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Vinacour M, Moiana M, Forné I, Jung K, Bertea M, Calero Valdayo PM, Nikel PI, Imhof A, Palumbo MC, Fernández Do Porto D, Ruiz JA. Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16. Appl Environ Microbiol 2023; 89:e0063023. [PMID: 38054732 PMCID: PMC10734416 DOI: 10.1128/aem.00630-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Fusaric acid (FA) is an important virulence factor produced by several Fusarium species. These fungi are responsible for wilt and rot diseases in a diverse range of crops. FA is toxic for animals, humans and soil-borne microorganisms. This mycotoxin reduces the survival and competition abilities of bacterial species able to antagonize Fusarium spp., due to its negative effects on viability and the production of antibiotics effective against these fungi. FA biodegradation is not a common characteristic among bacteria, and the determinants of FA catabolism have not been identified so far in any microorganism. In this study, we identified genes, enzymes, and metabolic pathways involved in the degradation of FA in the soil bacterium Burkholderia ambifaria T16. Our results provide insights into the catabolism of a pyridine-derivative involved in plant pathogenesis by a rhizosphere bacterium.
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Affiliation(s)
- Matias Vinacour
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Moiana
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Micaela Bertea
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Patricia M. Calero Valdayo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Miranda C. Palumbo
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Fernández Do Porto
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena A. Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Zhang K, Yin M, Lei S, Zhang H, Yin X, Niu Q. Bacillus sp. YC7 from intestines of Lasioderma serricorne degrades nicotine due to nicotine dehydrogenase. AMB Express 2023; 13:87. [PMID: 37603100 PMCID: PMC10441963 DOI: 10.1186/s13568-023-01593-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
A large number of nicotine-containing wastes produced during the tobacco manufacturing process are seriously harmful to the environment and human health. The degradation and transformation of nicotine-containing environmental contaminants to harmless substances has become an urgent requirement. Lasioderma serricorne can grow and reproduce in nicotine-rich sources, and their intestinal microbiota show promising potential to degrade and utilize nicotine. The purpose of this study is to screen and identify nicotine-degrading bacteria from the intestines of L. serricorne and explore their degradation characteristics. A dominant strain, YC7, with significant nicotine degradation capabilities was isolated from the intestines of L. serricorne. The strain was identified as Bacillus using a polyphasic approach. The test results showed it can produce multiple enzymes that include β-glucosidase, cellulase, proteases, and amylases. The nicotine-degrading bacteria were functionally annotated using databases. Nicotine dehydrogenase (NDH) was found by combining an activity tracking test and protein mass spectrometry analysis. The YC-7 NDH in the pathway was molecularly docked and functionally verified via the gene knockdown method. The binding ability of nicotine to nicotine-degrading enzymes was investigated using molecular docking. A high-efficiency nicotine-degrading bacteria, YC-7, was isolated and screened from tobacco, and the gene functions related to degradation were verified. This investigation provides a new hypothesis for screening nicotine-degrading bacteria and increases our knowledge of potential nicotine-degrading microbial sources.
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Affiliation(s)
- Ke Zhang
- College of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, 90 Wangcheng Road, Luoyang, 471023, Henan, China
| | - Mingshen Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Shengwei Lei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Hongxin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xiaoyan Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Yuan C, Zhao L, Tong L, Wang L, Ke Z, Yang Y, He J. Expression and Characterization of 3,6-Dihydroxy-picolinic Acid Decarboxylase PicC of Bordetella bronchiseptica RB50. Microorganisms 2023; 11:microorganisms11040854. [PMID: 37110277 PMCID: PMC10142695 DOI: 10.3390/microorganisms11040854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Picolinic acid (PA) is a typical mono-carboxylated pyridine derivative produced by human/animals or microorganisms which could be served as nutrients for bacteria. Most Bordetella strains are pathogens causing pertussis or respiratory disease in humans and/or various animals. Previous studies indicated that Bordetella strains harbor the PA degradation pic gene cluster. However, the degradation of PA by Bordetella strains remains unknown. In this study, a reference strain of genus Bordetella, B. bronchiseptica RB50, was investigated. The organization of pic gene cluster of strain RB50 was found to be similar with that of Alcaligenes faecalis, in which the sequence similarities of each Pic proteins are between 60% to 80% except for PicB2 (47% similarity). The 3,6-dihydroxypicolinic acid (3,6DHPA) decarboxylase gene (BB0271, designated as picCRB50) of strain RB50 was synthesized and over-expressed in E. coli BL21(DE3). The PicCRB50 showed 75% amino acid similarities against known PicC from Alcaligenes faecalis. The purified PicCRB50 can efficiently transform 3,6DHPA to 2,5-dihydroxypyridine. The PicCRB50 exhibits optimal activities at pH 7.0, 35 °C, and the Km and kcat values of PicCRB50 for 3,6DHPA were 20.41 ± 2.60 μM and 7.61 ± 0.53 S−1, respectively. The present study provided new insights into the biodegradation of PA by pathogens of Bordetella spp.
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Affiliation(s)
- Cansheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Lingling Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu Tong
- Suzhou Kaisiling Environmental Sci-Technology Co., Ltd., Suzhou 215413, China
| | - Lin Wang
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Zhuang Ke
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Jian He
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Wang K, Zhu G, Feng Q, Li X, Lv Y, Zhao Y, Pan H. Influence of applied voltage on bioelectrochemical enhancement of biomethanation for low-rank coal and microbial community distribution. BIORESOURCE TECHNOLOGY 2023; 369:128466. [PMID: 36503085 DOI: 10.1016/j.biortech.2022.128466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The performance of peat biomethanation was investigated in bioelectrochemical anaerobic digestion at different applied voltages, and compared to conventional anaerobic digestion. The methane yield was stabilized at 16 mL/g peat in the conventional anaerobic digestion. However, in the bioelectrochemical anaerobic digestion, the methane yield was significantly increased to 264 mL/g peat at the applied voltage of 4 V, followed by 1 V, 2 V, 0.5 V and 0 V. The bioelectrochemical system could enrich more electroactive microorganisms on the electrode, as well as in the bulk solution, and further improve the direct interspecies electron transfer for methane production. The 16S rRNA analysis showed a significant increase in the abundance of specific microorganisms in the bulk solution, including Firmicutes phylum and Proteobacteria phylum, in addition to a gradual increase in acetoclastic methanogenesis with an increase in applied voltage. These results provide a solution to turn low-rank coal into a new alternative energy.
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Affiliation(s)
- Keqiang Wang
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Guanyu Zhu
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Qing Feng
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Xiaoxiang Li
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Yaowei Lv
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Yong Zhao
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Hongda Pan
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
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Zhao L, Zhang F, Wang K, Zhang X, Hu G, Chen E, Qiu J, Yuan C, He J. Quinolinic acid catabolism is initiated by a novel four-component hydroxylase QuiA in Alcaligenes faecalis JQ191. ENVIRONMENTAL RESEARCH 2023; 216:114421. [PMID: 36162464 DOI: 10.1016/j.envres.2022.114421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Quinolinic acid (QA) is an essential nitrogen-containing aromatic heterocyclic compounds in organisms and it also acts as an important intermediate in chemical industry, which has strong neurotoxicity and cytotoxicity. The wide range of sources and applications caused the release and accumulation of QA in the environment which might poses a hazard to ecosystems and human health. However, few research on the degradation of QA by microorganisms and toxicity of QA and its metabolites were reported. Alcaligenes faecalis JQ191 could degrade QA but the genetic foundation of QA degradation has not been studied. In this study, the gene cluster quiA1A2A3A4 was identified from A. faecalis JQ191, which was responsible for the initial catabolism step of QA. The quiA1A2A3A4 gene cluster encodes a novel cytoplasmic four-component hydroxylase QuiA. The 1H nuclear magnetic resonance indicated that QuiA catalyzed QA to 6-hydroxyquinolinic acid (6HQA) and the H218O-labeling analysis confirmed that the hydroxyl group incorporating into 6HQA was derived from water. Toxicity tests showed that the QA could approximately inhibit 20%-80% growth of Chlorella ellipsoidea, and 6HQA could relieve at least 50% QA growth inhibition of Chlorella ellipsoidea, indicating that the 6-hydroxylation of QA by QuiA is a detoxification process. This research provides new insights into the metabolism of QA by microorganism and potential application in the bioremediation of toxic pyridine derivatives-contaminated environments.
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Affiliation(s)
- Lingling Zhao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Fuyin Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Kexin Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Xuan Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Gang Hu
- Laboratory Centre of Life Science, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - E Chen
- The Environmental Monitoring Center of Gansu Province, Lanzhou, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Cansheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing, Jiangsu, 210036, China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China; College of Rural Revitalization, Jiangsu Open University, Nanjing, Jiangsu, 210036, China.
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The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid. Appl Environ Microbiol 2022; 88:e0036022. [PMID: 35766505 PMCID: PMC9317849 DOI: 10.1128/aem.00360-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
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Mu Y, Peng JY, Wang HP, Song Y, Wang HM, Chen Q, Chen K. Xinfangfangia pollutisoli sp. nov., Isolated from Clopyralid-Contaminated Soil. Curr Microbiol 2022; 79:255. [PMID: 35834049 DOI: 10.1007/s00284-022-02958-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
With the aim of isolating clopyralid-degrading bacterial species for potential bioremediation, a pale-yellow, Gram-negative, rod-shaped, and non-motile designated as Clo-40T was isolated from soil which was about 10 years use of clopyralid in Zaozhuang city, Shandong province. Growth occurred within the ranges from 10 to 40 °C and 0-2.5% (w/v) NaCl. Strain could completely degrade 50 mg/L clopyralid within 2 days after induction and formed 3, 6-hydroxypicolinic acid, a major clopyralid metabolite, hydrolyze esculin, and reduce nitrates to nitrites, but could not hydrolyze gelatin. Based on phylogenetic analysis, strain clustered within the genus Xinfangfangia clade and branched with Xinfangfangia humi IMT-291T (97.6%) and Xinfangfangia soli ZQBWT (96.9%). Genome sequencing revealed a genome size of 4.41 Mbp and G + C content of 67.3%. The average nucleotide ANI values of strain with respect to X. humi IMT-291T and X. soli ZQBWT were 77.5% and 76.9%, respectively. The DDH estimated values between strain Clo-40T and X. humi IMT-291T and X. soli ZQBWT were 20.5% and 20.0%, respectively. The predominant fatty acids (> 5% of the total fatty acids) were C18:1 w7c (42.9%), C16:0 (28.8%), C17:0 cyclo (13.0%), and C14:0 (7.0%). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, unidentified glycolipid, and unidentified lipids. The predominant respiratory quinone was Q-10. Based on data from phenotypic, chemotaxonomic, and genotypic analyses in this study, strain Clo-40T represent a novel species in the genus of Xinfangfangia, for which the name Xinfangfangia pollutisoli sp. nov. is proposed. The type strain is Clo-40T (= KCTC 92089T = GDMCC 1.2845T).
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Affiliation(s)
- Yang Mu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Taizhou Center for Disease Prevention and Control, Taizhou, 225300, People's Republic of China
| | - Jia-Yi Peng
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Hui-Ping Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Yue Song
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Hong-Mei Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China.
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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Xu S, Wang X, Zhang F, Jiang Y, Zhang Y, Cheng M, Yan X, Hong Q, He J, Qiu J. PicR as a MarR Family Transcriptional Repressor Multiply Controls the Transcription of Picolinic Acid Degradation Gene Cluster pic in Alcaligenes faecalis JQ135. Appl Environ Microbiol 2022; 88:e0017222. [PMID: 35604228 PMCID: PMC9195942 DOI: 10.1128/aem.00172-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, pic, that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the pic cluster remains known. This study showed that the entire pic cluster was composed of 17 genes and transcribed as four operons: picR, picCDEF, picB4B3B2B1, and picT1A1A2A3T2T3MN. Deletion of picR, encoding a putative MarR-type regulator, greatly shortened the lag phase of PA degradation. An electrophoretic mobility shift assay and DNase I footprinting showed that PicR has one binding site in the picR-picC intergenic region and two binding sites in the picB-picT1 intergenic region. The DNA sequences of the three binding sites have the palindromic characteristics of TCAG-N4-CTNN: the space consists of four nonspecific bases, and the four palindromic bases on the left and the first two palindromic bases on the right are strictly conserved, while the last two bases on the right vary among the three binding sites. An in vivo β-galactosidase activity reporter assay indicated that 6-hydroxypicolinic acid but not PA acted as a ligand of PicR, preventing PicR from binding to promoter regions and thus derepressing the transcription of the pic cluster. This study revealed the negative transcriptional regulation mechanism of PA degradation by PicR in A. faecalis JQ135 and provides new insights into the structure and function of the MarR-type regulator. IMPORTANCE The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha-, Beta-, and Gammaproteobacteria. Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains. This study revealed that PicR binds to three sites of the promoter regions of the pic cluster to multiply regulate the transcription of the pic cluster, which enables A. faecalis JQ135 to efficiently utilize PA. Furthermore, the study also found a unique palindrome sequence for binding of the MarR-type regulator. This study enhanced our understanding of microbial catabolism of environmental toxic pyridine derivatives.
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Affiliation(s)
- Siqiong Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fuyin Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yinhu Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yanting Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Genome mining of Burkholderia ambifaria strain T16, a rhizobacterium able to produce antimicrobial compounds and degrade the mycotoxin fusaric acid. World J Microbiol Biotechnol 2022; 38:114. [PMID: 35578144 DOI: 10.1007/s11274-022-03299-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Burkholderia ambifaria T16 is a bacterium isolated from the rhizosphere of barley plants that showed a remarkable antifungal activity. This strain was also able to degrade fusaric acid (5-Butylpyridine-2-carboxylic acid) and detoxify this mycotoxin in inoculated barley seedlings. Genes and enzymes responsible for fusaric acid degradation have an important biotechnological potential in the control of fungal diseases caused by fusaric acid producers, or in the biodegradation/bio catalysis processes of pyridine derivatives. In this study, the complete genome of B. ambifaria T16 was sequenced and analyzed to identify genes involved in survival and competition in the rhizosphere, plant growth promotion, fungal growth inhibition, and degradation of aromatic compounds. The genomic analysis revealed the presence of several operons for the biosynthesis of antimicrobial compounds, such as pyrrolnitrin, ornibactin, occidiofungin and the membrane-associated AFC-BC11. These compounds were also detected in bacterial culture supernatants by mass spectrometry analysis. In addition, this strain has multiple genes contributing to its plant growth-promoting profile, including those for acetoin, 2,3-butanediol and indole-3-acetic acid production, siderophores biosynthesis, and solubilisation of organic and inorganic phosphate. A pan-genomic analysis demonstrated that the genome of strain T16 possesses large gene clusters that are absent in the genomes of B. ambifaria reference strains. According to predictions, most of these clusters would be involved in aromatic compounds degradation. One genomic region, encoding flavin-dependent monooxygenases of unknown function, is proposed as a candidate responsible for fusaric acid degradation.
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Zhao L, Jiang Y, Zhao Z, Wang K, Zhang X, Hong Q, Qiu J, He J. Biodegradation of Quinolinic acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ191. FEMS Microbiol Lett 2022; 369:6567840. [PMID: 35416242 DOI: 10.1093/femsle/fnac040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Quinolinic acid (QA) is a pyridine derivative that can be found in many organisms and is widely used in the chemical industry. However, QA possesses excitotoxic properties. To date, the catabolism of QA mediated by microorganisms has rarely been reported. In this study, a QA-degrading strain (JQ191) was isolated from sewage sludge. Based on phenotypic and 16S rRNA gene phylogenetic analysis, the strain was identified as Alcaligenes faecalis. Strain JQ191 was able to utilize QA as the sole source of carbon and nitrogen for growth. QA-cultured cells of JQ191 completely degrade 200 mg/L QA within 2 days in a mineral salt medium, whereas the LB-cultured cells experienced a 2-day lag period before degrading QA, indicating that the catabolic enzymes involved in QA degradation were induced by QA. 6-Hydroxypicolinic acid (6HPA) was identified as an intermediate of QA degradation by strain JQ191. A 6HPA monooxygenase gene picB was cloned, genetically disrupted, and heterologously expressed, and the results show that picB was responsible for catalyzing 6HPA to 3,6DHPA in JQ191. A new QA mineralization pathway was proposed. This study identifies a new bacterium candidate that has a potential application prospect in the bioremediation of QA-polluted environment, as well as provides new insights into the bacterial catabolism of QA.
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Affiliation(s)
- Lingling Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinhu Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenyang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kexin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Biochemical and structural characterization of an aromatic ring-hydroxylating dioxygenase for terephthalic acid catabolism. Proc Natl Acad Sci U S A 2022; 119:e2121426119. [PMID: 35312352 PMCID: PMC9060491 DOI: 10.1073/pnas.2121426119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SignificanceMore than 400 million tons of plastic waste is produced each year, the overwhelming majority of which ends up in landfills. Bioconversion strategies aimed at plastics have emerged as important components of enabling a circular economy for synthetic plastics, especially those that exhibit chemically similar linkages to those found in nature, such as polyesters. The enzyme system described in this work is essential for mineralization of the xenobiotic components of poly(ethylene terephthalate) (PET) in the biosphere. Our description of its structure and substrate preferences lays the groundwork for in vivo or ex vivo engineering of this system for PET upcycling.
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The TetR Family Repressor HpaR Negatively Regulates the Catabolism of 5-Hydroxypicolinic Acid in Alcaligenes faecalis JQ135 by Binding to Two Unique DNA Sequences in the Promoter of hpa Operon. Appl Environ Microbiol 2022; 88:e0239021. [PMID: 35138929 DOI: 10.1128/aem.02390-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5-Hydroxypicolinic acid (5HPA), an important natural pyridine derivative, is microbially degraded in the environment. Previously, a gene cluster hpa responsible for 5HPA degradation has been identified in Alcaligenes faecalis JQ135. However, the transcription regulation mechanism of the hpa cluster is still unknown. In this study, the transcription start site and promoter of hpa operon was identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR, whereas the transcription of hpaR itself was not regulated by HpaR. Electrophoretic mobility shift assay and DNase I footprinting revealed that HpaR bound to two DNA sequences, covering -35 region and -10 region, respectively, in the promoter region of hpa operon. Interestingly, the two binding sequences are partial-palindromic with 3-4 mismatches, and are complementary with each other. 5HPA acted as a ligand of HpaR preventing HpaR from binding to promoter region thus derepressing the transcription of hpa operon. The study revealed that HpaR binds to two unique complementary sequences of the promoter of hpa operon to negatively regulate the catabolism of 5HPA. IMPORTANCE This study revealed that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR. The binding of HpaR to the promoter of hpa operon has the following unique features: (1) HpaR has two independent binding sites in the promoter of the hpa operon, covering -35 region and -10 region, respectively. (2) the palindrome sequences of the two binding sites are complementary with each other. (3) both of the two binding sites include a 10-nt partial palindrome sequences with 3-4 mismatches. This study provides new insights into the binding features of the TetR family regulator with DNA sequences.
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Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N 2 and MocR-like Transcriptional Regulator DnfR in Alcaligenes faecalis JQ135. Appl Environ Microbiol 2022; 88:e0226121. [PMID: 35108103 DOI: 10.1128/aem.02261-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is an important process of both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH3→NH2OH→N2) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes and its genetic regulation remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N2 via NH2OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N2 in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N2O and trace amounts of N2 with nitrite as sole nitrogen source. Deletion of genes nirK and nosZ that are essential for denitrification did not impair the capability of JQ135 to oxidize ammonia to N2 (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 5'-TGGTCTGT-3' in the promotor region. Bioinformatic survey showed that homologs to dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that besides A. ammonioxydans, Dirammox also occurs in other bacteria, and is regulated by the MocR-family transcriptional regulator DnfR. Importance Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previous known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation (Anammox), and complete ammonia oxidation (Comammox)) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N2 (Dirammox), has been identified in the heterotrophic bacterium Alcaligenes ammonioxydans HO-1. This paper shows that in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by dnf genes, which are independent of the denitrification pathway. Bioinformatic survey suggests that homologs to dnf genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N2.
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Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195. Appl Environ Microbiol 2021; 87:e0092321. [PMID: 34232707 DOI: 10.1128/aem.00923-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cotinine is a stable toxic contaminant, produced as a by-product of smoking. It is of emerging concern due to its global distribution in aquatic environments. Microorganisms have the potential to degrade cotinine; however, the genetic mechanisms of this process are unknown. Nocardioides sp. strain JQ2195 is a pure-culture strain that has been reported to degrade cotinine at micropollutant concentrations. This strain utilizes cotinine as its sole carbon and nitrogen source. In this study, a 50-kb gene cluster (designated cot), involved in cotinine degradation, was predicted based on genomic and transcriptomic analyses. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3), which initiated cotinine catabolism, was identified and characterized. CotA from Shinella sp. strain HZN7 was heterologously expressed and purified and was shown to convert cotinine into 6-hydroxycotinine. H218O-labeling and electrospray ionization-mass spectrometry (ESI-MS) analysis confirmed that the hydroxyl group incorporated into 6-hydroxycotinine was derived from water. This study provides new molecular insights into the microbial metabolism of heterocyclic chemical pollutants. IMPORTANCE In the human body, cotinine is the major metabolite of nicotine, and 10 to 15% of generated cotinine is excreted in urine. Cotinine is a structural analogue of nicotine and is much more stable than nicotine. Increased tobacco consumption has led to high environmental concentrations of cotinine, which may have detrimental effects on aquatic ecosystems and human health. Nocardioides sp. strain JQ2195 is a unique cotinine-degrading bacterium. However, the underlying genetic and biochemical foundations of cotinine degradation are still unknown. In this study, a 50-kb gene cluster (designated cot) was identified by genomic and transcriptomic analyses as being involved in the degradation of cotinine. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3) catalyzed cotinine to 6-hydroxy-cotinine. This study provides new molecular insights into the microbial degradation and enzymatic transformation of cotinine.
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Chen G, An X, Li H, Lai F, Yuan E, Xia X, Zhang Q. Detoxification of azo dye Direct Black G by thermophilic Anoxybacillus sp. PDR2 and its application potential in bioremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 214:112084. [PMID: 33640726 DOI: 10.1016/j.ecoenv.2021.112084] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Direct Black G (DBG) is a highly toxic synthetic azo dye which is difficult to degrade. Biological treatment seems to be a promising option for the treatment of azo dye containing effluent. A thermophilic bacterial strain (Anoxybacillus sp. PDR2) previously isolated from the soil can effectively remove DBG. However, the molecular underpinnings of DBG degradation and the microbial detoxification ability remains unknown. In the present study, the genetic background of PDR2 for the efficient degradation of DBG and its adaptation to azo dye-contaminated environments was revealed by bioinformatics. Moreover, the possible biodegradation pathways were speculated based on the UV-vis spectral analysis, FTIR, and intermediates identified by LC-MS. Additionally, phytotoxicity and the comet experiment studies clearly indicated that PDR2 converts toxic azo dye (DBG) into low toxicity metabolites. The combination of biodegradation pathways and detoxification analysis were utilized to explore the molecular degradation mechanism and bioremediation of azo dye for future applications. These findings will provide a valuable theoretical basis for the practical treatment of azo dye wastewater.
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Affiliation(s)
- Guotao Chen
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Hanguang Li
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Fenju Lai
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - En Yuan
- College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330045, PR China
| | - Xiang Xia
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China.
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3-Hydroxypyridine Dehydrogenase HpdA Is Encoded by a Novel Four-Component Gene Cluster and Catalyzes the First Step of 3-Hydroxypyridine Catabolism in Ensifer adhaerens HP1. Appl Environ Microbiol 2020; 86:AEM.01313-20. [PMID: 32709720 DOI: 10.1128/aem.01313-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022] Open
Abstract
3-Hydroxypyridine (3HP) is an important natural pyridine derivative. Ensifer adhaerens HP1 can utilize 3HP as its sole sources of carbon, nitrogen, and energy to grow, but the genes responsible for the degradation of 3HP remain unknown. In this study, we predicted that a gene cluster, designated 3hpd, might be responsible for the degradation of 3HP. The analysis showed that the initial hydroxylation of 3HP in E. adhaerens HP1 was catalyzed by a four-component dehydrogenase (HpdA1A2A3A4) and led to the formation of 2,5-dihydroxypyridine (2,5-DHP). In addition, the SRPBCC component in HpdA existed as a separate subunit, which is different from other SRPBCC-containing molybdohydroxylases acting on N-heterocyclic aromatic compounds. Moreover, the results demonstrated that the phosphoenolpyruvate (PEP)-utilizing protein and pyruvate-phosphate dikinase were involved in the HpdA activity, and the presence of the gene cluster 3hpd was discovered in the genomes of diverse microbial strains. Our findings provide a better understanding of the microbial degradation of pyridine derivatives in nature and indicated that further research on the origin of the discovered four-component dehydrogenase with a separate SRPBCC domain and the function of PEP-utilizing protein and pyruvate-phosphate dikinase might be of great significance.IMPORTANCE 3-Hydroxypyridine is an important building block for the synthesis of drugs, herbicides, and antibiotics. Although the microbial degradation of 3-hydroxypyridine has been studied for many years, the molecular mechanisms remain unclear. Here, we show that 3hpd is responsible for the catabolism of 3-hydroxypyridine. The 3hpd gene cluster was found to be widespread in Actinobacteria, Rubrobacteria, Thermoleophilia, and Alpha-, Beta-, and Gammaproteobacteria, and the genetic organization of the 3hpd gene clusters in these bacteria shows high diversity. Our findings provide new insight into the catabolism of 3-hydroxypyridine in bacteria.
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