATM inhibitor enhances isoniazid mediated Mtb clearance in macrophages as well as in murine infection model, suggesting its utility for host directed adjunct therapy. Collectively, data suggests that DSBs inflicted by SecA2 secretome of Mtb provides survival niche through activation of ATM kinase.

The current state of animal models and genomic approaches towards identifying and validating molecular determinants of Mycobacterium tuberculosis infection and tuberculosis disease

Animal models are important in understanding both the pathogenesis of and immunity to tuberculosis (TB). Unfortunately, we are beginning to understand that no animal model perfectly recapitulates the human TB syndrome, which encompasses numerous different stages. Furthermore, Mycobacterium tuberculosis infection is a very heterogeneous event at both the levels of pathogenesis and immunity. This review seeks to establish the current understanding of TB pathogenesis and immunity, as validated in the animal models of TB in active use today. We especially focus on the use of modern genomic approaches in these models to determine the mechanism and the role of specific molecular pathways. Animal models have significantly enhanced our understanding of TB. Incorporation of contemporary technologies such as single cell transcriptomics, high-parameter flow cytometric immune profiling, proteomics, proteomic flow cytometry and immunocytometry into the animal models in use will further enhance our understanding of TB and facilitate the development of treatment and vaccination strategies.

Four superoxide dismutases of Bacillus cereus 0-9 are non-redundant and perform different functions in diverse living conditions

Superoxide dismutases (SODs) have been shown to exhibit high levels of conservation and exist in almost all aerobic organisms and even many strict anaerobes. There are four SODs in Bacillus cereus 0-9, and this coexistence of multiple homologous enzymes is of great significance in the evolution of bacteria. We hypothesized that the four sod genes in B. cereus 0-9 constituted non-redundant protection against oxidative damage in vivo and played unique roles in the pathogenicity of B. cereus 0-9 during different phases or growth environments. To test this hypothesis, we constructed four single-knockout mutants (∆sodA1, ∆sodA2, ∆sodS, and ∆sodC) and a mutant lacking all four sod genes (∆sod-4) of B. cereus 0-9 and assessed their various phenotypes. Our results indicated that sodA1 plays a major role in tolerance to intracellular oxidative stress and spore formation. The ∆sodA1 and ∆sod-4 mutants were very sensitive to oxidants. The spore formation of the ∆sodA1 mutant was dramatically delayed, and the ∆sod-4 mutant did not form any spores under our experimental conditions. The sodA2 gene may play an important role in negative regulation of swarming motility, pathogenicity, and phospholipase and haemolytic activity of B. cereus but also a role in positive regulation of biofilm formation under our experimental conditions. The other two genes, sodS and sodC, were key to the pathogenicity of B. cereus. The lethal rates of Helicoverpa armigera infected by the ∆sodS and ∆sodC mutants were only 26.67%, while wild-type B. cereus 0-9 caused lethality in up to 86.67% of the insects at 24 h after injection. Moreover, the ∆sod-4 mutant caused a reduced death rate of H. armigera of 46.70%, which was slightly higher than that caused by the ∆sodS and ∆sodC strains. Thus, these four sod genes were non-redundant for oxidative stress and may play different additional roles in B. cereus 0-9. These results can help us to further understand the biocontrol characteristics of B. cereus 0-9 and lay a theoretical foundation for further research.

Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses

Metabolic adaptation of Mycobacterium tuberculosis (M. tuberculosis) to microbicidal intracellular environment of host macrophages is fundamental to its pathogenicity. However, an in-depth understanding of metabolic adjustments through key reaction pathways and networks is limited. To understand how such changes occur, we measured the cellular metabolome of M. tuberculosis subjected to four microbicidal stresses using liquid chromatography-mass spectrometric multiple reactions monitoring (LC-MRM/MS). Overall, 87 metabolites were identified. The metabolites best describing the separation between stresses were identified through multivariate analysis. The coupling of the metabolite measurements with existing genome-scale metabolic model, and using constraint-based simulation led to several new concepts and unreported observations in M. tuberculosis; such as (i) the high levels of released ammonia as an adaptive response to acidic stress was due to increased flux through L-asparaginase rather than urease activity; (ii) nutrient starvation-induced anaplerotic pathway for generation of TCA intermediates from phosphoenolpyruvate using phosphoenolpyruvate kinase; (iii) quenching of protons through GABA shunt pathway or sugar alcohols as possible mechanisms of early adaptation to acidic and oxidative stresses; and (iv) usage of alternate cofactors by the same enzyme as a possible mechanism of rewiring metabolic pathways to overcome stresses. Besides providing new leads and important nodes that can be used for designing intervention strategies, the study advocates the strength of applying flux balance analyses coupled with metabolomics to get a global picture of complex metabolic adjustments.

Mechanisms of BCG immunotherapy and its outlook for bladder cancer

BCG immunotherapy is the gold-standard treatment for non-muscle-invasive bladder cancer at high risk of recurrence or progression. Preclinical and clinical studies have revealed that a robust inflammatory response to BCG involves several steps: attachment of BCG; internalization of BCG into resident immune cells, normal cells, and tumour urothelial cells; BCG-mediated induction of innate immunity, which is orchestrated by a cellular and cytokine milieu; and BCG-mediated initiation of tumour-specific immunity. As an added layer of complexity, variation between clinical BCG strains might influence development of tumour immunity. However, more than 40 years after the first use of BCG for bladder cancer, many questions regarding its mechanism of action remain unanswered. Clearly, a better understanding of the mechanisms underlying BCG-mediated tumour immunity could lead to improved efficacy, increased tolerance of treatment, and identification of novel immune-based therapies. Indeed, enthusiasm for bladder cancer immunotherapy, and the possibility of combining BCG with other therapies, is increasing owing to the availability of targeted immunotherapies, including checkpoint inhibitors. Understanding of the mechanism of action of BCG immunotherapy has advanced greatly, but many questions remain, and further basic and clinical research efforts are needed to develop new treatment strategies for patients with bladder cancer.

Distribution of reactive oxygen species defense mechanisms across domain bacteria

Bacteria are the most diverse and numerous organisms on the planet, inhabiting environments from the deep subsurface to particles in clouds. Across this range of conditions, bacteria have evolved a diverse suite of enzymes to mitigate cellular damage from reactive oxygen species (ROS). Here, we review the diversity and distribution of ROS enzymatic defense mechanisms across the domain Bacteria, using both peer-reviewed literature and publicly available genome databases. We describe the specific strategies used by well-characterized organisms in order to highlight differences in oxidative stress responses between aerobic, facultatively anaerobic, and anaerobic lifestyles. We present evidence from genome minimization experiments to suggest that ROS defenses are obligately required for life. This review clarifies the variability in ROS defenses across Bacteria, including the novel diversity found in currently uncharacterized Candidate Phyla.

Teleost contributions to the understanding of mycobacterial diseases

Few pathogens have shaped human medicine as the mycobacteria. From understanding biological phenomena driving disease spread, to mechanisms of host-pathogen interactions and antibiotic resistance, the Mycobacterium genus continues to challenge and offer insights into the basis of health and disease. Teleost fish models of mycobacterial infections have progressed significantly over the past three decades, now supplying a range of unique tools and new opportunities to define the strategies employed by these Gram-positive bacteria to overcome host defenses, as well as those host antimicrobial pathways that can be used to limit its growth and spread. Herein, we take a comparative perspective and provide an update on the contributions of teleost models to our understanding of mycobacterial diseases.

Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups

BACKGROUND

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. An improved understanding of the genetic diversity of C. burnetii is essential for the development of diagnostics, vaccines and therapeutics, but genotyping data is lacking from many parts of the world. Sporadic outbreaks of Q fever have occurred in the United Kingdom, but the local genetic make-up of C. burnetii has not been studied in detail.

RESULTS

Here, we report whole genome data for nine C. burnetii sequences obtained in the UK. All four genomes of C. burnetii from cattle, as well as one sheep sample, belonged to Multi-spacer sequence type (MST) 20, whereas the goat samples were MST33 (three genomes) and MST32 (one genome), two genotypes that have not been described to be present in the UK to date. We established the phylogenetic relationship between the UK genomes and 67 publically available genomes based on single nucleotide polymorphisms (SNPs) in the core genome, which confirmed tight clustering of strains within genomic groups, but also indicated that sub-groups exist within those groups. Variation is mainly achieved through SNPs, many of which are non-synonymous, thereby confirming that evolution of C. burnetii is based on modification of existing genes. Finally, we discovered genomic-group specific genome content, which supports a model of clonal expansion of previously established genotypes, with large scale dissemination of some of these genotypes across continents being observed.

CONCLUSIONS

The genetic make-up of C. burnetii in the UK is similar to the one in neighboring European countries. As a species, C. burnetii has been considered a clonal pathogen with low genetic diversity at the nucleotide level. Here, we present evidence for significant variation at the protein level between isolates of different genomic groups, which mainly affects secreted and membrane-associated proteins. Our results thereby increase our understanding of the global genetic diversity of C. burnetii and provide new insights into the evolution of this emerging zoonotic pathogen.

Interaction effects of oxytetracycline and copper at different ratios on marine microalgae Isochrysis galbana

Contamination with both oxytetracycline (OTC) and Cu is prevalent in water. OTC can chelate with Cu to form OTC + Cu composites. Through the study of the effects of the interaction of OTC and Cu on the algae Isochrysis galbana at multiple coordination ratios, it was found that the OTC + Cu complex was antagonistic to algae growth after 24 h of exposure but was synergistic in treatment (T) 3 and T4 after 48 and 72 h. Compared with OTC alone, the addition of Cu addition significantly inhibited the biosynthesis of chlorophyll a, but the ratio (R) in the OTC + Cu and OTC treatments gradually increased from T1 to T4. The addition of Cu also led to a significant increase in malondialdehyde and reactive oxygen species, but R gradually decreased and increased, respectively, from T1 to T4. The accumulation of OTC in algae was considerably promoted by the addition of Cu, with R increasing 1.5 in T2 to 2.6 in T4; moreover, the residue of OTC in water was reduced in the presence of algae. OTC alone dramatically inhibited the absorption of Cu by algae, while in the presence of OTC + Cu, only the two high-OTC treatments showed a significant decrease in Cu absorption. In addition, the absorption of Mg was markedly inhibited in all OTC treatments and the adsorption of K in the high-OTC treatment, but these inhibitory effects were alleviated in the OTC + Cu treatment. These results indicated that the effects of the OTC + Cu complex on algae were different from the effects of OTC and Cu alone.

Single and combined effects of microplastics and roxithromycin on Daphnia magna

There is a rising concern about the pollution of microplastics (plastic particles < 5 mm) in water due to their physicochemical properties, especially their interaction with organic contaminants; however, such knowledge is still limited. The mass production and consumption of medication for the treatment of infectious diseases in human and animals have led to the ubiquity of antibiotics in the environment. We studied the single and joint effects of microplastics (1-μm and 10-μm polystyrene particles, PS) and roxithromycin (ROX) on Daphnia magna through the acute and sublethal toxicity tests. The 48-h median effective concentration (EC₅₀) of 1-μm and 10-μm PS to D. magna was 66.97 mg/L and 199.94 mg/L, respectively, while the value of ROX was 20.28 mg/L. Malondialdehyde (MDA) levels and the activities of four enzymatic biomarkers, including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and glutathione S-transferase (GST), were further detected to assess the oxidative stress caused in D. magna caused. The results showed that 48-h exposure to PS (0.1 mg/L) or ROX (0.01 mg/L) alone activated the activities of CAT and GST and MDA levels. When compared with the ROX alone, the responses of GPx and MDA in D. magna co-exposed to 1-μm PS were significantly decreased, while co-exposure to 10-μm PS significantly decreased the responses of GST and MDA. Furthermore, the integrated biomarker response version 2 (IBRv2) analysis revealed that co-exposure to 1-μm PS and ROX led to the strongest biological responses in D. magna. Our findings underlined that microplastics should be a concern when they interact with the co-existence of pollutants in the aquatic environment.