Isolation and Characterization of Novel Pyridine Dicarboxylic Acid-Degrading Microorganisms

CHEMIJA. 2016. Vol. 27. No. 1. P. 74–83 © Lietuvos mokslų akademija, 2016 Isolation and characterization of novel pyridine dicarboxylic acid-degrading microorganisms Simonas Kutanovas, Five novel microorganisms capable of pyridine dicarboxylic acids degradation were isolated from a soil. Microorganisms utilizing pyridine-2,3-dicarboxylic acid as a sole carbon Laimonas Karvelis, source were identified as Rhodococcus sp. 23C1, Mycobacterium frederiksbergense 23ON and Cupriavidus campinensis 23K8. This is the first report describing the representatives Justas Vaitekūnas, of these genus capable of degrading this compound. A pyridine-2,3-dicarboxylic acid dehydrogenase (quinolinate dehydrogenase) activity was detected in Rhodococcus sp. 23C1 and Jonita Stankevičiūtė, Mycobacterium frederiksbergense 23ON. The enzyme was partially purified from Rho- dococcus sp. 23C1. Based on detection of nicotinic acid hydroxylase, 6-hydroxynicotinic Renata Gasparavičiūtė, acid hydroxylase and 2,5-dihydroxypyridine dioxygenase activities in the cell-free extract, a novel pathway of degradation of pyridine-2,3-dicarboxylic acid proceeding via forma- Rolandas Meškys* tion of nicotinic acid was proposed for Cupriavidus campinensis 23K8. A bacterial isolate aerobically degrading pyridine-2,6-dicarboxylic acid was identified as Achromobacter sp. Department of Molecular Microbiology and Biotechnology, JS18. A novel pathway of pyridine-2,6-dicarboxylic acid degradation with 3-hydroxypico- Institute of Biochemistry, linic acid as an intermediate was proposed for this bacteria. A pyridine-3,5-dicarboxylic Vilnius University, acid-degrading bacterial isolate 35KP identified as Xanthobacter sp. was characterized for Mokslininkų St. 12, the first time. A phenazine methosulphate-dependent pyridine-3,5-dicarboxylate dehydro- LT-08662 Vilnius, Lithuania genase activity was detected in the cell-free extract of Xanthobacter sp. 35KP. Keywords: pyridine-2,3-dicarboxylic acid, pyridine-2,6-dicarboxylic acid, pyridine-3,5- dicarboxylic acid, pyridine-3,5-dicarboxylate dehydrogenase, biodegradation INTRODUCTION ids also open ways for synthesis of industrially relevant hydroxylated derivatives. For example, 6-hydroxynicotinic acid In the past decades, biocatalysis has emerged as an important is an important material in the synthesis of imidacloprid, tool in the industrial synthesis of bulk chemicals, pharma- a potential insecticide, and modified nucleotides [17–20], ceutical and agrochemical intermediates, active pharma- and 2-hydroxynicotinic acid is the starting compound for ceuticals, and food ingredients. Selective hydroxylation of the synthesis of 2-chloronicotinic acid [21]. Catabolism and aromatic compounds is among the most challenging chemi- initial hydroxylation steps of monocarboxylated pyridines cal reactions in synthetic chemistry and has gained steadily such as 2-carboxypyridine (picolinic acid) [22–25], 3-car- increasing attention during recent years, particularly because boxypyridine (nicotinic acid) [26–28], and 4-carboxypyri- of the use of hydroxylated aromatics as precursors for phar- dine (isonicotinic acid) [29, 30] have been studied in detail. maceuticals [1–3]. The chemo- and regioselective hydroxyla- Nicotinate dehydrogenases, catalyzing the hydroxylation tion of the pyridine ring has few analogues in non-enzymatic reactions, were purified from Bacillus niacini [31], Pseu- chemistry, and biocatalysis represents a potential new and domonas fluorescens TN5 [32], Eubacterium barkeri (pre- mild synthetic route to substituted pyridinols, many of which viously Clostridium barkeri) [33], Ralstonia/Burkholderia are potential drugs or agrochemicals. Microbial hydroxyla- strain DSM 6920 [34] and Pseudomonas putida KT2440 tion of pyridines has been studied extensively [4–8]. Various [35]. Isonicotinate dehydrogenase was purified fromMyco - N-heterocyclic compounds and their derivatives are convert- bacterium sp. INA1 [29] and picolinic acid 6-hydroxylase ed into useful chemicals by microbial or enzymatic oxidation was purified and characterized from Arthrobacter picolino- [9–16]. The microbial conversions of pyridine carboxylic ac- philus [22]. The microbial conversion of pyridine dicarboxylic acids * Corresponding author. E-mail: [email protected] has been less studied. A putative degradation pathway of Isolation and characterization of novel pyridine dicarboxylic acid-degrading microorganisms 75 pyridine-2,6-dicarboxylic acid (dipicolinic acid) via 3-hydroxy- Preparation of bacterial cells for whole-cell dipicolinic acid [36, 37], the regioselective hydroxylation of bioconversion experiments pyridine-2,3-dicarboxylic acid (quinolinic acid), pyridine-2,4- The isolate 35KP was cultivated aerobically in 20 ml EFA dicarboxylic acid (lutidinic acid) and pyridine-2,5-dicarboxyl- medium supplemented with pyridine-3,5-dicarboxylic acid ic acid (isocinchomeronic acid) using microbial cells has been (0.05%) at 30 °C for 7 days. The cells were aseptically collected reported [38, 39]. 2,3-, 2,5-, 2,6 and 3,4-dicarboxypyridine were (3000 × g, 15 min), suspended into 200 ml KT medium supple- oxidized by phthalic acid-degrading microorganisms [40, 41]. mented with pyridine-3,5-dicarboxylic acid (0.05%) and cul- Fermentation of pyridine-2,6-dicarboxylic acid by the consor- tivated aerobically at 30 °C for 24 hours. The cells were asepti- tium of strictly anaerobic microorganisms has been also ob- cally collected (3000 × g, 15 min) and washed twice with 0.9% served [42]. However, microorganisms capable to use or con- NaCl. The isolates 23ON and 23K8 were cultivated aerobically vert pyridine-3,5-dicarboxylic acid (dinicotinic acid) have not in 200 ml EFA medium supplemented with pyridine-2,3-di- been isolated yet. carboxylic acid (0.05%) at 30 °C for 5 days. Then pyridine-2,3- The present work describes the isolation and characteri- dicarboxylic acid was aseptically added (final concentration zation of novel pyridine dicarboxylic acids-degrading bacteria 0.05%) and the cells were additionally cultivated for 24 hours. including the first identified microorganism able to degrade The biomass was aseptically collected (3000 × g, 15 min) and pyridine-3,5-dicarboxylic acid. The isolated microorganisms washed twice with 0.9% NaCl. The isolate 23C1 was culti- show a good potential to be applicable as biocatalysts as well vated aerobically in 200 ml EFA medium supplemented with as an interesting source for novel pyridine ring attacking oxy- pyridine-2,3-dicarboxylic acid (0.05%) at 30 °C for 24 hours. genases. Then the cells were aseptically collected (3000 × g, 15 min) and twice washed with 0.9% NaCl. The isolate JS18 was cultivated EXPERIMENTAL aerobically in 200 ml EFA medium supplemented with pyridine-2,6-dicarboxylic acid (0.05%) at 30 °C for 2 days. Then Chemicals pyridine-2,6-dicarboxylic acid was aseptically added (final Chemicals were purchased from Sigma-Aldrich and Flu- concentration 0.05%) and the cells were additionally cultivated ka (Buchs, Switzerland) and were of the highest purity at 30 °C for 24 hours. The biomass was aseptically collected available. Nutrient agar and yeast extract were purchased (3000 × g, 15 min) and washed twice with 0.9% NaCl. from Oxoid (Hampshire, UK). 2,5-Dihydroxypyridine was The same cultivation conditions were applied when other synthesized according to [43]. DEAE FF Sepharose and substrates were used as an inducer. Phenyl-Sepharose 6 FF were obtained from GE Healthcare For all experiments, biomass (equivalent amount as from (Helsinki, Finland). 10 ml of culture broth) was suspended in 1 ml of 50 mM po- tassium phosphate buffer (pH 7.2) containing 0.1–1 mM of the appropriate substrate. The reactions were carried out at Isolation of pyridine dicarboxylic acid utilizing 20 °C. microorganism Soils and the enrichment culture technique were used to isolate pyridine dicarboxylic acid-degrading microorganisms. Taxonomic affiliation and phylogenetic analysis Samples of soils (5 g) were suspended in 20 ml of the mineral DNA was extracted according to [44]. 16S rRNA encoding genes ′ medium (KT medium (per litre of distilled water): 5.0 g NaCl, were amplified using universal primers w001 (5 -AGAGTTT- ′ ′ 1.0 g NH H PO , 1.0 g K HPO , 0.4 g MgSO ∙ 7H O, pH 7.2 with GATCMTGGCTC-3 ) and w002 (5 -GNTACCTTGTTACGAC- 4 2 4 2 4 4 2 ′ KOH) containing an appropriate acid (0.05%) and cultivated TT-3 ) according to [45]. The PCR product was purified with aerobically at 30 °C for 1–3 weeks. After cultivation the ali- a DNA purification kit and cloned into the pTZ57R/T plasmid quots were diluted and spread on the agar plates containing (Thermo Fisher Scientific, Lithuania). The cloned 16S riboso- the KT medium supplemented with 0.05% of an appropriate mal DNA was sequenced at Macrogen (Netherlands). A phy- acid and cultivated aerobically at 30 °C for 2–7 days. The larg- logenetic tree was created by the neighbour-joining meth od est colonies were selected and purified by streaking repeatedly [46]. The robustness of the tree was analyzed by 1000 bootstrap on the Nutrient agar medium, EFA medium ((per litre of dis- replications [47]. The evolutionary distances were computed tilled water): 10.0 g K HPO , 4.0 g KH PO , 0.5 g yeast extract, using the maximum composite likelihood method [48] and are 2 4 2 4 in the units of the number of base substitutions per site. All po- 1.0 g (NH4)2SO4, 0.2 g MgSO4 ∙ 7H2O, salt solution 10 ml/l, pH 7.2; salt solution (per litre of 0.1 N HCl): 2.0 g CaCl ∙ 2H O, sitions containing gaps and missing data were

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