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Boiangiu RS, Brinza I, Honceriu I, Mihasan M, Hritcu L. Insights into Pharmacological Activities of Nicotine and 6-Hydroxy-L-nicotine, a Bacterial Nicotine Derivative: A Systematic Review. Biomolecules 2023; 14:23. [PMID: 38254623 PMCID: PMC10813004 DOI: 10.3390/biom14010023] [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: 11/21/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The purported cognitive benefits associated with nicotine and its metabolites in the brain are a matter of debate. In this review, the impact of the pharmacologically active metabolite of a nicotine derivative produced by bacteria named 6-hydroxy-L-nicotine (6HLN) on memory, oxidative stress, and the activity of the cholinergic system in the brain was examined. A search in the PubMed, Science Direct, Web of Science, and Google Scholar databases, limiting entries to those published between 1992 and 2023, was conducted. The search focused specifically on articles about nicotine metabolites, memory, oxidative stress, and cholinergic system activity, as well as enzymes or pathways related to nicotine degradation in bacteria. The preliminary search resulted in 696 articles, and following the application of exclusion criteria, 212 articles were deemed eligible for inclusion. This review focuses on experimental studies supporting nicotine catabolism in bacteria, and the chemical and pharmacological activities of nicotine and its metabolite 6HLN.
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Affiliation(s)
| | | | | | - Marius Mihasan
- BioActive Research Group, Department of Biology, Faculty of Biology, Alexandru Ioan Cuza University of Iasi, 700506 Iasi, Romania; (R.S.B.); (I.B.); (I.H.)
| | - Lucian Hritcu
- BioActive Research Group, Department of Biology, Faculty of Biology, Alexandru Ioan Cuza University of Iasi, 700506 Iasi, Romania; (R.S.B.); (I.B.); (I.H.)
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El-Sabeh A, Mlesnita AM, Munteanu IT, Honceriu I, Kallabi F, Boiangiu RS, Mihasan M. Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster. BMC Genomics 2023; 24:536. [PMID: 37697273 PMCID: PMC10494377 DOI: 10.1186/s12864-023-09644-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids. RESULTS In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway. CONCLUSIONS The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.
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Affiliation(s)
- Amada El-Sabeh
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | | | | | - Iasmina Honceriu
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | - Fakhri Kallabi
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Marius Mihasan
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania.
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Dang B, Jia W, Ma S, Zhang X, Huang Y, Huang W, Han D, Zhang K, Zhao F, Zhang Y, Xu Z. Characterization of a novel nornicotine-degrading strain Mycolicibacterium sp. SMGY-1XX from a nornicotine-degrading consortium and preliminary elucidation of its biodegradation pathway by multi-omics analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131777. [PMID: 37290356 DOI: 10.1016/j.jhazmat.2023.131777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/14/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Nicotine and nornicotine are all toxic alkaloids involved in the formation of carcinogenic tobacco-specific nitrosamines. Microbes play an important role in removing these toxic alkaloids and their derivatives from tobacco-polluted environments. By now, microbial degradation of nicotine has been well studied. However, limited information is available on the microbial catabolism of nornicotine. In the present study, a nornicotine-degrading consortium was enriched from a river sediment sample and characterized by metagenomic sequencing using a combination of Illumina and Nanopore technologies. The metagenomic sequencing analysis demonstrated that Achromobacter, Azospirillum, Mycolicibacterium, Terrimonas, and Mycobacterium were the dominant genera in the nornicotine-degrading consortium. A total of 7 morphologically distinct bacterial strains were isolated from the nornicotine-degrading consortium. These 7 bacterial strains were characterized by whole genome sequencing and examined for their ability to degrade nornicotine. Based on a combination of 16 S rRNA gene similarity comparisons, 16 S rRNA gene-based phylogenetic analysis, and ANI analysis, the accurate taxonomies of these 7 isolated strains were identified. These 7 strains were identified as Mycolicibacterium sp. strain SMGY-1XX, Shinella yambaruensis strain SMGY-2XX, Sphingobacterium soli strain SMGY-3XX, Runella sp. strain SMGY-4XX, Chitinophagaceae sp. strain SMGY-5XX, Terrimonas sp. strain SMGY-6XX, Achromobacter sp. strain SMGY-8XX. Among these 7 strains, Mycolicibacterium sp. strain SMGY-1XX, which has not been reported previously to have the ability to degrade nornicotine or nicotine, was found to be capable of degrading nornicotine, nicotine as well as myosmine. The degradation intermediates of nornicotine and myosmine by Mycolicibacterium sp. strain SMGY-1XX were determined and the nornicotine degradation pathway in strain SMGY-1XX was proposed. Three novel intermediates, myosmine, pseudooxy-nornicotine, and γ-aminobutyrate, were identified during the nornicotine degradation process. Further, the most likely candidate genes responsible for nornicotine degradation in Mycolicibacterium sp. strain SMGY-1XX were identified by integrating genomic analysis, transcriptomic analysis, and proteomic analysis. The findings in this study will help to expand our understanding on the microbial catabolism of nornicotine and nicotine and provide new insights into the nornicotine degradation mechanism by consortia and pure culture, laying a foundation for the application of strain SMGY-1XX for the removal, biotransformation, or detoxification of nornicotine.
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Affiliation(s)
- Bingjun Dang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wei Jia
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Shuanglong Ma
- College of Resources and Environmental Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoping Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China; Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Zhengzhou 450002, China
| | - Yao Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Wuxing Huang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Dan Han
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Kai Zhang
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Fanchong Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuwei Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Zicheng Xu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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Mihăşan M, Boiangiu RŞ, Guzun D, Babii C, Aslebagh R, Channaveerappa D, Dupree E, Darie CC. Time-Dependent Analysis of Paenarthrobacter nicotinovorans pAO1 Nicotine-Related Proteome. ACS OMEGA 2021; 6:14242-14251. [PMID: 34124447 PMCID: PMC8190789 DOI: 10.1021/acsomega.1c01020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/10/2021] [Indexed: 05/08/2023]
Abstract
Paenarthrobacter nicotinovorans is a soil Gram-positive nicotine-degrading microorganism (NDM) that harbors a 165 kb pAO1 catabolic megaplasmid. The nicotine catabolic genes on pAO1 have been sequenced, but not all the details on the regulation and interplay of this pathway with the general metabolism of the cell are available. To address this issue at the protein level, a time-based shotgun proteomics study was performed. P. nicotinovorans was grown in the presence or absence of nicotine, and the cells were harvested at three different time intervals: 7, 10, and 24 h after inoculation. The cells were lysed, separated on SDS-PAGE, and digested by in-gel digestion using trypsin, and the resulting peptide mixture was analyzed using nanoliquid chromatography tandem mass spectrometry. We found an extensive number of proteins that are both plasmidal- and chromosomal-encoded and that work together in the energetic metabolism via the Krebs cycle and nicotine pathway. These data provide insight into the adaptation of the bacterial cells to the nicotine metabolic intermediates and could serve as a basis for future attempts to genetically engineer the pAO1-encoded catabolic pathway for increased bioremediation efficiency or for the production of valuable chemicals. The mass-spectrometry-based proteomics data have been deposited to the PRIDE partner repository with the data set identifier PXD012577.
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Affiliation(s)
- Marius Mihăşan
- Biochemistry
and Molecular Biology Laboratory, Department of Biology, Alexandru Ioan Cuza University of Iasi, Carol I Blvd, no 20A, Iasi 700506, Romania
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States
| | - Răzvan Ştefan Boiangiu
- Biochemistry
and Molecular Biology Laboratory, Department of Biology, Alexandru Ioan Cuza University of Iasi, Carol I Blvd, no 20A, Iasi 700506, Romania
| | - Doina Guzun
- Biochemistry
and Molecular Biology Laboratory, Department of Biology, Alexandru Ioan Cuza University of Iasi, Carol I Blvd, no 20A, Iasi 700506, Romania
| | - Cornelia Babii
- Biochemistry
and Molecular Biology Laboratory, Department of Biology, Alexandru Ioan Cuza University of Iasi, Carol I Blvd, no 20A, Iasi 700506, Romania
| | - Roshanak Aslebagh
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States
| | - Devika Channaveerappa
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States
| | - Emmalyn Dupree
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States
| | - Costel C. Darie
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States
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Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
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Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Brandsch R, Mihasan M. A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements. J Biosci 2020. [DOI: 10.1007/s12038-020-00030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mu Y, Chen Q, Parales RE, Lu Z, Hong Q, He J, Qiu J, Jiang J. Bacterial catabolism of nicotine: Catabolic strains, pathways and modules. ENVIRONMENTAL RESEARCH 2020; 183:109258. [PMID: 32311908 DOI: 10.1016/j.envres.2020.109258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/22/2020] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
Nicotine, the major alkaloid in tobacco, is a toxic, carcinogenic, and addictive compound. In recent years, nicotine catabolism in prokaryotes, including the catabolic pathways for its degradation and the catabolic genes that encode the enzymes of these pathways, have been systemically investigated. In this review, the three known pathways for nicotine catabolism in bacteria are summarized: the pyridine pathway, the pyrrolidine pathway, and a variation of the pyridine and pyrrolidine pathway (VPP pathway). The three nicotine catabolic pathways appear to have evolved separately in three distantly related lineages of bacteria. However, the general mechanism for the breakdown of the nicotine molecule in all three pathways is conserved and can be divided into six major enzymatic steps or catabolic modules that involve hydroxylation of the pyridine ring, dehydrogenation of the pyrrolidine ring, cleavage of the side chain, cleavage of the pyridine ring, dehydrogenation of the side chain, and deamination of pyridine ring-lysis products. In addition to summarizing our current understanding of nicotine degradation pathways, we identified several potential nicotine-degrading bacteria whose genome sequences are in public databases by comparing the sequences of conserved catabolic enzymes. Finally, several uncharacterized genes that are colocalized with nicotine degradation genes and are likely to be involved in nicotine catabolism, including regulatory genes, methyl-accepting chemotaxis protein genes, transporter genes, and cofactor genes are discussed. This review provides a comprehensive overview of the catabolism of nicotine in prokaryotes and highlights aspects of the process that still require additional research.
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Affiliation(s)
- Yang Mu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China; Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Zhenmei Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qing Hong
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Frederick J, Hennessy F, Horn U, de la Torre Cortés P, van den Broek M, Strych U, Willson R, Hefer CA, Daran JMG, Sewell T, Otten LG, Brady D. The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. BMC Genomics 2020; 21:3. [PMID: 31898479 PMCID: PMC6941271 DOI: 10.1186/s12864-019-6405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.
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Affiliation(s)
- Joni Frederick
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
- Present Address: LadHyx, UMR CNRS 7646, École Polytechnique, 91128 Palaiseau, France
| | - Fritha Hennessy
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
| | - Uli Horn
- Meraka, CSIR, Meiring Naude Road, Brummeria, 0091 South Africa
| | - Pilar de la Torre Cortés
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ulrich Strych
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Present Address: Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX 77030 USA
| | - Richard Willson
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Chemical and Biomolecular Engineering, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
| | - Charles A. Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002 South Africa
- Present Address: AgResearch Limited, Lincoln Research Centre, Private Bag 4749, Christchurch, 8140 New Zealand
| | - Jean-Marc G. Daran
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Trevor Sewell
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
| | - Linda G. Otten
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dean Brady
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO, Wits, 2050 South Africa
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Mihăşan M, Babii C, Aslebagh R, Channaveerappa D, Dupree EJ, Darie CC. Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:515-529. [DOI: 10.1007/978-3-030-15950-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Sekowska A, Ashida H, Danchin A. Revisiting the methionine salvage pathway and its paralogues. Microb Biotechnol 2019; 12:77-97. [PMID: 30306718 PMCID: PMC6302742 DOI: 10.1111/1751-7915.13324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by-products of S-adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.
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Affiliation(s)
- Agnieszka Sekowska
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
| | - Hiroki Ashida
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
- Institute of Synthetic BiologyShenzhen Institutes of Advanced StudiesShenzhenChina
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11
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Heuson E, Charmantray F, Petit JL, de Berardinis V, Gefflaut T. Enantioselective Synthesis ofd- andl-α-Amino Acids by Enzymatic Transamination Using Glutamine as Smart Amine Donor. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Egon Heuson
- Université Clermont Auvergne, CNRS, SIGMA Clermont; ICCF; F-63000 Clermont-Ferrand France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont; ICCF; F-63000 Clermont-Ferrand France
| | - Jean-Louis Petit
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry; Univ Paris-Saclay; 91057 Evry France
| | - Véronique de Berardinis
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry; Univ Paris-Saclay; 91057 Evry France
| | - Thierry Gefflaut
- Université Clermont Auvergne, CNRS, SIGMA Clermont; ICCF; F-63000 Clermont-Ferrand France
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12
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Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1. Sci Rep 2018; 8:16239. [PMID: 30390017 PMCID: PMC6214936 DOI: 10.1038/s41598-018-34687-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022] Open
Abstract
Paenarthrobacter nicotinovorans is a nicotine-degrading microorganism that shows a promising biotechnological potential for the production of compounds with industrial and pharmaceutical importance. Its ability to use nicotine was linked to the presence of the catabolic megaplasmid pAO1. Although extensive work has been performed on the molecular biology of nicotine degradation in this bacterium, only half of the genes putatively involved have been experimentally linked to nicotine. In the current approach, we used nanoLC-MS/MS to identify a total of 801 proteins grouped in 511 non-redundant protein clusters when P. nicotinovorans was grown on citrate, nicotine and nicotine and citrate as the only carbon sources. The differences in protein abundance showed that deamination is preferred when citrate is present. Several putative genes from the pAO1 megaplasmid have been shown to have a nicotine-dependent expression, including a hypothetical polyketide cyclase. We hypothesize that the enzyme would hydrolyze the N1-C6 bond from the pyridine ring with the formation of α-keto- glutaramate. Two chromosomally-encoded proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly up-regulated when nicotine was the sole carbon source and could be related to the production the α-keto-glutarate. The data have been deposited to the ProteomeXchange with identifier PXD008756.
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13
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Pan D, Sun M, Wang Y, Lv P, Wu X, Li QX, Cao H, Hua R. Characterization of Nicotine Catabolism through a Novel Pyrrolidine Pathway in Pseudomonas sp. S-1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:7393-7401. [PMID: 29932673 DOI: 10.1021/acs.jafc.8b01868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nicotine is a major toxic alkaloid in wastes generated from tobacco production and cigarette manufacturing. In the present work, a nicotine-degrading bacterial strain was isolated from tobacco powdery waste. The isolate was identified as Pseudomonas sp. S-1 based on morphology, physiology, and 16S rRNA gene sequence. Suitable conditions of isolate S-1 for nicotine degradation were pH 7.0 and 30 °C. Catabolic intermediates of nicotine were isolated with preparative-HPLC and characterized with LC-HRMS and NMR. The catabolic pathways of nicotine were involved in dehydrogenation, oxidation, hydrolysis, and hydroxylation. Interestingly, nicotine catabolism in strain S-1 undergoes a new pyrrolidine pathway that differs from the other three catabolic pathways in bacterial species. This work sheds light on catabolic diversity of nicotine and heteroaromatics.
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Affiliation(s)
- Dandan Pan
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Mengmeng Sun
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Yawen Wang
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Pei Lv
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Xiangwei Wu
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , 1955 East-West Road , Honolulu , Hawaii 96822 , United States
| | - Haiqun Cao
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
| | - Rimao Hua
- College of Resources and Environment , Anhui Agricultural University , Key Laboratory of Agri-Food Safety of Anhui Province , Hefei 230036 , China
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14
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Wang H, Zhi XY, Qiu J, Shi L, Lu Z. Characterization of a Novel Nicotine Degradation Gene Cluster ndp in Sphingomonas melonis TY and Its Evolutionary Analysis. Front Microbiol 2017; 8:337. [PMID: 28337179 PMCID: PMC5343071 DOI: 10.3389/fmicb.2017.00337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Sphingomonas melonis TY utilizes nicotine as a sole source of carbon, nitrogen, and energy through a variant of the pyridine and pyrrolidine pathways (VPP). A 31-kb novel nicotine-degrading gene cluster, ndp, in strain TY exhibited a different genetic organization with the vpp cluster in strains Ochrobactrum rhizosphaerae SJY1 and Agrobacterium tumefaciens S33. Genes in vpp were separated by a 20-kb interval sequence, while genes in ndp were localized together. Half of the homolog genes were in different locus in ndp and vpp. Moreover, there was a gene encoding putative transporter of nicotine or other critical metabolite in ndp. Among the putative nicotine-degrading related genes, the nicotine hydroxylase, 6-hydroxy-L-nicotine oxidase, 6-hydroxypseudooxynicotine oxidase, and 6-hydroxy-3-succinyl-pyridine monooxygenase responsible for catalyzing the transformation of nicotine to 2, 5-dihydropyridine in the initial four steps of the VPP were characterized. Hydroxylation at C6 of the pyridine ring and dehydrogenation at the C2–C3 bond of the pyrrolidine ring were the key common reactions in the VPP, pyrrolidine and pyridine pathways. Besides, VPP and pyrrolidine pathway shared the same latter part of metabolic pathway. After analysis of metabolic genes in the pyridine, pyrrolidine, and VPP pathways, we found that both the evolutionary features and metabolic mechanisms of the VPP were more similar to the pyrrolidine pathway. The linked ndpHFEG genes shared by the VPP and pyrrolidine pathways indicated that these two pathways might share the same origin, but variants were observed in some bacteria. And we speculated that the pyridine pathway was distributed in Gram-positive bacteria and the VPP and pyrrolidine pathways were distributed in Gram-negative bacteria by using comprehensive homologs searching and phylogenetic tree construction.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University Kunming, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Longxiang Shi
- Institution of System Engineering, College of Computer Science and Technology, Zhejiang University Hangzhou, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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15
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Wang H, Xie C, Zhu P, Zhou NY, Lu Z. Two Novel Sets of Genes Essential for Nicotine Degradation by Sphingomonas melonis TY. Front Microbiol 2017; 7:2060. [PMID: 28144232 PMCID: PMC5239795 DOI: 10.3389/fmicb.2016.02060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
Nicotine is a type of environmental pollutant present in the tobacco waste that is generated during tobacco manufacturing. Sphingomonas melonis TY can utilize nicotine as a sole source of carbon, nitrogen and energy via a variant of the pyridine and pyrrolidine pathway (the VPP pathway). In this study, we report the identification of two novel sets of genes, ndrA1A2A3, and ndrB1B2B3B4, which are crucial for nicotine degradation by strain TY. ndrA1A2A3 and ndrB1B2B3B4 exhibit similarity with both nicotine dehydrogenase ndh from Arthrobacter nicotinovorans and nicotine hydroxylase vppA from Ochrobactrum sp. SJY1. The transcriptional levels of ndrA1A2A3 and ndrB1B2B3B4 in strain TY were significantly upregulated in the presence of nicotine. Furthermore, ndrA1 or ndrB2 knockout resulted in a loss of the ability to degrade nicotine, whereas gene complementation restored the capacity of each mutant to utilize nicotine for growth. Biodegradation assays indicated that the mutant strains retained the ability to degrade the first intermediate in the pathway, 6-hydroxynicotine (6 HN). However, heterologous expression of ndrA1A2A3 and ndrB1B2B3B4 did not confer nicotine dehydrogenase activity to E. coli DH5α, Pseudomonas putida KT2440 or Sphingomonas aquatilis. These results provide information on the VPP pathway of nicotine degradation in S. melonis TY, and we conclude that these two sets of genes have essential functions in the conversion of nicotine to 6 HN in strain TY.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Cuixiao Xie
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Panpan Zhu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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16
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Gong X, Ma G, Duan Y, Zhu D, Chen Y, Zhang KQ, Yang J. Biodegradation and metabolic pathway of nicotine in Rhodococcus sp. Y22. World J Microbiol Biotechnol 2016; 32:188. [PMID: 27677748 DOI: 10.1007/s11274-016-2147-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/22/2016] [Indexed: 10/20/2022]
Abstract
Nicotine in tobacco is harmful to health and the environment, so there is an environmental requirement to remove nicotine from tobacco and tobacco wastes. In this study, the biotransformation of nicotine by Rhodococcus sp. Y22 was investigated, and three metabolites (NIC1, NIC4 and NIC5) were isolated by column separation, preparative TLC and solid plate's method, respectively. NIC1 was identified as 6-hydoxynicotine based on the results of NMR, MS, HPLC-UV and HRESIMS analysis; NIC4 was a novel compound and identified as 5-(3-methyl-[1,3]oxazinan-2-ylidene)-5H-pyridin-2-one based on the results of NMR, MS and UV analysis; NIC5 was identified as nicotine blue based on the results of NMR and MS analysis. Meanwhile, two metabolites NIC2 and NIC3 were identified as 6-hydroxy-N-methylmyosmine and 6-hydroxypseudooxynicotine by HRESIMS analysis, respectively. According to these metabolites, the possible pathway of nicotine degradation by Rhodococcus sp. Y22 was proposed. The nicotine can be transformed to nicotine blue through two pathways (A and B), and 6-hydroxy-N-methylmyosmine is the key compound, which can be converted to 6-hydroxypseudooxynicotine (pathway A) and 5-(3-methyl-[1,3]oxazinan-2-ylidene)-5H-pyridin-2-one (pathway B), respectively. Moreover, the encoding gene of nicotine dehydrogenase, ndh, was amplified from Rhodococcus sp. Y22, and its transcriptional level could be up-regulated obviously under nicotine induction. Our studies reported the key metabolites and possible biotransformation pathway of nicotine in Rhodococcus sp. Y22, and provided new insights into the microbial metabolism of nicotine.
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Affiliation(s)
- Xiaowei Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- R & D Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650024, People's Republic of China
| | - Guanghui Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
- Yunnan Comtestor Co., Ltd., Kunming, 650106, People's Republic of China
| | - Yanqing Duan
- R & D Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650024, People's Republic of China
| | - Donglai Zhu
- R & D Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650024, People's Republic of China
| | - Yongkuan Chen
- R & D Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650024, People's Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People's Republic of China.
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17
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HPLC determination of α-ketoglutaramate [5-amino-2,5-dioxopentanoate] in biological samples. Anal Biochem 2016; 494:52-4. [PMID: 26576832 DOI: 10.1016/j.ab.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/22/2022]
Abstract
α-Ketoglutaramate is an important glutamine metabolite in mammals, plants, and many bacteria. It is also a nicotine metabolite in certain bacteria. Previously published methods for the determination of α-ketoglutaramate in biological samples have considerable drawbacks. Here, we describe a relatively simple high-performance liquid chromatography (HPLC)-based method for measurement of α-ketoglutaramate in plasma and deproteinized tissues that overcomes these drawbacks. Concentrations of α-ketoglutaramate in normal rat liver, kidney, brain, and plasma were found to be approximately 216, 13, 6, and 19 μM, respectively. The HPLC method should be useful for studying the role of α-ketoglutaramate in eukaryotic glutamine metabolism and in bacterial nicotine metabolism.
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18
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A 2-Hydroxypyridine Catabolism Pathway in Rhodococcus rhodochrous Strain PY11. Appl Environ Microbiol 2015; 82:1264-1273. [PMID: 26655765 DOI: 10.1128/aem.02975-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/04/2015] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus rhodochrous PY11 (DSM 101666) is able to use 2-hydroxypyridine as a sole source of carbon and energy. By investigating a gene cluster (hpo) from this bacterium, we were able to reconstruct the catabolic pathway of 2-hydroxypyridine degradation. Here, we report that in Rhodococcus rhodochrous PY11, the initial hydroxylation of 2-hydroxypyridine is catalyzed by a four-component dioxygenase (HpoBCDF). A product of the dioxygenase reaction (3,6-dihydroxy-1,2,3,6-tetrahydropyridin-2-one) is further oxidized by HpoE to 2,3,6-trihydroxypyridine, which spontaneously forms a blue pigment. In addition, we show that the subsequent 2,3,6-trihydroxypyridine ring opening is catalyzed by the hypothetical cyclase HpoH. The final products of 2-hydroxypyridine degradation in Rhodococcus rhodochrous PY11 are ammonium ion and α-ketoglutarate.
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19
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ω-Amidase: an underappreciated, but important enzyme in l-glutamine and l-asparagine metabolism; relevance to sulfur and nitrogen metabolism, tumor biology and hyperammonemic diseases. Amino Acids 2015; 48:1-20. [DOI: 10.1007/s00726-015-2061-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/24/2015] [Indexed: 12/29/2022]
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20
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Ellens KW, Richardson LGL, Frelin O, Collins J, Ribeiro CL, Hsieh YF, Mullen RT, Hanson AD. Evidence that glutamine transaminase and omega-amidase potentially act in tandem to close the methionine salvage cycle in bacteria and plants. PHYTOCHEMISTRY 2015; 113:160-169. [PMID: 24837359 DOI: 10.1016/j.phytochem.2014.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/07/2014] [Accepted: 04/12/2014] [Indexed: 06/03/2023]
Abstract
S-Adenosylmethionine is converted enzymatically and non-enzymatically to methylthioadenosine, which is recycled to methionine (Met) via a salvage pathway. In plants and bacteria, enzymes for all steps in this pathway are known except the last: transamination of α-ketomethylthiobutyrate to give Met. In mammals, glutamine transaminase K (GTK) and ω-amidase (ω-Am) are thought to act in tandem to execute this step, with GTK forming α-ketoglutaramate, which ω-Am hydrolyzes. Comparative genomics indicated that GTK and ω-Am could function likewise in plants and bacteria because genes encoding GTK and ω-Am homologs (i) co-express with the Met salvage gene 5-methylthioribose kinase in Arabidopsis, and (ii) cluster on the chromosome with each other and with Met salvage genes in diverse bacteria. Consistent with this possibility, tomato, maize, and Bacillus subtilis GTK and ω-Am homologs had the predicted activities: GTK was specific for glutamine as amino donor and strongly preferred α-ketomethylthiobutyrate as amino acceptor, and ω-Am strongly preferred α-ketoglutaramate. Also consistent with this possibility, plant GTK and ω-Am were localized to the cytosol, where the Met salvage pathway resides, as well as to organelles. This multiple targeting was shown to result from use of alternative start codons. In B. subtilis, ablating GTK or ω-Am had a modest but significant inhibitory effect on growth on 5-methylthioribose as sole sulfur source. Collectively, these data indicate that while GTK, coupled with ω-Am, is positioned to support significant Met salvage flux in plants and bacteria, it can probably be replaced by other aminotransferases.
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Affiliation(s)
- Kenneth W Ellens
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.
| | - Lynn G L Richardson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Joseph Collins
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Cintia Leite Ribeiro
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Yih-Feng Hsieh
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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21
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Liu J, Ma G, Chen T, Hou Y, Yang S, Zhang KQ, Yang J. Nicotine-degrading microorganisms and their potential applications. Appl Microbiol Biotechnol 2015; 99:3775-85. [PMID: 25805341 DOI: 10.1007/s00253-015-6525-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 11/29/2022]
Abstract
Nicotine-degrading microorganisms (NDMs) are a special microbial group which can use nicotine as the sole carbon and nitrogen source for growth. Since the 1950s, the bioconversion of nicotine by microbes has received increasing attention, and several NDMs have been identified, such as Arthrobacter nicotinovorans, Microsporum gypseum, Pellicularia filamentosa JTS-208, and Pseudomonas sp. 41. In recent years, increasing numbers of NDMs have been isolated and identified from tobacco plantation soil, leaf, and tobacco waste. Meanwhile, the metabolic pathway and degradation mechanism of nicotine have been elucidated in several NDMs, such as A. nicotinovorans, Agrobacterium tumefaciens S33, Aspergillus oryzae, and Pseudomonas putida S16. Moreover, several NDMs have been used in improving the quality of cigarettes, treating tobacco waste, and producing valuable intermediates of nicotine. Here, we summarize the diversity, phylogenetic analysis, and potential applications of NDMs.
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Affiliation(s)
- Jianli Liu
- Tobacco Company of Chongqing, Chongqing, 400023, People's Republic of China
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22
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A novel (S)-6-hydroxynicotine oxidase gene from Shinella sp. strain HZN7. Appl Environ Microbiol 2014; 80:5552-60. [PMID: 25002425 DOI: 10.1128/aem.01312-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nicotine is an important environmental toxicant in tobacco waste. Shinella sp. strain HZN7 can metabolize nicotine into nontoxic compounds via variations of the pyridine and pyrrolidine pathways. However, the catabolic mechanism of this variant pathway at the gene or enzyme level is still unknown. In this study, two 6-hydroxynicotine degradation-deficient mutants, N7-M9 and N7-W3, were generated by transposon mutagenesis. The corresponding mutant genes, designated nctB and tnp2, were cloned and analyzed. The nctB gene encodes a novel flavin adenine dinucleotide-containing (S)-6-hydroxynicotine oxidase that converts (S)-6-hydroxynicotine into 6-hydroxy-N-methylmyosmine and then spontaneously hydrolyzes into 6-hydroxypseudooxynicotine. The deletion and complementation of the nctB gene showed that this enzyme is essential for nicotine or (S)-6-hydroxynicotine degradation. Purified NctB could also convert (S)-nicotine into N-methylmyosmine, which spontaneously hydrolyzed into pseudooxynicotine. The kinetic constants of NctB toward (S)-6-hydroxynicotine (Km = 0.019 mM, kcat = 7.3 s(-1)) and nicotine (Km = 2.03 mM, kcat = 0.396 s(-1)) indicated that (S)-6-hydroxynicotine is the preferred substrate in vivo. NctB showed no activities toward the R enantiomer of nicotine or 6-hydroxynicotine. Strain HZN7 could degrade (R)-nicotine into (R)-6-hydroxynicotine without any further degradation. The tnp2 gene from mutant N7-W3 encodes a putative transposase, and its deletion did not abolish the nicotine degradation activity. This study advances the understanding of the microbial diversity of nicotine biodegradation.
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23
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Mihasan M, Brandsch R. pAO1 of Arthrobacter nicotinovorans and the spread of catabolic traits by horizontal gene transfer in gram-positive soil bacteria. J Mol Evol 2014; 77:22-30. [PMID: 23884627 DOI: 10.1007/s00239-013-9576-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 165-kb megaplasmid pAO1 of Arthrobacter nicotinovorans carries two large gene clusters, one involved in nicotine catabolism (nic-gene cluster) and one in carbohydrate utilization (ch-gene cluster). Here, we propose that both gene clusters were acquired by A. nicotinovorans by horizontal gene transfer mediated by pAO1. Protein-protein blast search showed that none of the published Arthrobacter genomes contains nic-genes, but Rhodococcus opacus carries on its chromosome a nic-gene cluster highly similar to that of pAO1. Analysis of the nic-genes in the two species suggested a recombination event between their nic-gene clusters. Apparently, there was a gene exchange between pAO1, or a precursor plasmid, and a nic-gene cluster of an as yet unidentified Arthrobacter specie or other soil bacterium, possibly related to Rhodococcus, leading to the transfer by pAO1 of this catabolic trait to A. nicotinovorans. Analysis of the pAO1 ch-gene cluster revealed a virtually identical counterpart on the chromosome of Arthrobacter phenanthrenivorans. Moreover, the sequence analysis of the genes flanking the ch-gene cluster suggested that it was acquired by pAO1 by Xer-related site directed recombination and transferred via the plasmid to A. nicotinovorans. The G+C content, the level of sequence identity, gene co-linearity of nic- and ch-gene clusters as well as the signs of recombination events clearly supports the notion of pAO1 and its precursor plasmids as vehicles in HGT among Gram + soil bacteria.
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Affiliation(s)
- Marius Mihasan
- Laboratory of Biochemistry, Faculty of Biology, University "A. I. Cuza" Iasi, Bulevardul Carol I, Nr. 20 A, 700506, Iasi, Romania,
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24
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Liu Y, Wang L, Huang K, Wang W, Nie X, Jiang Y, Li P, Liu S, Xu P, Tang H. Physiological and biochemical characterization of a novel nicotine-degrading bacterium Pseudomonas geniculata N1. PLoS One 2014; 9:e84399. [PMID: 24416227 PMCID: PMC3885553 DOI: 10.1371/journal.pone.0084399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022] Open
Abstract
Management of solid wastes with high nicotine content, such as those accumulated during tobacco manufacturing, poses a major challenge, which can be addressed by using bacteria such as Pseudomonas and Arthrobacter. In this study, a new species of Pseudomonas geniculata, namely strain N1, which is capable of efficiently degrading nicotine, was isolated and identified. The optimal growth conditions for strain N1 are a temperature of 30°C, and a pH 6.5, at a rotation rate of 120 rpm min−1 with 1 g l−1 nicotine as the sole source of carbon and nitrogen. Myosmine, cotinine, 6-hydroxynicotine, 6-hydroxy-N-methylmyosmine, and 6-hydroxy-pseudooxynicotine were detected as the five intermediates through gas chromatography-mass and liquid chromatography-mass analyses. The identified metabolites were different from those generated by Pseudomonas putida strains. The analysis also highlighted the bacterial metabolic diversity in relation to nicotine degradation by different Pseudomonas strains.
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Affiliation(s)
- Yanghui Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lijuan Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Kaiming Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xueling Nie
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yi Jiang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Pengpeng Li
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Shanshan Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University Shanghai, People's Republic of China
- Shanghai Nuclear Engineering Research & Design Institute, Shanghai, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- * E-mail:
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25
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Isolation, transposon mutagenesis, and characterization of the novel nicotine-degrading strain Shinella sp. HZN7. Appl Microbiol Biotechnol 2013; 98:2625-36. [PMID: 24026891 DOI: 10.1007/s00253-013-5207-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/08/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Nicotine is a significant toxic waste generated in tobacco manufacturing. Biological methods for the degradation of nicotine waste are in high demand. In this study, we report the identification and characterization of the novel nicotine-degrading strain Shinella sp. HZN7. This strain can degrade 500 mg/L nicotine completely within 3 h at 30 °C and pH values of 6.5 ∼ 8.0. The biodegradation of nicotine by Shinella sp. HZN7 involves five intermediate metabolites: 6-hydroxy-nicotine (6HN), 6-hydroxy-N-methylmyosmine, 6-hydroxypseudooxynicotine (6HPON), 6-hydroxy-3-succinoyl-pyridine (HSP), and 2,5-dihydroxypyridine, as detected by ultraviolet spectrophotometry, HPLC, and LC-MS. We generated three mutants, N7-W18, N7-X5, and N7-M17, by transposon mutagenesis, in which the nicotine-degrading pathway terminated at 6HN, 6HPON, and HSP, respectively. The production of the five intermediate metabolites and their order in the degradation pathway were confirmed in the three mutants, indicating that strain HZN7 degrades nicotine via a variant of the pyridine and pyrrolidine pathways. The mutant gene from strain N7-X5, orf2, was cloned by self-formed adaptor PCR, but the nucleotide and amino acid sequence showed no similarity to any gene or gene product with defined function. However, orf2 disruption and complementation suggested that the orf2 gene is essential for the conversion of 6HPON to HSP in strain HZN7. This is the first study to provide genetic evidence for this variant nicotine degradation pathway.
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