Chloramphenicol is a substrate for a novel nitroreductase pathway in Haemophilus influenzae

ChlOR, a GMC family oxidoreductase that evolved independently from the actinomycete, confers resistance to amphenicol antibiotics

Overuse of the amphenicol antibiotics chloramphenicol (CHL) and thiamphenicol (TAP) poses a great threat to ecosystem safety and human health. The strain, Nocardioides sp. LMS-CY, Nocardioides sp. QY071 and Nocardioides sp. L-11A, classified as a gram-positive actinomycete, harbours a complete CHL metabolic pathway. However, the metabolic genes (clusters) involved in the entire pathway in gram-positive actinomycetes are still limited. Here, chlORLMS , chlORQY071 and chlORL-11A completely from the actinomycete Nocardioides spp. were found to act on the C1 -OH of the CHL/TAP side chain, directly converting CHL/TAP to 4-nitrobenzaldehyde (PNBD)/4-methylsulfonyl benzaldehyde (PMBD) and transforming PNBD/PMBD into 4-nitrobenzyl alcohol (PNBM)/4-methylsulfonyl phenyl methanol (PMBM). Furthermore, oxidoreductases can transform PNBM into 4-nitrobenzoate (PNBA). The oxidoreductases ChlORLMS , ChlORQY071 and ChlORL-11A were all classified as cellobiose dehydrogenases from the glucose methanol choline (GMC) family. Based on the Swiss-Prot database, ChlORQY071 exhibited a lower identity (27.12%-35.10% similarity) with the reported oxidoreductases. Enzymatic and molecular docking analyses showed that ChlORQY071 and ChlORL-11A from the two similar genomes were remarkably more effective in metabolizing CHL than ChlORLMS . Overall, the detailed resistance mechanism of CHL/TAP by actinomycete strains isolated from soil and livestock manure will provide insights into the occurrence of CHL/TAP resistance genes in the environment, resistance risk and bioremediation of CHL/TAP-contaminated environments.

Biotransformation of chloramphenicol by white-rot-fungi Trametes versicolor under cadmium stress

The recalcitrant chloramphenicol (CAP) combined with heavy metals cadmium (Cd) commonly co-existed in the environment, posing threat to environment health. The capacity of Trametes versicolor to remove/biodegrade CAP in air-pulse fluidized-bed reactor was evaluated, even under Cd stress. T. versicolor could remove 44 % CAP of 5 mg/L in 15 days, even 51 % CAP under 1 mg/L Cd stress. Sustained Cd stress inhibited CAP biodegradation and Cd removal in a 5-batches of a 5-days cycle sequential batch reactor. Nine transformation products and two novel pathways were proposed, with initial multi-step transformation reaction into CP2 and allylic alcohol, respectively. Furthermore, the main mechanism of Cd removal by T. versicolor was extracellular surface bioadsorption and intracellular accumulation. This study filled the gap of the mechanism of simultaneous CAP removal/biodegradation and Cd removal by white-rot fungi T. versicolor, which offer a theoretical basis for future application of biological removal of CAP containing wastewater.

The capability of chloramphenicol biotransformation of Klebsiella sp. YB1 under cadmium stress and its genome analysis

Co-contamination by antibiotics and heavy metal is common in the environment, however, there is scarce information about antibiotics biodegradation under heavy metals stress. In this study, Klebsiella sp. Strain YB1 was isolated which is capable of biodegrading chloramphenicol (CAP) with a biodegradation efficiency of 22.41% at an initial CAP of 10 mg L^-1 within 2 days. CAP biodegradation which fitted well with the first-order kinetics. YB1 still degrades CAP under Cd stress, however 10 mg L^-1 Cd inhibited CAP biodegradation by 15.1%. Biotransformation pathways remained the same under Cd stress, but two new products (Cmpd 19 and Cmpd 20) were identified. Five parallel metabolism pathways of CAP were proposed with/without Cd stress, including one novel pathway (pathway 5) that has not been reported before. In pathway 5, the initial reaction was oxidation of CAP by disruption of C-C bond at the side chain of C1 and C2 with the formation of 4-nitrobenzyl alcohol and CY7, then these intermediates were oxidized into p-nitrobenzoic acid and CY1, respectively. CAP acetyltransferase and nitroreductase and 2,3/4,5-dioxygenase may play an important role in CAP biodegradation through genome analysis and prediction. This study deepens our understanding of mechanism of antibiotic degradation under heavy metal stress in the environment.

The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification

Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.

Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

BACKGROUND

As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance genes. Microbes play a vital role in the decomposition of chloramphenicol in the environment, and the biotransformation processes are especially dependent on synergistic interactions and metabolite exchanges among microbes. Herein, the comprehensive chloramphenicol biotransformation pathway, key metabolic enzymes, and interspecies interactions in an activated sludge-enriched consortium were elucidated using integrated multi-omics and cultivation-based approaches.

RESULTS

The initial biotransformation steps were the oxidization at the C₁-OH and C₃-OH groups, the isomerization at C₂, and the acetylation at C₃-OH of chloramphenicol. Among them, the isomerization is an entirely new biotransformation pathway of chloramphenicol discovered for the first time. Furthermore, we identified a novel glucose-methanol-choline oxidoreductase responsible for the oxidization of the C₃-OH group in Sphingomonas sp. and Caballeronia sp. Moreover, the subsequent biotransformation steps, corresponding catalyzing enzymes, and the microbial players responsible for each step were deciphered. Synergistic interactions between Sphingomonas sp. and Caballeronia sp. or Cupriavidus sp. significantly promoted chloramphenicol mineralization, and the substrate exchange interaction network occurred actively among key microbes.

CONCLUSION

This study provides desirable strain and enzyme resources for enhanced bioremediation of chloramphenicol-contaminated hotspot sites such as pharmaceutical wastewater and livestock and poultry wastewater. The in-depth understanding of the chloramphenicol biotransformation mechanisms and microbial interactions will not only guide the bioremediation of organic pollutants but also provide valuable knowledge for environmental microbiology and biotechnological exploitation. Video Abstract.

Human Gut Microbiota and Drug Metabolism

The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.

Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens

Phylogenetically diverse bacteria can carry out chloramphenicol reduction, but only a single enzyme has been described that efficiently catalyzes this reaction, the NfsB nitroreductase from Haemophilus influenzae strain KW20. Here, we tested the hypothesis that some NfsB homologs function as housekeeping enzymes with the potential to become chloramphenicol resistance enzymes. We found that expression of H. influenzae and Neisseria spp. nfsB genes, but not Pasteurella multocida nfsB, allows Escherichia coli to resist chloramphenicol by nitroreduction. Mass spectrometric analysis confirmed that purified H. influenzae and N. meningitides NfsB enzymes reduce chloramphenicol to amino-chloramphenicol, while kinetics analyses supported the hypothesis that chloramphenicol reduction is a secondary activity. We combined these findings with atomic resolution structures of multiple chloramphenicol-reducing NfsB enzymes to identify potential key substrate-binding pocket residues. Our work expands the chloramphenicol reductase family and provides mechanistic insights into how a housekeeping enzyme might confer antibiotic resistance. IMPORTANCE The question of how new enzyme activities evolve is of great biological interest and, in the context of antibiotic resistance, of great medical importance. Here, we have tested the hypothesis that new antibiotic resistance mechanisms may evolve from promiscuous housekeeping enzymes that have antibiotic modification side activities. Previous work identified a Haemophilus influenzae nitroreductase housekeeping enzyme that has the ability to give Escherichia coli resistance to the antibiotic chloramphenicol by nitroreduction. Herein, we extend this work to enzymes from other Haemophilus and Neisseria strains to discover that expression of chloramphenicol reductases is sufficient to confer chloramphenicol resistance to Es. coli, confirming that chloramphenicol reductase activity is widespread across this nitroreductase family. By solving the high-resolution crystal structures of active chloramphenicol reductases, we identified residues important for this activity. Our work supports the hypothesis that housekeeping proteins possessing multiple activities can evolve into antibiotic resistance enzymes.

Rapid removal of chloramphenicol via the synergy of Geobacter and metal oxide nanoparticles

The wide use of chloramphenicol and its residues in the environments are an increasing threat to human beings. Electroactive microorganisms were proven with the ability of biodegradation of chloramphenicol, but the removal rate and efficiency need to be improved. In this study, a model electricigens, Geobacter metallireducens, was supplied with and Fe₃O₄ and MnO₂ nanoparticles. Five times higher chloramphenicol removal rate (0.71 d^-1) and two times higher chloramphenicol removal efficiency (100%) was achieved. Fe₃O₄ and MnO₂ nanoparticles highly increased the current density and NADH-quinone oxidoreductase expression. Fe₃O₄ nanoparticles enhanced the expression of alcohol dehydrogenase and c-type cytochrome, while MnO₂ nanoparticles increased the transcription of pyruvate dehydrogenase and Type IV pili assembly genes. Chloramphenicol was reduced to a type of dichlorination reducing product named CPD3 which is a benzene ring containing compound. Collectively, Fe₃O₄ and MnO₂ nanoparticles increased the chloramphenicol removal capacity in MFCs by enhancing electron transfer efficiency. This study provides new enhancing strategies for the bioremediation of chloramphenicol in the environments.

Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles

Nitroheterocycle antibiotics, particularly 5-nitroimidazoles, are frequently used for treating anaerobic infections. The antimicrobial activities of these drugs heavily rely on the in vivo bioactivation, mainly mediated by widely distributed bacterial nitroreductases (NTRs). However, the bioactivation can also lead to severe toxicities and drug resistance. Mechanistic understanding of NTR-mediated 5-nitroimidazole metabolism can potentially aid addressing these issues. Here, we report the metabolism of structurally diverse nitroimidazole drug molecules by a NTR from a human pathogen Haemophilus influenzae (HiNfsB). Our detailed bioinformatic analysis uncovered that HiNfsB represents a group of unexplored oxygen-insensitive NTRs. Biochemical characterization of the recombinant enzyme revealed that HiNfsB effectively metabolizes ten clinically used nitroimidazoles. Furthermore, HiNfsB generated not only canonical nitroreduction metabolites but also stable, novel dimeric products from three nitroimidazoles, whose structures were proposed based on the results of high resolution MS and tandem MS analysis. X-ray structural analysis of the enzyme coupled with site-directed mutagenesis identified four active site residues important to its catalysis and broad substrate scope. Finally, transient expression of HiNfsB sensitized an E. coli mutant strain to 5-nitroimidazoles under anaerobic conditions. Together, these results advance our understanding of the metabolism of nitroimidazole antibiotics mediated by a new NTR group and reinforce the research on the natural antibiotic resistome for addressing the antibiotic resistance crisis.

The nitroreductase of Haemophilus influenzae metabolizes clinically used nitroimidazoles, generates dimeric metabolites and anaerobically sensitizes an E. coli mutant to antibiotics. We further uncover its biochemical and structural details.

Chloramphenicol biodegradation by enriched bacterial consortia and isolated strain Sphingomonas sp. CL5.1: The reconstruction of a novel biodegradation pathway

Figuring out the comprehensive metabolic mechanism of chloramphenicol (CAP) is critical to improving CAP removal in the bioremediation process. In this study, CAP biodegradation by six consortia and isolated Sphingomonas sp. CL5.1 were systematically investigated using the combination of high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry, second-generation, and third-generation sequencing technologies. The CAP-degrading capability of six consortia was enhanced while CAP mineralization rate declined after long-term enrichment. The microbial community structures of six consortia were all simplified with 69%-82% decline in species richness after continuous passages for one year. The core genera of consortia CL and CH included Sphingomonas, Cupriavidus, Burkholderia, Chryseobacterium, and Pigmentiphaga, which accounted for over 98% of the total population. Sphingomonas was discovered as a new CAP degrader that could subsist on CAP as the sole carbon, nitrogen, and energy sources. Sphingomonas sp. CL5.1 was able to completely remove 120 mg/L CAP within 48 hours with a mineralization rate of 50.4%. The presence of acetate or nitrite could inhibit CAP metabolization by strain CL5.1. Four CAP metabolic pathways were constructed, including modification of the C₃ hydroxyl group of CAP via acetylation, oxidization, dehydration and the bond cleavage between C₁ and C₂. C₃ hydroxyl group dehydration and C₁-C₂ bond-cleavage were first reported regarding to CAP biotransformation. Strain CL5.1 played a core role in the consortia and was responsible for C3 hydroxyl oxidation, C3 dehydration, and C1-C2 bond cleavage. Genomic information of strain CL5.1 revealed the further mineralization pathways of downstream product p-nitrobenzoic acid via ortho- and meta-cleavage.

Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues

Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary trajectory, an aspect that is often overlooked in laboratory directed evolution studies. We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. Analysis of every possible intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions. In both cases, improved chloramphenicol detoxification was only observed after an R225 substitution that largely eliminated activity with endogenous quinones. Error-prone PCR mutagenesis reinforced the importance of R225 substitutions, found in 100% of selected variants. This strong activity trade-off demonstrates that endogenous cellular metabolites hold considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, emphasising the importance of negative selection to effect enzyme specialisation, and offering an application for the evolved genes as dual-purpose selectable/counter-selectable markers.

In the cell, most tasks are performed by big molecules called proteins, which behave like molecular machines. Although proteins are often described as having one job each, this is not always true, and many proteins can perform different roles. Enzymes are a type of protein that facilitate chemical reactions. They are often specialised to one reaction, but they can also accelerate other side-reactions. During evolution, these side-reactions can become more useful and, as a result, the role of the enzyme may change over time.

The main role of the enzyme called NfsA in Escherichia coli bacteria is thought to be to convert molecules called quinones into hydroquinones, which can protect the cell from toxic molecules produced in oxidation reactions. As a side-reaction, NfsA has the potential to protect bacteria from an antibiotic called chloramphenicol, but it generally does this with such low efficacy that the effects are negligible. Producing hydroquinones is helpful to the cell in some situations, but if bacteria are regularly exposed to chloramphenicol, NfsA’s role aiding antibiotic resistance could become more important. Over time, the enzyme could evolve to become better at neutralising chloramphenicol. Therefore, NfsA provides an opportunity to study the evolution of proteins and how bacteria adapt to antibiotics.

To see how evolution might affect the activity of NfsA, Hall et al. generated 250 million E. coli with either random or targeted changes to the gene that codes for the NfsA enzyme. The resulting variants of NfsA that were most effective against chloramphenicol all had a change that eliminated the enzyme’s ability to convert quinones. This result demonstrates a key trade-off between roles for NfsA, where one must be lost for the other to improve.

These results demonstrate the interplay between a protein’s different roles and provide insight into bacterial drug resistance. Additionally, the experiments showed that the bacteria with improved resistance to chloramphenicol also became more sensitive to another antibiotic, metronidazole. These findings could inform the fight against drug-resistant bacterial infections and may also be helpful in guiding the design of proteins with different roles.

Novel Pathway for Chloramphenicol Catabolism in the Activated Sludge Bacterial Isolate Sphingobium sp. CAP-1

The chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a refractory contaminant that is widely present in various environments. However, few CAP-mineralizing bacteria have been documented, and a complete CAP catabolism pathway has yet to be identified. In this study, the bacterial strain Sphingobium sp. CAP-1 was isolated from an activated sludge sample and was shown to be capable of aerobically subsisting on CAP as the sole carbon, nitrogen, and energy source while simultaneously and efficiently degrading CAP. p-Nitrobenzoic acid (PNBA), p-nitrobenzaldehyde (PNBD), protocatechuate (PCA), and the novel side chain C₃-hydroxy-oxygenated product of CAP (O-CAP) were identified during CAP degradation. Strain CAP-1 was able to convert O-CAP to intermediate product PNBA. The putative functional genes associated with PNBA catabolism into the tricarboxylic acid cycle via PCA and floc formation were also identified by genome sequencing and comparative proteome analysis. A complete pathway for CAP catabolism was proposed. The discovery of a novel CAP oxidation/detoxification process and a complete pathway for CAP catabolism enriches the fundamental understanding of the bacterial catabolism of antibiotics, providing new insights into the microbial-mediated fate, transformation, and resistance risk of CAP in the environment. The molecular basis of CAP catabolism and floc formation in strain CAP-1 also offers theoretical guidance for the enhanced bioremediation of CAP-containing environments.

Gut microbiota in reductive drug metabolism

Gut bacteria are predominant microorganisms in the gut microbiota and have been recognized to mediate a variety of biotransformations of xenobiotic compounds in the gut. This review is focused on one of the gut bacterial xenobiotic metabolisms, reduction. Xenobiotics undergo different types of reductive metabolisms depending on chemically distinct groups: azo (-NN-), nitro (-NO₂), alkene (-CC-), ketone (-CO), N-oxide (-NO), and sulfoxide (-SO). In this review, we have provided select examples of drugs in six chemically distinct groups that are known or suspected to be subjected to the reduction by gut bacteria. For some drugs, responsible enzymes in specific gut bacteria have been identified and characterized, but for many drugs, only circumstantial evidence is available that indicates gut bacteria-mediated reductive metabolism. The physiological roles of even known gut bacterial enzymes have not been well defined.

High-efficiency biodegradation of chloramphenicol by enriched bacterial consortia: Kinetics study and bacterial community characterization

The risk of environmental pollution caused by chloramphenicol has necessitated special attention. Biodegradation has tremendous potential for chloramphenicol removal in the environment. Six chloramphenicol-degrading consortia were acclimated under different culture conditions to investigate their chloramphenicol biodegradation behaviors, and the bacterial community structures were comprehensively characterized. The enriched consortia CL and CH which utilized chloramphenicol as their sole carbon and energy source could thoroughly degrade 120 mg/L chloramphenicol within 5 days, and the mineralization rate reached up to 90%. Chloramphenicol biodegradation kinetics by different enriched consortia fit the modified Gompertz model or the first-order decay model (R²≥0.97). Consortia CL could almost completely degrade 1-500 mg/L CAP with a final mineralization rate of 87.8-91.7%. Chloramphenicol 3-acetate was identified to be a major intermediate of CAP biodegradation by metabolite analysis and enzyme activity assay. 16S rRNA sequencing analysis revealed that the diversities and abundances of the main genera in the enriched consortia were distinct from each other. Forty-one core OTUs belonging to 18 genera were the core bacteria which might be related to chloramphenicol biodegradation. Among them, the genera Sphingomonas, Chryseobacterium, Cupriavidus, Bradyrhizobium, Burkholderia, and Afipia with high abundance may play potential roles for chloramphenicol biodegradation.

Mild Nitration of Pyrazolin-5-ones by a Combination of Fe(NO3 )3 and NaNO2 : Discovery of a New Readily Available Class of Fungicides, 4-Nitropyrazolin-5-ones

4-Nitropyrazolin-5-ones have been synthesized by the nitration of pyrazolin-5-ones at room temperature by employing the Fe(NO₃ )₃ /NaNO₂ system. The method demonstrated selectivity towards the 4-position of pyrazolin-5-ones even in the presence of NPh and allyl substituents, which are sensitive to nitration. It was shown that other systems containing Fe^III and nitrites, namely Fe(NO₃ )₃ /tBuONO, Fe(ClO₄ )₃ /NaNO₂ , and Fe(ClO₄ )₃ /tBuONO, were also effective. Presumably, Fe^III oxidizes the nitrite (NaNO₂ or tBuONO) to form the NO₂ free radical, which serves as the nitrating agent for pyrazolin-5-ones. The synthesized 4-nitropyrazolin-5-ones were discovered to be a new class of fungicides. Their in vitro activities against phytopathogenic fungi were found comparable or even superior to those of commercial fungicides (fluconazole, clotrimazole, triadimefon, and kresoxim-methyl). These results represent a promising starting point for the development of a new type of plant protection agents that can be easily synthesized from widely available reagents.

Investigating the promiscuity of the chloramphenicol nitroreductase from Haemophilus influenzae towards the reduction of 4-nitrobenzene derivatives

Chloramphenicol nitroreductase (CNR), a drug-modifying enzyme from Haemophilus influenzae, has been shown to be responsible for the conversion of the nitro group into an amine in the antibiotic chloramphenicol (CAM). Since CAM structurally bears a 4-nitrobenzene moiety, we explored the substrate promiscuity of CNR by investigating its nitroreduction of 4-nitrobenzyl derivatives. We tested twenty compounds containing a nitrobenzene core, two nitropyridines, one compound with a vinylogous nitro group, and two aliphatic nitro compounds. In addition, we also synthesized twenty-eight 4-nitrobenzyl derivatives with ether, ester, and thioether substituents and assessed the relative activity of CNR in their presence. We found several of these compounds to be modified by CNR, with the enzyme activity ranging from 1 to 150% when compared to CAM. This data provides insights into two areas: (i) chemoenzymatic reduction of select compounds to avoid harsh chemicals and heavy metals routinely used in reductions of nitro groups and (ii) functional groups that would aid CAM in overcoming the activity of this enzyme.

Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol

Widespread antibiotic resistance has led to the reappraisal of abandoned antibiotics including chloramphenicol. However, enzyme(s) underlying one form of chloramphenicol resistance, nitroreduction, have eluded identification. Here we demonstrate that expression of the Haemophilus influenzae nitroreductase gene nfsB confers chloramphenicol resistance in Escherichia coli. We characterized the enzymatic product of H. influenzae NfsB acting on chloramphenicol and found it to be amino-chloramphenicol. Kinetic analysis revealed reduction of diverse substrates including the incomplete reduction of 5-nitro antibiotics metronidazole and nitrofurantoin, likely resulting in activation of these antibiotic pro-drugs to their cytotoxic forms. We observed that expression of the H. influenzae nfsB gene in E. coli results in significantly increased susceptibility to metronidazole. Finally, we found that in this strain metronidazole attenuates chloramphenicol resistance synergistically, and in vitro metronidazole weakly inhibits chloramphenicol reduction by NfsB. Our findings reveal the underpinnings of a chloramphenicol resistance mechanism nearly 70 years after its description.

Chloramphenicol Derivatives as Antibacterial and Anticancer Agents: Historic Problems and Current Solutions

Chloramphenicol (CAM) is the D-threo isomer of a small molecule, consisting of a p-nitrobenzene ring connected to a dichloroacetyl tail through a 2-amino-1,3-propanediol moiety. CAM displays a broad-spectrum bacteriostatic activity by specifically inhibiting the bacterial protein synthesis. In certain but important cases, it also exhibits bactericidal activity, namely against the three most common causes of meningitis, Haemophilus influenzae, Streptococcus pneumoniae and Neisseria meningitidis. Resistance to CAM has been frequently reported and ascribed to a variety of mechanisms. However, the most important concerns that limit its clinical utility relate to side effects such as neurotoxicity and hematologic disorders. In this review, we present previous and current efforts to synthesize CAM derivatives with improved pharmacological properties. In addition, we highlight potentially broader roles of these derivatives in investigating the plasticity of the ribosomal catalytic center, the main target of CAM.

Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione

Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key enzymes initiating the biotransformation of this herbicide. Two enzymes (called NfrA1 and NfrA2/YcnD) were identified, and functionally and structurally characterized. Both belong to the NfsA FRP family of the nitro-FMN reductase superfamily (type I oxygen-insensitive nitroreductase) and show optimal pH and temperature of 6–6.5 and 23–25°C, respectively. Both undergo a Ping Pong Bi Bi mechanism, with NADPH and NADPH/NADH as cofactors for NfrA1 and NfrA2/YcnD, respectively. It is interesting that both can also reduce various nitro compounds including pesticides, antibiotics, one prodrug and 4-methylsulfonyl-2-nitrobenzoic acid, one of the mesotrione metabolites retrieved from the environment. The present study constitutes the first identification of mesotrione-transforming enzymes. These enzymes (or their corresponding genes) could be used as biomarkers to predict the capacity of ecosystems to transform mesotrione and assess their contamination by both the parent molecule and/or the metabolites.

Effect of temperature switchover on the degradation of antibiotic chloramphenicol by biocathode bioelectrochemical system

Exposure to chloramphenicol (CAP), a chlorinated nitroaromatic antibiotic, can induce CAP-resistant bacteria/genes in diverse environments. A biocathode bioelectrochemical system (BES) was applied to reduce CAP under switched operational temperatures. When switching from 25 to 10°C, the CAP reduction rate (kCAP) and the maximum amount of the dechlorinated reduced amine product (AMCl, with no antibacterial activity) by the biocathode communities were both markedly decreased. The acetate and ethanol yield from cathodophilic microbial glucose fermentation (with release of electrons) was also reduced. Formation of the product AMCl was enhanced by the biocathode dechloridation reaction compared with that produced from pure electrochemical or microbial dechloridation processes. The electrochemical and morphological analyses of cathode biofilms demonstrated that some cathodophilic microbes could adapt to low temperature and play a key role in CAP degradation. The resilient biocathode BES has a potential for the treatment of CAP-containing wastewater in temperature fluctuating environments.

The Saccharomyces cerevisiae quinone oxidoreductase Lot6p: stability, inhibition and cooperativity

Lot6p (EC 1.5.1.39; Ylr011wp) is the sole quinone oxidoreductase in the budding yeast, Saccharomyces cerevisiae. Using hexahistidine tagged, recombinant Lot6p, we determined the steady-state enzyme kinetic parameters with both NADH and NADPH as electron donors; no cooperativity was observed with these substrates. The NQO1 inhibitor curcumin, the NQO2 inhibitor resveratrol, the bacterial nitroreductase inhibitor nicotinamide and the phosphate mimic vanadate all stabilise the enzyme towards thermal denaturation as judged by differential scanning fluorimetry. All except vanadate have no observable effect on the chemical cross-linking of the two subunits of the Lot6p dimer. These compounds all inhibit Lot6p's oxidoreductase activity, and all except nicotinamide exhibit negative cooperativity. Molecular modelling suggests that curcumin, resveratrol and nicotinamide all bind over the isoalloxazine ring of the FMN cofactor in Lot6p. Resveratrol was predicted to contact an α-helix that links the two active sites. Mutation of Gly-142 (which forms part of this helix) to serine does not greatly affect the thermal stability of the enzyme. However, this variant shows less cooperativity towards resveratrol than the wild type. This suggests a plausible hypothesis for the transmission of information between the subunits and, thus, the molecular mechanism of negative cooperativity in Lot6p.

Application of 6-nitrocoumarin as a substrate for the fluorescent detection of nitroreductase activity in Sporothrix schenckii

Introduction

Sporothrix schenckii is a thermal dimorphic pathogenic fungus causing a subcutaneous mycosis, sporotrichosis. Nitrocoumarin represents a fluorogenic substrate class where the microbial nitroreductase activity produces several derivatives, already used in several other enzyme assays. The objective of this study was the analysis of 6-nitrocoumarin (6-NC) as a substrate to study the nitroreductase activity in Sporothrix schenckii.

Methods

Thirty-five samples of S. schenckii were cultivated for seven, 14 and 21 days at 35 °C in a microculture containing 6-nitrocoumarin or 6-aminocoumarin (6-AC) dissolved in dimethyl sulfoxide or dimethyl sulfoxide as a negative control, for posterior examination under an epifluorescence microscope. The organic layer of the seven, 14 and 21-day cultures was analyzed by means of direct illumination with 365 nm UV light and by means of elution on G silica gel plate with hexane:ethyl acetate 1:4 unveiled with UV light.

Results

All of the strains showed the presence of 6-AC (yellow fluorescence) and 6-hydroxylaminocoumarin (blue fluorescence) in thin layer chromatography, which explains the green fluorescence observed in the fungus structure.

Conclusion

The nitroreductase activity is widely distributed in the S. schenckii complex and 6-NC is a fluorogenic substrate of easy access and applicability for the nitroreductase activity detection.

Accelerated reduction of chlorinated nitroaromatic antibiotic chloramphenicol by biocathode

Chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a priority pollutant in wastewaters. A fed-batch bioelectrochemical system (BES) with biocathode with applied voltage of 0.5 V (served as extracellular electron donor) and glucose as intracellular electron donor was applied to reduce CAP to amine product (AMCl2). The biocathode BES converted 87.1 ± 4.2% of 32 mg/L CAP in 4 h, and the removal efficiency reached 96.0 ± 0.9% within 24 h. Conversely, the removal efficiency of CAP in BES with an abiotic cathode was only 73.0 ± 3.2% after 24 h. When the biocathode was disconnected (no electrochemical reaction but in the presence of microbial activities), the CAP removal rate was dropped to 62.0% of that with biocathode BES. Acetylation of one hydroxyl of CAP was noted exclusive in the biocatalyzed process, while toxic intermediates, hydroxylamino (HOAM), and nitroso (NO), from CAP reduction were observed only in the abiotic cathode BES. Electrochemical hydrodechlorination and dehalogenase were responsible for dechlorination of AMCl2 to AMCl in abiotic and microbial cathode BES, respectively. The cyclic voltammetry (CV) highlighted higher peak currents and lower overpotentials for CAP reduction at the biocathode compared with abiotic cathode. With the biocathode BES, antibacterial activity of CAP was completely removed and nitro group reduction combined with dechlorination reaction enhanced detoxication efficiency of CAP. The CAP cathodic transformation pathway was proposed based on intermediates analysis. Bacterial community analysis indicated that the dominate bacteria on the biocathode were belonging to α, β, and γ-Proteobacteria. The biocathode BES could serve as a potential treatment process for CAP-containing wastewater.

Isolation, identification and characterization of human intestinal bacteria with the ability to utilize chloramphenicol as the sole source of carbon and energy

Five aerobic intestinal bacterial strains that utilized chloramphenicol (CAP) as sole carbon and energy source were isolated from fecal samples collected from healthy volunteers. Based on 16S rRNA gene sequence analysis, four of the five strains were identified as Klebsiella pneumoniae and one as Escherichia fergusonii. The degradation rate of strain I-10-CHL (E. fergusonii) varied with the initial concentration of CAP. The pH value also had an effect on the degradation rate of CAP and bacterial growth. A pH of 6.5 was optimal for CAP degradation and growth of strain I-10-CHL (E. fergusonii). In mixed substrate batch cultivations, where CAP was one of the components, glucose, acetamide and CAP were utilized simultaneously. The presence of glucose and acetamide increased the growth and substrate degradation rates of CAP. During incubation with E. fergusonii cells, reduction intermediates (1-p-nitrophenyl-2-amino-1,3-propanediol) were observed. The strains capable of utilizing CAP were CAP-susceptible, which indicates that the mechanism of CAP assimilation by the strains is independent on that of CAP resistance. The role of this CAP reduction pathway in the physiology of K. pneumoniae and E. fergusonii is unknown.

Inactivation of chloramphenicol and florfenicol by a novel chloramphenicol hydrolase

Chloramphenicol and florfenicol are broad-spectrum antibiotics. Although the bacterial resistance mechanisms to these antibiotics have been well documented, hydrolysis of these antibiotics has not been reported in detail. This study reports the hydrolysis of these two antibiotics by a specific hydrolase that is encoded by a gene identified from a soil metagenome. Hydrolysis of chloramphenicol has been recognized in cell extracts of Escherichia coli expressing a chloramphenicol acetate esterase gene, estDL136. A hydrolysate of chloramphenicol was identified as p-nitrophenylserinol by liquid chromatography-mass spectroscopy and proton nuclear magnetic resonance spectroscopy. The hydrolysis of these antibiotics suggested a promiscuous amidase activity of EstDL136. When estDL136 was expressed in E. coli, EstDL136 conferred resistance to both chloramphenicol and florfenicol on E. coli, due to their inactivation. In addition, E. coli carrying estDL136 deactivated florfenicol faster than it deactivated chloramphenicol, suggesting that EstDL136 hydrolyzes florfenicol more efficiently than it hydrolyzes chloramphenicol. The nucleotide sequences flanking estDL136 encode proteins such as amidohydrolase, dehydrogenase/reductase, major facilitator transporter, esterase, and oxidase. The most closely related genes are found in the bacterial family Sphingomonadaceae, which contains many bioremediation-related strains. Whether the gene cluster with estDL136 in E. coli is involved in further chloramphenicol degradation was not clear in this study. While acetyltransferases for chloramphenicol resistance and drug exporters for chloramphenicol or florfenicol resistance are often detected in numerous microbes, this is the first report of enzymatic hydrolysis of florfenicol resulting in inactivation of the antibiotic.

Pre-electrospray ionisation manifold methylation and post-electrospray ionisation manifold cleavage/ion cluster formation observed during electrospray ionisation of chloramphenicol in solutions of methanol and acetonitrile for liquid chromatography-mass spectrometry employing a commercial quadrupole ion trap mass analyser

We have observed unusual mass spectra of chloramphenicol (CAP) in solutions of methanol or acetonitrile showing intense ions at m/z 297, m/z 311, m/z 325 and m/z 339. The observed ions were different from those which are traditionally observed in the full scan ESI mass spectra of CAP with ions of m/z 321, m/z 323 and m/z 325. We have evidence to show that this process starts with offline methylation of CAP in solutions of methanol or acetonitrile to give m/z 339. Investigations using nuclear magnetic resonance (NMR) spectroscopy showed that there is a methylene group somewhere within the CAP molecule but not attached to any of the carbon atoms when the CAP is dissolved in methanol or acetonitrile before infusion into the mass spectrometer. The possible locations of attachment were speculated to be the electronegative atoms apart from the chlorine atoms due to valence considerations. The methylene group is attached to the nitrogen atom and forms a bond as observed in the MS/MS spectra of m/z 297, m/z 311, m/z 325 and m/z 339 which give m/z 183 as the base peak in all cases. Further experiments showed that there is cleavage of the methylated CAP molecule followed by cluster ion formation involving addition of methylene groups to the CAP fragment with m/z 183 to produce ions of m/z including m/z 297, m/z 311, m/z 325 and m/z 339. This process occurs in the mass spectrometer in the region housing the tube lens and is triggered when the ions are accelerated through this region by application of a negative tube lens offset voltage. This region affords collision of the charged droplets with a collision gas in this case nitrogen to strip the droplets of their solvent molecules. Experiments to follow the intensities of m/z 183, m/z 311, m/z 321, m/z 323, m/z 325 and m/z 339 as the tube lens offset voltage was varied were done in which the intensities of m/z 311, m/z 325 and m/z 339 were observed to be at their peak when the tube lens offset voltage was set at -40 V. When the tube lens offset voltage is swung to +40 V, thus decelerating the ions through the capillary skimmer region via the tube lens, the traditionally observed spectra with m/z 321, m/z 323 and m/z 325 were observed.

Viability of Mycoplasma agalactiae and Mycoplasma mycoides subsp. capri in goat milk samples stored under different conditions

Control programs for contagious agalactia (CA) involve monitoring milk samples to detect this disease. This study was designed to establish the effects of the preservatives generally used in dairy laboratories and storage temperature on the viability of Mycoplasma (M.) agalactiae (Ma) and M. mycoides subsp. capri (Mmc) in goat milk samples. In total, 1440 determinations were conducted for each mycoplasma species in milk samples subjected to different storage temperatures (refrigeration at 4°C or freezing at -20°C), preservation strategies (no preservative, NP; azidiol, AZ; or bronopol, BR) and storage times at each temperature (0, 2, 4, 6, 8, 10 and 24h at 4°C and 48h, 1 week, 2 weeks and 4 weeks at -20°C). Our findings reveal the similar viability of Mmc in milk samples stored at 4°C for 24h under the three preservation conditions examined. In contrast, the isolation of Ma in refrigerated milk samples was compromised by the presence of BR, and in smaller measure by the treatments AZ and NP. Freezing milk samples considerably reduced the viability of both mycoplasmas. Given the different sensitivity of the two mycoplasma species to BR, refrigerated milk samples treated with AZ could be used to detect infections caused by both species through culture-based methods.