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Wang K, Xu L, Ma J, Zhou Y, Jiang Y, Zha J, Cai Y, He J, Jiang J, Qiu J, Mu Y. Characterization of cotinine degradation in a newly isolated Gram-negative strain Pseudomonas sp. JH-2. Arch Microbiol 2024; 206:316. [PMID: 38904699 DOI: 10.1007/s00203-024-04036-x] [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: 02/23/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Cotinine, the primary metabolite of nicotine in the human body, is an emerging pollutant in aquatic environments. It causes environmental problems and is harmful to the health of humans and other mammals; however, the mechanisms of its biodegradation have been elucidated incompletely. In this study, a novel Gram-negative strain that could degrade and utilize cotinine as a sole carbon source was isolated from municipal wastewater samples, and its cotinine degradation characteristics and kinetics were determined. Pseudomonas sp. JH-2 was able to degrade 100 mg/L (0.56 mM) of cotinine with high efficiency within 5 days at 30 ℃, pH 7.0, and 1% NaCl. Two intermediates, 6-hydroxycotinine and 6-hydroxy-3-succinoylpyridine (HSP), were identified by high-performance liquid chromatography and liquid chromatograph mass spectrometer. The draft whole genome sequence of strain JH-2 was obtained and analyzed to determine genomic structure and function. No homologs of proteins predicted in Nocardioides sp. JQ2195 and reported in nicotine degradation Pyrrolidine pathway were found in strain JH-2, suggesting new enzymes that responsible for cotinine catabolism. These findings provide meaningful insights into the biodegradation of cotinine by Gram-negative bacteria.
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Affiliation(s)
- Kexin Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lu Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiale Ma
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Zhou
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinhu Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Zha
- Taizhou Center for Disease Prevention and Control, Taizhou, 225300, China
| | - Yanqiu Cai
- Taizhou Center for Disease Prevention and Control, Taizhou, 225300, China
| | - Jian He
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yang Mu
- Taizhou Center for Disease Prevention and Control, Taizhou, 225300, China.
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Guan Y, Zhu Z, Peng Q, Li M, Li X, Yang JW, Lu YH, Wang M, Xie BB. Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota. Curr Genomics 2024; 25:226-235. [PMID: 39086996 PMCID: PMC11288164 DOI: 10.2174/0113892029302230240319042208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Methods To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of human microbiota. A total of 26,295 genomes and 1,596 metagenomes for human microbiota were downloaded from public databases and five types of NDEs were annotated with a custom pipeline. We found 959 NdhB, 785 NdhL, 987 NicX, three NicA1, and three NicA2 homologs. Results Genomic classification revealed that six phylum-level taxa, including Proteobacteria, Firmicutes, Firmicutes_A, Bacteroidota, Actinobacteriota, and Chloroflexota, can produce NDEs, with Proteobacteria encoding all five types of NDEs studied. Analysis of NicX prevalence revealed differences among body sites. NicX homologs were found in gut and oral samples with a high prevalence but not found in lung samples. NicX was found in samples from both smokers and non-smokers, though the prevalence might be different. Conclusion This study represents the first systematic investigation of NDEs from the human microbiota, providing new insights into the physiology and ecological functions of human microbiota and shedding new light on the development of nicotine-degrading probiotics for the treatment of smoking-related diseases.
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Affiliation(s)
- Ying Guan
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Qiyuan Peng
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Xuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jia-Wei Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yan-Hong Lu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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Mastenbrook J, Pathak E, Beaver C, Stull F, Koestler BJ. Breaking the habit: isolating nicotine-degrading bacteria in undergraduate microbiology teaching labs. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024:e0015223. [PMID: 38602406 DOI: 10.1128/jmbe.00152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/24/2024] [Indexed: 04/12/2024]
Abstract
Nicotine is a major alkaloid in tobacco plants and an addictive component of tobacco products. Some bacteria grow on tobacco plants and have evolved the ability to metabolize nicotine. As part of our microbiology teaching lab, we used minimal media with nicotine as the sole carbon source to isolate nicotine-degrading bacteria from tobacco leaves and commercial tobacco products. Students then identified these bacteria using 16S rRNA sequencing and biochemical assays and assessed their ability to catabolize nicotine using UV spectroscopy. Students were able to isolate and identify 14 distinct genera that can metabolize nicotine. This modification of the commonly used unknown project gave students firsthand experience using selective media, and students got the opportunity to work with largely uncharacterized microbes with a real-world connection to public health, which increased student engagement. Students had the opportunity to think critically about why nicotine-degrading microorganisms associate with tobacco plants, why there are different bacteria that use the same specialized metabolism, and how these organisms are isolated from other bacteria using selective media.
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Affiliation(s)
- J Mastenbrook
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - E Pathak
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - C Beaver
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - F Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
| | - B J Koestler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
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Wang H, Guo D, Zhang M, Wu G, Shi Y, Zhou J, Ding N, Chen X, Li X. Correlation study on microbial communities and volatile flavor compounds in cigar tobacco leaves of diverse origins. Appl Microbiol Biotechnol 2024; 108:236. [PMID: 38407656 PMCID: PMC10896874 DOI: 10.1007/s00253-024-13032-6] [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: 08/28/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
To elucidate the significant influence of microorganisms on geographically dependent flavor formation by analyzing microbial communities and volatile flavor compounds (VFCs) in cigar tobacco leaves (CTLs) obtained from China, Dominica, and Indonesia. Microbiome analysis revealed that the predominant bacteria in CTLs were Staphylococcus, Aerococcus, Pseudomonas, and Lactobacillus, while the predominant fungi were Aspergillus, Wallemia, and Sampaiozyma. The microbial communities of CTLs from different origins differed to some extent, and the diversity and abundance of bacteria were greater than fungi. Metabolomic analysis revealed that 64 VFCs were identified, mainly ketones, of which 23 VFCs could be utilized to identify the geographical origins of CTLs. Sixteen VFCs with OAV greater than 1, including cedrol, phenylacetaldehyde, damascone, beta-damascone, and beta-ionone, play important roles in shaping the flavor profile of CTLs from different origins. Combined with the correlation analysis, bacterial microorganisms were more closely related to key VFCs and favored a positive correlation. Bacillus, Vibrio, and Sphingomonas were the main flavor-related bacteria. The study demonstrated that the predominant microorganisms were essential for the formation of key flavor qualities in CTLs, which provided a theoretical reference for flavor control of CTLs by microbial technology. KEY POINTS: • It is the high OAV VFCs that determine the flavor profile of CTLs. • The methylerythritol phosphate (MEP) pathway and the carotenoid synthesis pathway are key metabolic pathways for the formation of VFCs in CTLs. • Microbial interactions influence tobacco flavor, with bacterial microorganisms contributing more to the flavor formation of CTLs.
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Affiliation(s)
- Haiqing Wang
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Danxia Road 485#, 230601, Hefei City, Anhui Province, People's Republic of China
| | - Dongfeng Guo
- China Tobacco Anhui Industrial Co., Ltd, Huangshan Road 606#, 230088, Hefe City, Anhui Province, People's Republic of China.
| | - Mingzhu Zhang
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Danxia Road 485#, 230601, Hefei City, Anhui Province, People's Republic of China
| | - Guanglong Wu
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Danxia Road 485#, 230601, Hefei City, Anhui Province, People's Republic of China
| | - Yaqi Shi
- China Tobacco Anhui Industrial Co., Ltd, Huangshan Road 606#, 230088, Hefe City, Anhui Province, People's Republic of China
| | - Jinglong Zhou
- China Tobacco Anhui Industrial Co., Ltd, Huangshan Road 606#, 230088, Hefe City, Anhui Province, People's Republic of China
| | - Naihong Ding
- China Tobacco Anhui Industrial Co., Ltd, Huangshan Road 606#, 230088, Hefe City, Anhui Province, People's Republic of China
| | - Xiangsong Chen
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei City, 230009, Anhui Province, People's Republic of China
| | - Xingjiang Li
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Danxia Road 485#, 230601, Hefei City, Anhui Province, People's Republic of China.
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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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Ren M, Qin Y, Zhang L, Zhao Y, Zhang R, Shi H. Effects of fermentation chamber temperature on microbes and quality of cigar wrapper tobacco leaves. Appl Microbiol Biotechnol 2023; 107:6469-6485. [PMID: 37665370 DOI: 10.1007/s00253-023-12750-7] [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: 06/11/2023] [Revised: 08/13/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023]
Abstract
The natural fermentation of cigar tobacco leaves usually utilizes natural temperature and humidity for fermentation. Cigars produced in China are often fermented in winter, and the low environmental temperatures can lead to slow heating of the tobacco stack, affecting the cigar tobacco leaves quality. This study aimed to determine the minimum chamber temperature required to initiate the process of fermentation for cigar tobacco leaves and to explore the impact of temperature on the microbial community of tobacco leaves. Here, the cigar variety "Dexue 1" were subjected to stacking fermentation under three temperature parameters (20 ℃, 27 ℃, 34 ℃). With an increase in environmental temperature, the temperature inside the stack of cigar leaves increased significantly, the protein, total sugar, starch, and total alkaloid content in fermented tobacco leaves decreased, and the aroma components and amino acid content increased. Microbial richness and community diversity associated with fermented tobacco were highest at chamber temperatures of above 27 ℃. The relative abundance of Chryseobacterium and Rhodococcus was significantly negatively correlated with protein, alkaloids, total sugar, and starch, and positively correlated with amino acids and aroma components. Chryseobacterium and Rhodococcus may be responsible for the degradation of macromolecular substances and the conversion of favorable aromatic substances, thus improving the tobacco leaves quality. This study demonstrated that increasing the fermentation chamber temperature above 27 ℃ was conductive to raising the inner-stack temperature, increased microbial diversity and aromatic quality, reduced the strength and irritation, and extremely enhanced the overall quality of fermented cigar tobacco leaves. KEY POINTS: • The environmental temperature of the fermentation chamber has a significant impact on the quality of tobacco • Temperature > 27 ℃ can initiate the process of cigar tobacco leaves fermentation and increase inner-stack temperature and microbial diversity and abundance • Chryseobacterium and Rhodococcus may be related to the degradation of macromolecular substances and the transformation of aromatic substances, thereby improving the quality of tobacco leaves.
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Affiliation(s)
- Mengjuan Ren
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Yanqing Qin
- Sichuan Provincial Tobacco Company, Chengdu, 600041, Sichuan Province, China
| | - Lanyue Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Yuanyuan Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Ruina Zhang
- Deyang Branch of Sichuan Provincial Tobacco Company, Deyang, 618400, Sichuan Province, China
| | - Hongzhi Shi
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China.
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7
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Si H, Zhou K, Zhao T, Cui B, Liu F, Zhao M. The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves. BIORESOUR BIOPROCESS 2023; 10:74. [PMID: 38647588 PMCID: PMC10992852 DOI: 10.1186/s40643-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 04/25/2024] Open
Abstract
Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.
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Affiliation(s)
- Hongyang Si
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Kun Zhou
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Tingyi Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Bing Cui
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China.
| | - Fang Liu
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Mingqin Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China.
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Xu Z, Zhang T, Hu H, Liu W, Xu P, Tang H. Characterization on nicotine degradation and research on heavy metal resistance of a strain Pseudomonas sp. NBB. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132145. [PMID: 37557045 DOI: 10.1016/j.jhazmat.2023.132145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 08/11/2023]
Abstract
The remediation of polluted sites containing multiple contaminants like nicotine and heavy metals poses significant challenges, due to detrimental effects like cell death. In this study, we isolated a new strain Pseudomonas sp. NBB capable of efficiently degrading nicotine even in high level of heavy metals. It degraded nicotine through pyrrolidine pathway and displayed minimum inhibitory concentrations of 2 mM for barium, copper, and lead, and 5 mM for manganese. In the presence of 2 mM Ba2+ or Pb2+, 3 g L-1 nicotine could be completely degraded within 24 h. Moreover, under 0.5 mM Cu2+ or 5 mM Mn2+ stress, 24.13% and 72.56% of nicotine degradation were achieved in 60 h, respectively. Strain NBB tolerances metal stress by various strategies, including morphological changes, up-regulation of macromolecule transporters, cellular response to DNA damage, and down-regulation of ABC transporters. Notably, among the 153 up-regulated genes, cds_821 was identified as manganese exporter (MneA) after gene disruption and recovery experiments. This study presents a novel strain capable of efficiently degrading nicotine and displaying remarkable resistance to heavy metals. The findings of this research provide valuable insights into the potential application of nicotine bioremediation in heavy metal-contaminated areas.
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Affiliation(s)
- Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd., Zhengzhou 450000, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd., Zhengzhou 450000, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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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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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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11
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Wang Y, Luo X, Chu P, Shi H, Wang R, Li J, Zheng S. Cultivation and application of nicotine-degrading bacteria and environmental functioning in tobacco planting soil. BIORESOUR BIOPROCESS 2023; 10:10. [PMID: 38647817 PMCID: PMC10992035 DOI: 10.1186/s40643-023-00630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Nicotine, a toxic and addictive alkaloid from tobacco, is an environmental pollutant. However, nicotine-degrading bacteria (NDB) and their function in tobacco planting soil are not fully understood. First, 52 NDB strains belonging to seven genera were isolated from tobacco soil. The most dominant genera were Flavobacterium (36.5%), Pseudomonas (30.8%), and Arthrobacter (15.4%), and Chitinophaga and Flavobacterium have not been previously reported. Then, two efficient NDB strains, Arthrobacter nitrophenolicus ND6 and Stenotrophomonas geniculata ND16, were screened and inoculated in the compost fertilizer from tobacco waste. The nicotine concentrations were reduced from 1.5 mg/g (DW) to below the safety threshold of 0.5 mg/g. Furthermore, strain ND6 followed the pyridine pathway of nicotine degradation, but the degrading pathway in strain ND16 could not be determined according to genomic analysis and color change. Finally, the abundance of nicotine-degrading genes in tobacco rhizosphere soil was investigated via metagenomic analysis. Five key genes, ndhA, nctB, kdhL, nboR, and dhponh, represent the whole process of nicotine degradation, and their abundance positively correlated with soil nicotine concentrations (p < 0.05). In conclusion, various NDB including unknown species live in tobacco soil and degrade nicotine efficiently. Some key nicotine-degrading genes could be used in monitoring nicotine degradation in the environment. The fermentation of compost from tobacco waste is a promising application of efficient NDB.
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Affiliation(s)
- Yiting Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiangyan Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Peng Chu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Heli Shi
- Enshi Branch, Hubei Tobacco Company, Enshi, 445000, Hubei, People's Republic of China
| | - Rui Wang
- Enshi Branch, Hubei Tobacco Company, Enshi, 445000, Hubei, People's Republic of China
| | - Jiale Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shixue Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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12
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Fu Y, Wang B, Cao Z. Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorg Chem 2022; 61:20501-20512. [DOI: 10.1021/acs.inorgchem.2c03229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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13
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Chen B, Sun L, Zeng G, Shen Z, Wang K, Yin L, Xu F, Wang P, Ding Y, Nie Q, Wu Q, Zhang Z, Xia J, Lin J, Luo Y, Cai J, Krausz KW, Zheng R, Xue Y, Zheng MH, Li Y, Yu C, Gonzalez FJ, Jiang C. Gut bacteria alleviate smoking-related NASH by degrading gut nicotine. Nature 2022; 610:562-568. [PMID: 36261549 PMCID: PMC9589931 DOI: 10.1038/s41586-022-05299-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/31/2022] [Indexed: 01/04/2023]
Abstract
Tobacco smoking is positively correlated with non-alcoholic fatty liver disease (NAFLD)1-5, but the underlying mechanism for this association is unclear. Here we report that nicotine accumulates in the intestine during tobacco smoking and activates intestinal AMPKα. We identify the gut bacterium Bacteroides xylanisolvens as an effective nicotine degrader. Colonization of B. xylanisolvens reduces intestinal nicotine concentrations in nicotine-exposed mice, and it improves nicotine-exacerbated NAFLD progression. Mechanistically, AMPKα promotes the phosphorylation of sphingomyelin phosphodiesterase 3 (SMPD3), stabilizing the latter and therefore increasing intestinal ceramide formation, which contributes to NAFLD progression to non-alcoholic steatohepatitis (NASH). Our results establish a role for intestinal nicotine accumulation in NAFLD progression and reveal an endogenous bacterium in the human intestine with the ability to metabolize nicotine. These findings suggest a possible route to reduce tobacco smoking-exacerbated NAFLD progression.
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Affiliation(s)
- Bo Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Zhe Shen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Limin Yin
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology, Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Feng Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Pengcheng Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Qing Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Jialin Xia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Yuhong Luo
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Cai
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ruimao Zheng
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Yanxue Xue
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, China
| | - Ming-Hua Zheng
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,Key Laboratory of Diagnosis and Treatment for The Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China.
| | - Yang Li
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology, Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Chaohui Yu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China. .,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China. .,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China. .,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China.
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14
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Wu X, Cai W, Zhu P, Peng Z, Zheng T, Li D, Li J, Zhou G, Du G, Zhang J. Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco. BMC Microbiol 2022; 22:197. [PMID: 35965316 PMCID: PMC9377114 DOI: 10.1186/s12866-022-02597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background The aging process in the tobacco production, as in other food industries, is an important process for improving the quality of raw materials. In the spontaneous aging, the complex components in flue-cured tobacco (FT) improve flavor or reduce harmful compounds through chemical reactions, microbial metabolism, and enzymatic catalysis. Some believed that tobacco-microbe played a significant part in this process. However, little information is available on how microbes mediate chemical composition to improve the quality of FT, which will lay the foundation for the time-consuming spontaneous aging to seek ways to shorten the aging cycle. Results Comparing aged and unaged FT, volatile and non-volatile differential compounds (DCs) were multi-dimensionally analyzed with the non-targeted metabolomes based on UPLC-QTOP-MS (the ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry), GC–MS (gas chromatography-mass spectrometer) assisted derivatization and HP-SPME-GC/MS (headspace solid-phase micro-extraction assisted GC–MS). Products associated with the degradation pathways of terpenoids or higher fatty acids were one of the most important factors in improving FT quality. With the microbiome, the diversity and functions of microbial flora were analyzed. The high relative abundance function categories were in coincidence with DCs-related metabolic pathways. According to the correlation analysis, Acinetobacter, Sphingomonas and Aspergillus were presumed to be the important contributor, in which Aspergillus was associated with the highest number of degradation products of terpenoids and higher fatty acids. At last, the screened Aspergillus nidulans strain F4 could promote the degradation of terpenoids and higher fatty acids to enhance tobacco flavor by secreting highly active lipoxygenase and peroxidase, which verified the effect of tobacco-microbes on FT quality. Conclusions By integrating the microbiome and metabolome, tobacco-microbe can mediate flavor-related substances to improve the quality of FT after aging, which provided a basis for identifying functional microorganisms for reforming the traditional spontaneous aging. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02597-9.
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Affiliation(s)
- Xinying Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Wen Cai
- Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., 56 Chenglong Road, 610000, Chengdu, China
| | - Pengcheng Zhu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., 56 Chenglong Road, 610000, Chengdu, China
| | - Zheng Peng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Tianfei Zheng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Dongliang Li
- Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., 56 Chenglong Road, 610000, Chengdu, China
| | - Jianghua Li
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Guanyu Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
| | - Juan Zhang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
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15
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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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16
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Biodegradation of Quinoline by a Newly Isolated Salt-Tolerating Bacterium Rhodococcus gordoniae Strain JH145. Microorganisms 2022; 10:microorganisms10040797. [PMID: 35456847 PMCID: PMC9029321 DOI: 10.3390/microorganisms10040797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/05/2023] Open
Abstract
Quinoline is a typical nitrogen-heterocyclic compound with high toxicity and carcinogenicity which exists ubiquitously in industrial wastewater. In this study, a new quinoline-degrading bacterial strain Rhodococcus sp. JH145 was isolated from oil-contaminated soil. Strain JH145 could grow with quinoline as the sole carbon source. The optimum growth temperature, pH, and salt concentration were 30 °C, 8.0, and 1%, respectively. 100 mg/L quinoline could be completely removed within 28 h. Particularly, strain JH145 showed excellent quinoline biodegradation ability under a high-salt concentration of 7.5%. Two different quinoline degradation pathways, a typical 8-hydroxycoumarin pathway, and a unique anthranilate pathway were proposed based on the intermediates identified by liquid chromatography–time of flight mass spectrometry. Our present results provided new candidates for industrial application in quinoline-contaminated wastewater treatment even under high-salt conditions.
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17
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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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18
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An NAD-Specific 6-Hydroxy-3-Succinoyl-Semialdehyde-Pyridine Dehydrogenase from Nicotine-Degrading Agrobacterium tumefaciens Strain S33. Microbiol Spectr 2021; 9:e0092421. [PMID: 34378958 PMCID: PMC8552603 DOI: 10.1128/spectrum.00924-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens strain S33 can catabolize nicotine via a hybrid of the pyridine and pyrrolidine pathways. Most of the enzymes involved in this biochemical pathway have been identified and characterized, except for the one catalyzing the oxidation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine. Based on a previous genomic and transcriptomic analysis, an open reading frame (ORF) annotated to encode aldehyde dehydrogenase (Ald) in the nicotine-degrading cluster was predicted to be responsible for this step. In this study, we heterologously expressed the enzyme and identified its function by biochemical assay and mass spectrum analysis. It was found that Ald catalyzes the NAD-specific dehydrogenation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine. With the nonhydroxylated analog 3-succinoyl-semialdehyde-pyridine (SAP) as a substrate, Ald had a specific activity of 10.05 U/mg at pH 9.0 and apparent Km values of around 58.68 μM and 0.41 mM for SAP and NAD+, respectively. Induction at low temperature and purification and storage in low-salt buffers were helpful to prevent its aggregation and precipitation. Disruption of the ald gene caused a lower growth rate and biomass of strain S33 on nicotine but not on 6-hydroxy-3-succinoylpyridine. Ald has a broad range of substrates, including benzaldehyde, furfural, and acetaldehyde. Recombinant Escherichia coli cells harboring the ald gene can efficiently convert furfural to 2-furoic acid at a specific rate of 0.032 mmol min−1 g dry cells−1, extending the application of Ald in the catalysis of bio-based furan compounds. These findings provide new insights into the biochemical mechanism of the nicotine-degrading hybrid pathway and the possible application of Ald in industrial biocatalysis. IMPORTANCE Nicotine is one of the major toxic N-heterocyclic aromatic alkaloids produced in tobacco plants. Manufacturing tobacco and smoking may lead to some environmental and public health problems. Microorganisms can degrade nicotine by various biochemical pathways, but the biochemical mechanism for nicotine degradation has not been fully elucidated. In this study, we identified an aldehyde dehydrogenase responsible for the oxidation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine; this was the only uncharacterized enzyme in the hybrid of the pyridine and pyrrolidine pathways in Agrobacterium tumefaciens S33. Similar to the known aldehyde dehydrogenase, the NAD-specific homodimeric enzyme presents a broad substrate range with high activity in alkaline and low-salt-containing buffers. It can catalyze not only the aldehyde from nicotine degradation but also those of benzaldehyde, furfural, and acetaldehyde. It was found that recombinant Escherichia coli cells harboring the ald gene could efficiently convert furfural to valuable 2-furoic acid, demonstrating its potential application for enzymatic catalysis.
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Shimasaki T, Masuda S, Garrido-Oter R, Kawasaki T, Aoki Y, Shibata A, Suda W, Shirasu K, Yazaki K, Nakano RT, Sugiyama A. Tobacco Root Endophytic Arthrobacter Harbors Genomic Features Enabling the Catabolism of Host-Specific Plant Specialized Metabolites. mBio 2021; 12:e0084621. [PMID: 34044592 PMCID: PMC8262997 DOI: 10.1128/mbio.00846-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/17/2021] [Indexed: 01/04/2023] Open
Abstract
Plant roots constitute the primary interface between plants and soilborne microorganisms and harbor microbial communities called the root microbiota. Recent studies have demonstrated a significant contribution of plant specialized metabolites (PSMs) to the assembly of root microbiota. However, the mechanistic and evolutionary details underlying the PSM-mediated microbiota assembly and its contribution to host specificity remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant specifically in the tobacco endosphere and that its enrichment in the tobacco endosphere is partially mediated by a combination of two unrelated classes of tobacco-specific PSMs, santhopine and nicotine. We isolated and sequenced Arthrobacter strains from tobacco roots as well as soils treated with these PSMs and identified genomic features, including but not limited to genes for santhopine and nicotine catabolism, that are associated with the ability to colonize tobacco roots. Phylogenomic and comparative analyses suggest that these genes were gained in multiple independent acquisition events, each of which was possibly triggered by adaptation to particular soil environments. Taken together, our findings illustrate a cooperative role of a combination of PSMs in mediating plant species-specific root bacterial microbiota assembly and suggest that the observed interaction between tobacco and Arthrobacter may be a consequence of an ecological fitting process. IMPORTANCE Host secondary metabolites have a crucial effect on the taxonomic composition of its associated microbiota. It is estimated that a single plant species produces hundreds of secondary metabolites; however, whether different classes of metabolites have distinctive or common roles in the microbiota assembly remains unclear. Here, we show that two unrelated classes of secondary metabolites in tobacco play a cooperative role in the formation of tobacco-specific compositions of the root bacterial microbiota, which has been established as a consequence of independent evolutionary events in plants and bacteria triggered by different ecological effects. Our findings illustrate mechanistic and evolutionary aspects of the microbiota assembly that are mediated by an arsenal of plant secondary metabolites.
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Affiliation(s)
- Tomohisa Shimasaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Takashi Kawasaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
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Liu F, Wu Z, Zhang X, Xi G, Zhao Z, Lai M, Zhao M. Microbial community and metabolic function analysis of cigar tobacco leaves during fermentation. Microbiologyopen 2021; 10:e1171. [PMID: 33970539 PMCID: PMC8483401 DOI: 10.1002/mbo3.1171] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/19/2022] Open
Abstract
Cigar tobacco leaves (CTLs) contain abundant bacteria and fungi that are vital to leaf quality during fermentation. In this study, artificial fermentation was used for the fermentation of CTLs since it was more controllable and efficient than natural aging. The bacterial and fungal community structure and composition in unfermented and fermented CTLs were determined to understand the effects of microbes on the characteristics of CTLs during artificial fermentation. The relationship between the chemical contents and alterations in the microbial composition was evaluated, and the functions of bacteria and fungi in fermented CTLs were predicted to determine the possible metabolic pathways. After artificial fermentation, the bacterial and fungal community structure significantly changed in CTLs. The total nitrate and nicotine contents were most readily affected by the bacterial and fungal communities, respectively. FAPROTAX software predictions of the bacterial community revealed increases in functions related to compound transformation after fermentation. FUNGuild predictions of the fungal community revealed an increase in the content of saprotrophic fungi after fermentation. These data provide information regarding the artificial fermentation mechanism of CTLs and will inform safety and quality improvements.
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Affiliation(s)
- Fang Liu
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Zhiyong Wu
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Xiaoping Zhang
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Gaolei Xi
- China Tobacco Henan Ind Co Ltd, Ctr TechnolZhengzhouChina
| | - Zhe Zhao
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Miao Lai
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
| | - Mingqin Zhao
- College of Tobacco ScienceHenan Agricultural UniversityZhengzhouChina
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Huang H, Shang J, Wang S. Physiology of a Hybrid Pathway for Nicotine Catabolism in Bacteria. Front Microbiol 2020; 11:598207. [PMID: 33281798 PMCID: PMC7688666 DOI: 10.3389/fmicb.2020.598207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Nicotine is a major N-heterocyclic aromatic alkaloid produced in tobacco plants and the main toxic chemical in tobacco waste. Due to its complex physiological effects and toxicity, it has become a concern both in terms of public health and the environment. A number of bacteria belonging to the genera Arthrobacter and Pseudomonas can degrade nicotine via the pyridine and pyrrollidine pathways. Recently, a novel hybrid of the pyridine and pyrrolidine pathways (also known as the VPP pathway) was found in the Rhizobiale group bacteria Agrobacterium tumefaciens S33, Shinella sp. HZN7 and Ochrobactrum sp. SJY1 as well as in other group bacteria. The special mosaic pathway has attracted much attention from microbiologists in terms of the study of their molecular and biochemical mechanisms. This will benefit the development of new biotechnologies in terms of the use of nicotine, the enzymes involved in its catabolism, and the microorganisms capable of degrading the alkaloid. In this pathway, some metabolites are hydroxylated in the pyridine ring or modified in the side chain with active groups, which can be used as precursors for the synthesis of some important compounds in the pharmaceutical and agricultural industries. Moreover, some enzymes may be used for industrial biocatalysis to transform pyridine derivatives into desired chemicals. Here, we review the molecular and biochemical basis of the hybrid nicotine-degrading pathway and discuss the electron transport in its oxidative degradation for energy conservation and bacterial growth.
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Affiliation(s)
- Haiyan Huang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, China
| | - Jinmeng Shang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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