稻田细菌分离株sp. CPD - 03的比较基因组学：毒死蜱降解潜力分析
Comparative Genomics of a Paddy Field Bacterial Isolate sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential.
作者信息
Nayak Tanmaya, Panda Ananta N, Kumari Khushbu, Adhya Tapan Kumar, Raina Vishakha
机构信息
Environmental Biotechnology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology-KIIT (Deemed to be University), Bhubaneswar, Odisha 751024 India.
出版信息
Indian J Microbiol. 2020 Sep;60(3):325-333. doi: 10.1007/s12088-020-00864-9. Epub 2020 Apr 2.
Abstract
genus is known to catabolize aromatic compounds. This study reports a complete genome sequence of sp. CPD-03 (~ 4.6 Mb of chromosomal features) responsible for chlorpyrifos (CP) isolated form a paddy field (20.3588° N, 85.8333° E) in Bhubaneswar, India. A comparative genomics approach was performed between CPD-03 and eight closely related genomes of other strains in order to deepen our knowledge, to establish its phylogenetic and functional relationships. The involvement of CP degrading genes indicated a versatile role of CPD-03 in additional field trails. This research would provide the genetic information for its use in natural environment for the depletion of organophosphorus (OP) compounds.
摘要
已知该属可分解芳香族化合物。本研究报告了从印度布巴内斯瓦尔的一块稻田（北纬20.3588°，东经85.8333°）分离出的负责降解毒死蜱（CP）的菌株CPD - 03的完整基因组序列（约4.6 Mb的染色体特征）。为了加深我们的认识，建立其系统发育和功能关系，对CPD - 03与其他菌株的八个密切相关基因组进行了比较基因组学研究。CP降解基因的参与表明CPD - 03在其他田间试验中具有多种作用。这项研究将为其在自然环境中用于消耗有机磷（OP）化合物提供遗传信息。
相似文献
1
Comparative Genomics of a Paddy Field Bacterial Isolate sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential.稻田细菌分离株sp. CPD - 03的比较基因组学：毒死蜱降解潜力分析
Indian J Microbiol. 2020 Sep;60(3):325-333. doi: 10.1007/s12088-020-00864-9. Epub 2020 Apr 2.
2
Biodegradation of chlorpyrifos and its hydrolysis product 3,5,6-trichloro-2-pyridinol using a novel bacterium Ochrobactrum sp. JAS2: A proposal of its metabolic pathway.利用新型细菌苍白杆菌属JAS2对毒死蜱及其水解产物3,5,6-三氯-2-吡啶醇进行生物降解：其代谢途径的推测
Pestic Biochem Physiol. 2016 Jan;126:13-21. doi: 10.1016/j.pestbp.2015.07.001. Epub 2015 Jul 16.
3
Biodegradation of organophosphate pesticide quinalphos by Ochrobactrum sp. strain HZM.食酸菌属菌株HZM对有机磷农药喹硫磷的生物降解作用
J Appl Microbiol. 2014 Nov;117(5):1283-92. doi: 10.1111/jam.12627. Epub 2014 Oct 3.
4
Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms.实验室微宇宙中联合生物刺激与生物强化降解毒死蜱的研究
3 Biotech. 2021 Oct;11(10):439. doi: 10.1007/s13205-021-02980-9. Epub 2021 Sep 18.
5
Characterization and genome functional analysis of the DDT-degrading bacterium Ochrobactrum sp. DDT-2.滴滴涕降解菌 Ochrobactrum sp. DDT-2 的特性描述和基因组功能分析。
Sci Total Environ. 2017 Aug 15;592:593-599. doi: 10.1016/j.scitotenv.2017.03.052. Epub 2017 Mar 18.
6
Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.夸氏杆菌属一新种，来自马铃薯根际的群体感应淬灭细菌，以及与相关模式菌株的比较基因组分析。
PLoS One. 2019 Jan 22;14(1):e0210874. doi: 10.1371/journal.pone.0210874. eCollection 2019.
7
Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links.来自临床和环境来源的苍白杆菌属物种的泛基因组揭示了不同的种群和可能的联系。
Genomics. 2020 Sep;112(5):3003-3012. doi: 10.1016/j.ygeno.2020.04.030. Epub 2020 May 17.
8
Genome sequence of strain SUBG007, a plant pathogen and potential xenobiotic compounds degradation bacterium.菌株SUBG007的基因组序列，该菌株是一种植物病原体及潜在的异生素化合物降解细菌。
Genom Data. 2017 Jan 4;11:116-117. doi: 10.1016/j.gdata.2017.01.001. eCollection 2017 Mar.
9
Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains.从地层水中分离和鉴定原油降解细菌：中间苍白杆菌环境分离株与临床菌株的比较基因组分析
J Zhejiang Univ Sci B. 2015 Oct;16(10):865-74. doi: 10.1631/jzus.B1500029.
10
Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis.基于recA和16S rRNA基因的比较序列分析对属于苍白杆菌-布鲁氏菌属菌群的细菌的遗传多样性和系统发育关系
Syst Appl Microbiol. 2008 Mar;31(1):1-16. doi: 10.1016/j.syapm.2007.10.004. Epub 2008 Jan 28.
引用本文的文献
1
Genomic Characteristics and Functional Analysis of sp. Strain WY7 Isolated from Antarctic Krill.从南极磷虾中分离出的sp.菌株WY7的基因组特征与功能分析
Microorganisms. 2023 Sep 11;11(9):2281. doi: 10.3390/microorganisms11092281.
2
Environmental Distribution, Metabolic Fate, and Degradation Mechanism of Chlorpyrifos: Recent and Future Perspectives.毒死蜱的环境分布、代谢归宿及降解机制：近期与未来展望
Appl Biochem Biotechnol. 2022 May;194(5):2301-2335. doi: 10.1007/s12010-021-03713-7. Epub 2022 Jan 11.
3
Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms.实验室微宇宙中联合生物刺激与生物强化降解毒死蜱的研究
3 Biotech. 2021 Oct;11(10):439. doi: 10.1007/s13205-021-02980-9. Epub 2021 Sep 18.
4
Myco-remediation of Chlorinated Pesticides: Insights Into Fungal Metabolic System.氯代农药的真菌修复：对真菌代谢系统的见解
Indian J Microbiol. 2021 Sep;61(3):237-249. doi: 10.1007/s12088-021-00940-8. Epub 2021 Apr 20.
本文引用的文献
1
Kinetics and Catabolic Pathways of the Insecticide Chlorpyrifos, Annotation of the Degradation Genes, and Characterization of Enzymes TcpA and Fre in Cupriavidus nantongensis X1.杀虫剂毒死蜱的动力学和分解代谢途径、降解基因注释以及铜绿假单胞菌 X1 中 tcpA 和 fre 酶的特性。
J Agric Food Chem. 2019 Feb 27;67(8):2245-2254. doi: 10.1021/acs.jafc.9b00173. Epub 2019 Feb 15.
2
Efficiency of the intestinal bacteria in the degradation of the toxic pesticide, chlorpyrifos.肠道细菌对有毒杀虫剂毒死蜱的降解效率。
3 Biotech. 2013 Apr;3(2):137-142. doi: 10.1007/s13205-012-0078-0. Epub 2012 Aug 1.
3
Developmental neurotoxicity of succeeding generations of insecticides.后续几代杀虫剂的发育神经毒性。
Environ Int. 2017 Feb;99:55-77. doi: 10.1016/j.envint.2016.11.019. Epub 2016 Nov 28.
4
Complete genome sequence of a novel chlorpyrifos degrading bacterium, Cupriavidus nantongensis X1.新型毒死蜱降解菌南通贪铜菌X1的全基因组序列
J Biotechnol. 2016 Jun 10;227:1-2. doi: 10.1016/j.jbiotec.2016.04.012. Epub 2016 Apr 8.
5
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.MEGA7：适用于更大数据集的分子进化遗传学分析版本7.0
Mol Biol Evol. 2016 Jul;33(7):1870-4. doi: 10.1093/molbev/msw054. Epub 2016 Mar 22.
6
Biodegradation of chlorpyrifos and its hydrolysis product 3,5,6-trichloro-2-pyridinol using a novel bacterium Ochrobactrum sp. JAS2: A proposal of its metabolic pathway.利用新型细菌苍白杆菌属JAS2对毒死蜱及其水解产物3,5,6-三氯-2-吡啶醇进行生物降解：其代谢途径的推测
Pestic Biochem Physiol. 2016 Jan;126:13-21. doi: 10.1016/j.pestbp.2015.07.001. Epub 2015 Jul 16.
7
OrthoANI: An improved algorithm and software for calculating average nucleotide identity.OrthoANI：一种用于计算平均核苷酸一致性的改进算法及软件。
Int J Syst Evol Microbiol. 2016 Feb;66(2):1100-1103. doi: 10.1099/ijsem.0.000760. Epub 2015 Nov 9.
8
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap.ClustVis：一种使用主成分分析和热图可视化多变量数据聚类的网络工具。
Nucleic Acids Res. 2015 Jul 1;43(W1):W566-70. doi: 10.1093/nar/gkv468. Epub 2015 May 12.
9
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.OrthoVenn：一个用于跨多个物种进行全基因组直系同源簇比较和注释的网络服务器。
Nucleic Acids Res. 2015 Jul 1;43(W1):W78-84. doi: 10.1093/nar/gkv487. Epub 2015 May 11.
10
Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.氯氰菊酯富集培养物的细菌群落分析及氯氰菊酯污染土壤的生物修复
J Basic Microbiol. 2015 Jul;55(7):819-29. doi: 10.1002/jobm.201400805. Epub 2015 Feb 5.
Zotero 插件