6-Hydroxynicotinic acid as an intermediate in the oxidation of nicotinic acid by Pseudomonas fluorescens

"Are we barking up the wrong tree? Too much emphasis on Cutibacterium acnes and ignoring other pathogens"- a study based on next-generation sequencing of normal and diseased discs

BACKGROUND

The majority of literature on bacterial flora in the disc stands disadvantaged in utilizing traditional culture methods and targeting a single bacterium, Cutibacterium acnes.

PURPOSE

Our objective was to document the diversity in the bacterial flora between normal and degenerated discs for shortlisting potential pathogens using next-generation genomic tools.

STUDY DESIGN

Experimental case-control study.

METHODS

Researchers employed 16S metagenome sequencing to profile bacterial diversity in magnetic resonance imaging normal healthy discs from brain-dead organ voluntary donors (n=20) and 40 degenerated disc samples harvested during surgery (Modic [MC]=20 and non-Modic [NMC]=20). The V3-V4 region was amplified using universal bacterial primers 341F and 806R, and the libraries were sequenced using Illumina NovoSeq 6000 platform. Statistical significance was set at bacteria with a minimum of 100 operational taxonomic unit (OTU) and present in at least 70% of the samples. The quality check-filtered reads were processed using the QIIME-2 pipeline. The OTU clustering and taxonomic classification were carried out for the merged reads using the Greengenes/SILVA reference database. Validation was done by identification of bacterial metabolites in samples using the liquid chromatography-mass spectrometry approach.

RESULTS

Abundant bacteria differing widely in diversity, as evidenced by Alfa and Beta diversity analysis, were present in all control and degenerative samples. The number of bacterial genera was 27 (14-gram-positive: 13-gram-negative) in the control group, 23 (10-gram-positive: 11-gram-negative) in the Modic group, and 16 (11-gram-positive: 5-gram-negative) in the non-Modic group. In the Modic group, gram-negative bacteria OTUs were found to be predominant (more than 50% of the total bacteria identified), whereas in control and non-Modic groups the OTUs of gram-positive bacteria were predominant. Species-level analysis revealed an abundance of opportunistic gram-negative pathogens like Pseudomonas aeruginosa, Sphingomonos paucibacillus, and Ochrobactrum quorumnocens in the discs with Modic changes, more than in non-Modic discs. The presence of bacterial metabolites and quorum-sensing molecules like N-decanoyl-L-homoserine lactone, 6-hydroxynicotinic acid, 2-aminoacetophenone, 4-hydroxy-3-polyprenylbenzoate, PE (16:1(9Z)/18:0) and phthalic acid validated the colonization and cell-cell communication of bacteria in disc ruling out contamination theory. Cutibacterium acnes was not the predominant bacteria in any of the three groups of discs and in fact was in the 16th position in the order of abundance in the control discs (0.72%), seventh position in the Modic discs (1.41%), and 12th position (0.53%) in the non-Modic discs.

CONCLUSION

This study identified a predominance of gram-negative bacteria in degenerated discs and highlights that Cutibacterium acnes may not be the only degeneration-causing bacteria. This may be attributed to the environment, diet, and lifestyle habits of the sample population. Though the study does not reveal the exact pathogen, it may pave the way for future studies on the subject.

CLINICAL SIGNIFICANCE

These findings invite further investigation into causal relationships of bacterial profile with disc degeneration phenotypes as well as phenotype-driven clinical treatment protocols.

Synthesis and Biological Evaluation of a Novel 18F-Labeled Radiotracer for PET Imaging of the Adenosine A2A Receptor

The adenosine A_2A receptor (A_2AR) has emerged as a potential non-dopaminergic target for the treatment of Parkinson’s disease and, thus, the non-invasive imaging with positron emission tomography (PET) is of utmost importance to monitor the receptor expression and occupancy during an A_2AR-tailored therapy. Aiming at the development of a PET radiotracer, we herein report the design of a series of novel fluorinated analogs (TOZ1-TOZ7) based on the structure of the A_2AR antagonist tozadenant, and the preclinical evaluation of [¹⁸F]TOZ1. Autoradiography proved A_2AR-specific in vitro binding of [¹⁸F]TOZ1 to striatum of mouse and pig brain. Investigations of the metabolic stability in mice revealed parent fractions of more than 76% and 92% of total activity in plasma and brain samples, respectively. Dynamic PET/magnetic resonance imaging (MRI) studies in mice revealed a brain uptake but no A_2AR-specific in vivo binding.

Cloning, expression and functional analysis of nicotinate dehydrogenase gene cluster from Comamonas testosteroni JA1 that can hydroxylate 3-cyanopyridine

A nicotinate dehydrogenase (NaDH) gene cluster was cloned from Comamonas testosteroni JA1. The enzyme, termed NaDH(JA1), is composed of 21, 82, and 46 kDa subunits, respectivley containing [2Fe2S], Mo(V) and cytochrome c domains. The recombinant NaDH(JA1) can catalyze the hydroxylation of nicotinate and 3-cyanopyridine. NaDH(JA1) protein exhibits 52.8% identity to the amino acid sequence of NaDH(KT2440) from P. putida KT2440. Sequence alignment analysis showed that the [2Fe2S] domain in NaDH(JA1) had a type II [2Fe-2S] motif and a type I [2Fe-2S] motif, while the same domain in NaDH(KT2440) had only a type II [2Fe-2S] motif. NaDH(KT2440) had an additional hypoxanthine dehydrogenase motif that NaDH(JA1) does not have. When the small unit of NaDH(JA1) was replaced by the small subunit from NaDH(KT2440), the hybrid protein was able to catalyze the hydroxylation of nicotinate, but lost the ability to catalyze hydroxylation of 3-cyanopyridine. In contrast, after replacement of the small subunit of NaDH(KT2440) with the small subunit from NaDH(JA1), the resulting hybrid protein NaDH(JAS+KTL) acquired the ability to hydroxylate 3-cyanopyridine. The subunits swap results indicate the [2Fe2S] motif determines the 3-cyanopyridine hydroxylation ability, which is evidently different from the previous belief that the Mo motif determines substrate specificity.

Cloning, heterologous expression, and functional characterization of the nicotinate dehydrogenase gene from Pseudomonas putida KT2440

6-hydroxynicotinate can be used for the production of drugs, pesticides and intermediate chemicals. Some Pseudomonas species were reported to be able to convert nicotinic acid to 6-hydroxynicotinate by nicotinate dehydrogenase. So far, previous reports on NaDH in Pseudomonas genus were confused and contradictory each other. Recently, Ashraf et al. reported an NaDH gene cloned from Eubacterium barkeri and suggested some deducted NaDH genes from other nine bacteria. But they did not demonstrate the activity of recombinant NaDH and did not mention NaDH gene in Pseudomonas. In this study we cloned the gene of NaDH, ndhSL, from Pseudomonas putida KT2440. NdhSL in P. putida KT2440 is composed of two subunits. The small subunit contains [2Fe2S] iron sulfur domain, while the large subunit contains domains of molybdenum cofactor and cytochrome c. Expression of recombinant ndhSL in P. entomophila L48, which lacks the ability to produce 6-hydroxynicotinate, enabled the resting cell and cell extract of engineering P. entomophila L48 to hydroxylate nicotinate. Gene knockout and recovery studies further confirmed the ndhSL function.

Enzymatic functionalization of aromatic N-heterocycles: Hydroxylation and carboxylation

Aromatic N-heterocycles are common structural motifs and versatile building blocks for the synthesis of various biologically active compounds. The application of microbial catalysis is considerably advantageous for the synthesis of N-heterocycle derivatives. Recent progress in the microbial functionalization of aromatic N-heterocyclic compounds is reviewed, focusing on the regiospecific hydroxylation and the carboxylation of aromatic N-heterocycles.

THE METABOLISM OF HALOGEN-SUBSTITUTED BENZOIC ACIDS BY PSEUDOMONAS FLUORESCENS

1. Washed suspensions of Pseudomonas fluorescens, grown with benzoate as sole carbon source, oxidize monohalogenobenzoates in the following descending order of effectiveness: benzoate, fluorobenzoates, chlorobenzoates, bromobenzoates, iodobenzoates. 2. Cells grown on asparagine oxidize benzoate after an adaptive period of 90-120min. This adaptive period is increased by halogenobenzoates in the following approximate descending order of effectiveness: chlorobenzoates, fluorobenzoates (=bromobenzoates), iodobenzoates. This inhibition of adaptation by halogeno analogues depends on the concentration of benzoate and is thus apparently competitive. 3. Cells do not adapt to oxidize the halobenzoates when the halogeno analogues are inducers. However, the fluorobenzoates reduce the lag period taken to form the benzoate-oxidizing system. 4. The halogenobenzoates inhibit adaptation to citrate and nicotinate but not so effectively as benzoate itself. This is presumably a ;diauxic' effect. The analogues do not inhibit adaptation to catechol. 5. The halogenobenzoates are not used as sole carbon source for growth nor do they increase growth when cells grow with asparagine as the main carbon source. 6. It is suggested that this inability to use the analogues for growth is due partly to inability of the cells to liberate the halogen and to carry the oxidation to a stage at which carbon may be assimilated and partly to the inhibition of the induction of the oxidizing enzymes.

Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions

Our review of the metabolic pathways of pyridines and aza-arenes showed that biodegradation of heterocyclic aromatic compounds occurs under both aerobic and anaerobic conditions. Depending upon the environmental conditions, different types of bacteria, fungi, and enzymes are involved in the degradation process of these compounds. Our review indicated that different organisms are using different pathways to biotransform a substrate. Our review also showed that the transformation rate of the pyridine derivatives is dependent on the substituents. For example, pyridine carboxylic acids have the highest transformation rate followed by mono-hydroxypyridines, methylpyridines, aminopyridines, and halogenated pyridines. Through the isolation of metabolites, it was possible to demonstrate the mineralization pathway of various heterocyclic aromatic compounds. By using 14C-labeled substrates, it was possible to show that ring fission of a specific heterocyclic compound occurs at a specific position of the ring. Furthermore, many researchers have been able to isolate and characterize the microorganisms or even the enzymes involved in the transformation of these compounds or their derivatives. In studies involving 18O labeling as well as the use of cofactors and coenzymes, it was possible to prove that specific enzymes (e.g., mono- or dioxygenases) are involved in a particular degradation step. By using H2 18O, it could be shown that in certain transformation reactions, the oxygen was derived from water and that therefore these reactions might also occur under anaerobic conditions.

Fluorometric determination of alpha-ketosuccinamic acid in rat tissues

A method for the fluorometric determination of alpha-ketosuccinamic acid, the alpha-keto acid analog of asparagine, is described. The procedure involves the hydrolysis of alpha-ketosuccinamate to oxaloacetate by omega-amidase followed by NADH-dependent reduction of oxaloacetate to malate by malate dehydrogenase. A correction for endogenous oxaloacetate is made by using control samples lacking omega-amidase. Of the rat tissues investigated, liver contained the highest concentration, followed by kidney (53 +/- 6 (n = 11) and 18 +/- 3 (n = 3) mumol/kg wet wt, respectively). alpha-Ketosuccinamate was not detected in brain (less than 8 mumol/kg wet wt). Some chemical properties of alpha-ketosuccinamate were investigated. Concentrated solutions of sodium alpha-ketosuccinamate frozen for extended periods and the solid sodium salt of alpha-ketosuccinamate dimer heated to 130 degrees C are converted to at least 10 products by processes involving dimerization, dehydration, and decarboxylation. Isobutane chemical ionization mass spectral analysis (170-230 degrees C) of the free acid monomer yielded similar products. Many of the breakdown products were identified as di- and monoheterocyclic compounds, some of which are known to be of biological importance.

Availability of 6-hydroxynicotinic acid for rapid identification of Pseudomonas aeruginosa and Serratia marcescens

Gas chromatography--mass spectrometry has been used to identify specific metabolites produced by Gram-negative bacteria such as Pseudomonas aeruginosa, Serratia marcescens, Klebsiella pneumoniae and Escherichia coli in a defined medium. 6-Hydroxynicotinic acid was detected in spent culture media of Pseudomonas aeruginosa and Serratia marcescens, but could not be detected in those of Klebsiella pneumoniae and Escherichia coli. The production of 6-hydroxynicotinic acid was recognized by the addition of nicotinic acid in urine with Pseudomonas aeruginosa or Serratia marcescens, but not without the addition of nicotinic acid. Among 10(5) Pseudomonas aeruginosa per 1 ml of urine (criteria for the diagnosis of urinary tract infection), 0.15 microgram of 6-hydroxynicotinic acid was detected in urine at 4 h incubation with nicotinic acid at the optimum pH of 6.9, 38 degrees C. The production of 6-hydroxynicotinic acid was proportional to the number of the bacteria and displayed a time dependency. These results suggest that the availability of 6-hydroxynicotinic acid might make for more rapid identification of bacteria than current methods.

Selective enrichment of Pseudomonas spp. defective in catabolism after exposure to halogenated substrates

Significant selective enrichments of mutants defective in catabolic pathways can be achieved by exposure of pseudomonad cells to halogenated analogs of growth substrates. Between 3 and 95% of viable clones rescued from such enrichments have been defective in specific catabolic pathways. This has been demonstrated for eight different catabolic pathways for aromatic compounds in pseudomonads, in which the genes are located on plasmids or on the chromosome. The plasmid-encoded pathways studied include those for the catabolism of p-cymene (CYM), m- and p-xylenes (TOL), naphthalene (NAH), salicylate (SAL), and 4-methylphthalate (MOP), and the chromosome-encoded pathways include those for p-hydroxybenzoate, monohydric phenols, and p-anisate utilization. The recalcitrance of halogenated compounds may, in part, be explained by these observations, which introduce an as yet not widely recognized factor in assessment of biodegradability of halogenated compounds and their effects on the transformation of the natural substrates.

Microbial metabolism of the pyridine ring. The hydroxylation of 4-hydroxypyridine to pyridine-3,4-diol (3,4-dihydroxypyridine) by 4-hydroxypyridine-3-hydroxylase

1. The first metabolic step in the biodegradation of 4-hydroxypyridine by an Agrobacterium sp. was hydroxylation to form pyridine-3,4-diol. 2. Extracts required 1mol of O(2) and 1mol of NADH or NADPH for the conversion of 4-hydroxypyridine into pyridine-3,4-diol, suggesting that the enzyme responsible, 4-hydroxypyridine-3-hydroxylase, was a mixed function mono-oxygenase. 3. After treatment with acidic (NH(4))(2)SO(4) the enzyme required FAD for activity; FMN and riboflavin would not substitute for FAD. 4. The rate of anaerobic reduction of FAD by NAD(P)H was increased more than tenfold in the presence of 4-hydroxypyridine, suggesting that the mechanism of hydroxylation was similar to that of other aromatic hydroxylases which are of the mono-oxygenase type. 5. The partially purified enzyme was extremely specific for its heterocyclic substrate but would utilize either NADH or NADPH. 6. 4-Hydroxypyridine-3-hydroxylase was strongly inhibited by high substrate concentration (above 0.5mm) especially below pH7.5. 8. The inflexion at pH8.4 in a pK(m) versus pH plot, together with strong inhibition by p-chloromercuribenzoate, suggested a role for thiol groups in substrate binding.

The oxidation of nicotinic acid by Pseudomonas ovalis Chester. The terminal oxidase

In cell-free extracts of Pseudomonas ovalis nicotinic acid oxidase is confined to the wallmembrane fraction. It is associated with an electron-transport chain comprising b- and c-type cytochromes only, differing proportions of which are reduced by nicotinate and NADH. CO difference-spectra show two CO-binding pigments, cytochrome o (absorption maximum at 417nm) and another component absorbing maximally at 425nm. Cytochrome o is not reduced by NADH or by succinate but is by nicotinate, which can also reduce the ;425' CO-binding pigment. The effects of inhibitors of terminal oxidation support the idea of two terminal oxidases and a scheme involving the ;425' CO-binding pigment and the other components of the electron-transport chain is proposed.

Oxidation of nicotinic acid by a Bacillus species: purification and properties of nicotinic acid and 6-hydroxynicotinic acid hydroxylases

The enzymes of a Bacillus species that hydroxylate nicotinic acid to 6-hydroxynicotinic acid and 6-hydroxynicotinic acid to 2,6-dihydroxynicotinic acid were purified and characterized. The purified enzymes contained approximately two molecules of flavine and eight molecules of iron per molecule of enzyme. The enzymes were large (molecular weight, 400,000 to 450,000) and appeared to consist of subunits.

Cometabolism of m-chlorobenzoate by an Arthrobacter

Twenty isolates representing nine bacterial genera were obtained from enrichment cultures and were shown to cometabolize one or more of 22 substituted benzoates. One of the isolates, an Arthrobacter sp., cometabolized m-chlorobenzoate to a product identified as 4-chlorocatechol by thin-layer chromatography and ultraviolet and infrared spectroscopy. The data indicate that cometabolism by the arthrobacter results from the formation of products by its benzoate-oxiding enzyme system that are not acted upon by the catechol-metabolizing enzymes of the bacterium.

The utilization of some halogenated aromatic acids by Nocardia. Effects on growth and enzyme induction

1. Halogen analogues of benzoate and p-nitrobenzoate did not support growth of Nocardia erythropolis. 2. These analogues, when present together with the parent compounds, inhibited growth of the organism. 3. The halogen analogues similarly inhibited oxidation of benzoate or p-nitrobenzoate by competent cells. 4. Fluoroacetate and 2-fluoro-4-nitrobenzoate caused comparable inhibition of growth on p-nitrobenzoate and both led to some citrate accumulation. 5. The induction of the p-nitrobenzoate-oxidation system was strongly inhibited by all the 2-halogeno-4-nitrobenzoates although the 2-fluoro and 2-chloro derivatives also acted as inducers. 6. Halogen analogues of benzoate also induced the benzoate-oxidation system.