Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungi

Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa

The bacterial cell envelope is the structure with which the bacterium engages with, and is protected from, its environment. Within this envelop is a conserved peptidoglycan polymer which confers shape and strength to the cell envelop. The enzymatic processes that build, remodel, and recycle the chemical components of this cross-linked polymer are preeminent targets of antibiotics and exploratory targets for emerging antibiotic structures. We report a comprehensive kinetic and structural analysis for one such enzyme, the Pseudomonas aeruginosa anhydro-N-acetylmuramic acid (anhNAM) kinase (AnmK). AnmK is an enzyme in the peptidoglycan-recycling pathway of this pathogen. It catalyzes the pairing of hydrolytic ring opening of anhNAM with concomitant ATP-dependent phosphoryl transfer. AnmK follows a random-sequential kinetic mechanism with respect to its anhNAM and ATP substrates. Crystallographic analyses of four distinct structures (apo AnmK, AnmK:AMPPNP, AnmK:AMPPNP:anhNAM, and AnmK:ATP:anhNAM) demonstrate that both substrates enter the active site independently in an ungated conformation of the substrate subsites, with protein loops acting as gates for anhNAM binding. Catalysis occurs within a closed conformational state for the enzyme. We observe this state crystallographically using ATP-mimetic molecules. A remarkable X-ray structure for dimeric AnmK sheds light on the precatalytic and postcatalytic ternary complexes. Computational simulations in conjunction with the high-resolution X-ray structures reveal the full catalytic cycle. We further report that a P. aeruginosa strain with disrupted anmK gene is more susceptible to the β-lactam imipenem compared to the WT strain. These observations position AnmK for understanding the nexus among peptidoglycan recycling, susceptibility to antibiotics, and bacterial virulence.

Kinetics and mechanism of sulfate radical-and hydroxyl radical-induced disinfection of bacteria and fungal spores by transition metal ions-activated peroxymonosulfate

Peroxymonosulfate(PMS)-based advanced oxidation process have been recognized as efficient disinfection processes. This study comprehensively investigated the role of sulfate radical (SO4•-) and hydroxyl radical (•OH)-driven disinfection of bacteria and fungal spores by the PMS/metals ions (Me(II)) systems and modeled the CT value based on the relationship between survival and ∫[Radical]dt, with the aim to provide an accurate and quantitative kinetic data of inactivation processes. The results indicated that •OH played a more central role than SO4•- in the inactivation process, and bacteria were more vulnerable to radical attack than fungal spores due to the differences in antioxidant mechanisms and external structures. The k value of •OH -induced inactivation of E. coli was approximately 3-fold higher than that of A. niger, and the shoulder length of •OH -induced inactivation of E. coli was closely 52-fold shorter than that of A. niger after treated with the PMS/Co(II) system. The morphological and biochemical changes revealed that PMS/Me(II) treatment caused membrane damage, intracellular ROS accumulation and esterase activity loss in microorganisms. This study significantly improved the understanding of the contribution of radicals in the process of microbial inactivation by PMS/Me(II) and would provide important implications for the further development of technologies to cope with the highly resistant fungal spores in drinking water.

Occurrence and control of fungi in water: New challenges in biological risk and safety assurance

Recently, the contamination of fungi in water has aroused widespread concern, which will pose a threat to water quality and safety, and raise diseases risk in the immunocompromised individuals. In this review, the characteristics and different physiological state of fungi in water are summarized. A comprehensive evaluation of the control efficiency and mechanism of waterborne fungi by the commonly used disinfection methods is provided as well. During the disinfection processes of chlorine, chlorine dioxide, chloramine and advanced disinfection processes (ADPs) such as O₃-based ADPs and UV-based ADPs, the fungal spores firstly lost their culturability, followed by membrane integrity, and the intracellular reactive oxygen species level increased at the same time, eventually the fungal spores were completely inactivated. The security strategies of drinking water against the contamination of fungi are also discussed in terms of water sources, water treatment plants and pipe network. Finally, future researches need to be explored are proposed: the rapid detection methods, the production laws and control of mycotoxin, and the outbreak conditions of fungi in water. Specifically, exploring efficient, safe and economical technologies, especially ADPs, is still the main direction in the disinfection of fungi in future studies. This review can offer a comprehensive understanding on the occurrence and control of fungi in water to fill the knowledge gap and provide guidance for the future research.

Sequential use of UV-LEDs irradiation and chlorine to disinfect waterborne fungal spores: Efficiency, mechanism and photoreactivation

In this work, sequential applications of light-emitting diodes (UV-LEDs) with two wavelengths and chlorine (Cl₂) were performed for fungal spores disinfection: UV-Cl₂, Cl₂-UV, UV/Cl₂-UV, UV-UV/Cl₂, Cl₂-UV/Cl₂-Cl₂. Overall comparisons of the sequential processes with respect to the inhibitory effect on photoreactivation were also evaluated. According to the evaluation of culturability and membrane permeability, inactivation of fungal spores by UV was not enhanced by prior or post exposure to Cl₂, but in the UV/Cl₂ process with pre or post UV treatment, the inactivation efficiency was greatly enhanced. Take P. polonicum for example, pre-treatments by UV₂₆₅ and UV₂₈₀ (40 mJ/cm²) caused the log count reduction (LCR) of 1.05 log and 0.95 log, then the followed UV₂₆₅/Cl₂ and UV₂₈₀/Cl₂ at the same UV fluence caused additional LCR of 1.80 log and 2.00 log. The permeabilization of P. polonicum was also accelerated in the processes of UV/Cl₂-UV and UV-UV/Cl₂, especially at the wavelength of 280 nm. In the sequential processes, especially those containing UV/Cl₂ or at the wavelength of 280 nm, could promote the formation of intracellular reactive oxygen species (ROS), thus leading to more severe damage to the spores as reflected in the culturability reduction, membrane permeability and inhibition of photoreactivation.

Efficacy of UV-LED based advanced disinfection processes in the inactivation of waterborne fungal spores: Kinetics, photoreactivation, mechanism and energy requirements

The contamination of fungi in water supply systems poses great risks to environment and human health. In this work, UV light-emitting diodes (UV-LEDs)-based advanced disinfection processes (ADPs) including UV-LEDs/hydrogen peroxide (H₂O₂), UV-LEDs/persulfate (PS) and UV-LEDs/peroxymonosulfate (PMS), were adopted for waterborne fungal spores inactivation. Overall comparisons of the UV-LEDs-based ADPs with respect to the control efficiency of photoreactivation and energy consumption were also evaluated. Results showed that culturability reduction of the fungal spores treated by UV-LEDs was not enhanced with the addition H₂O₂, PMS, and PS according to the results of heterotrophic plate counts and reaction rate constants; A. niger was expected to have higher UV resistance followed by T. harzianum and P. polonicum. However, UV-LEDs-ADPs inactivation, especially at the wavelengths of 280 and 265/280 nm, could accelerate the permeabilization of fungal spores as characterized by flow cytometry. Take P. polonicum for example, the percentage of membrane permeabilized spores was 98.0%, 98.7%, 97.6% and 82.6% after treatment by UV₂₈₀/H₂O₂, UV₂₈₀/PS, UV₂₈₀/PMS and UV₂₈₀ alone, respectively at the fluence of 100 mJ/cm². The direct attack of free radicals in the processes of UV-LEDs-ADPs further enhanced the membrane damage and lowered the photoreactivation level, thus improved the inactivation efficiency. UV-LEDs/H₂O₂ was considered as an effective process in the disinfection of fungal spores with the advantages of enhancing the damage of membrane, inhibiting photoreactivation and comparable energy consumption compared with UV-LEDs alone.

Proteomics and genetic analyses reveal the effects of arsenite oxidation on metabolic pathways and the roles of AioR in Agrobacterium tumefaciens GW4

A heterotrophic arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 isolated from As(III)-rich groundwater sediment showed high As(III) resistance and could oxidize As(III) to As(V). The As(III) oxidation could generate energy and enhance growth, and AioR was the regulator for As(III) oxidase. To determine the related metabolic pathways mediated by As(III) oxidation and whether AioR regulated other cellular responses to As(III), isobaric tags for relative and absolute quantitation (iTRAQ) was performed in four treatments, GW4 (+AsIII)/GW4 (-AsIII), GW4-ΔaioR (+AsIII)/GW4-ΔaioR (-AsIII), GW4-ΔaioR (-AsIII)/GW4 (-AsIII) and GW4-ΔaioR (+AsIII)/GW4 (+AsIII). A total of 41, 71, 82 and 168 differentially expressed proteins were identified, respectively. Using electrophoretic mobility shift assay (EMSA) and qRT-PCR, 12 genes/operons were found to interact with AioR. These results indicate that As(III) oxidation alters several cellular processes related to arsenite, such as As resistance (ars operon), phosphate (Pi) metabolism (pst/pho system), TCA cycle, cell wall/membrane, amino acid metabolism and motility/chemotaxis. In the wild type with As(III), TCA cycle flow is perturbed, and As(III) oxidation and fermentation are the main energy resources. However, when strain GW4-ΔaioR lost the ability of As(III) oxidation, the TCA cycle is the main way to generate energy. A regulatory cellular network controlled by AioR is constructed and shows that AioR is the main regulator for As(III) oxidation, besides, several other functions related to As(III) are regulated by AioR in parallel.

New insights into a hot environment for early life

Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB. In vivo, the formation process of the 1,6-anhydro bond of sugars on the peptidoglycan of prokaryotic cell wall is parallel to in vitro processes, suggesting that the 1,6-anhydro bond is an ideal CMB-like analogue that suggests a hot setting for early life. The CMB-like 1,6-anhydro bond is involved in the life cycle of viruses and the metabolism of eukaryotes, underlying this notion. From a novel perspective, the application of the concept of the CMB to microbial ecology may give new insights into a hot environment, such as hydrothermal vents, supporting early life and providing hypotheses to test in molecular palaeontology.

Bioconversion of anhydrosugars: Emerging concepts and strategies

As methods for the use of anhydrosugars in chemical and biofuel production continue to develop, our collective knowledge of anhydrosugar processing enzymes continues to improve, including their mechanistic details, structural dynamics and modes of substrate binding. Of particular interest, anhydrosugar kinases, such as levoglucosan kinase (LGK) and 1,6-anhydro-N-acetylmuramic acid kinase (AnmK), utilize an unusual mechanism whereby the sugar substrate is both cleaved and phosphorylated. The phosphorylated sugar can then be routed to other metabolic pathways, thereby allowing its further bioconversion. Advanced engineering efforts to improve the catalytic efficiency and stability of LGK have been steadily progressing. Other enzymes that cleave the glycosidic bond of disaccharide sugars containing an anhydrosugar component are also being identified and characterized. Accordingly, the potential future use of these enzymes in large-scale production strategies is becoming increasingly viable. Here, a mini-review of the observed characteristics of anhydrosugar processing enzymes is presented along with recent developments in the bioconversion of these sugars. © 2016 IUBMB Life 68(9):700-708, 2016.