从系统生物学角度看微生物生物降解网络的组织
The organization of the microbial biodegradation network from a systems-biology perspective.
作者信息
Pazos Florencio, Valencia Alfonso, De Lorenzo Víctor
机构信息
ALMA Bioinformatics, Centro Empresarial Euronova, Ronda de Poniente 4, Tres Cantos, 28760 Madrid, Spain.
出版信息
EMBO Rep. 2003 Oct;4(10):994-9. doi: 10.1038/sj.embor.embor933. Epub 2003 Sep 5.
Abstract
Microbial biodegradation of environmental pollutants is a field of growing importance because of its potential use in bioremediation and biocatalysis. We have studied the characteristics of the global biodegradation network that is brought about by all the known chemical reactions that are implicated in this process, regardless of their microbial hosts. This combination produces an efficient and integrated suprametabolism, with properties similar to those that define metabolic networks in single organisms. The characteristics of this network support an evolutionary scenario in which the reactions evolved outwards from the central metabolism. The properties of the global biodegradation network have implications for predicting the fate of current and future environmental pollutants.
摘要
由于微生物对环境污染物的生物降解在生物修复和生物催化方面的潜在应用，该领域的重要性日益凸显。我们研究了由该过程中所有已知化学反应所构成的全球生物降解网络的特征，无论这些反应的微生物宿主是什么。这种组合产生了一种高效且整合的超代谢，其特性类似于定义单个生物体代谢网络的特性。该网络的特征支持一种进化情景，即反应从中心代谢向外演化。全球生物降解网络的特性对于预测当前和未来环境污染物的归宿具有重要意义。
相似文献
1
The organization of the microbial biodegradation network from a systems-biology perspective.从系统生物学角度看微生物生物降解网络的组织
EMBO Rep. 2003 Oct;4(10):994-9. doi: 10.1038/sj.embor.embor933. Epub 2003 Sep 5.
2
Untapped potential: exploiting fungi in bioremediation of hazardous chemicals.未开发的潜力：利用真菌进行有害化学物质的生物修复。
Nat Rev Microbiol. 2011 Mar;9(3):177-92. doi: 10.1038/nrmicro2519. Epub 2011 Feb 7.
3
Planetary systems biology.行星系统生物学
Mol Cell. 2005 Feb 18;17(4):471-2. doi: 10.1016/j.molcel.2005.02.005.
4
Systems biology approaches to bioremediation.生物修复的系统生物学方法。
Curr Opin Biotechnol. 2008 Dec;19(6):579-89. doi: 10.1016/j.copbio.2008.10.004. Epub 2008 Nov 19.
5
Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology.将生态进化原理与环境生物技术相结合以增强微生物污染物的降解。
Trends Microbiol. 2021 Oct;29(10):908-918. doi: 10.1016/j.tim.2021.03.002. Epub 2021 Mar 31.
6
The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics.明尼苏达大学生物催化/生物降解数据库：用于功能基因组学的特殊代谢
Nucleic Acids Res. 1999 Jan 1;27(1):373-6. doi: 10.1093/nar/27.1.373.
7
The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes.明尼苏达大学生物催化/生物降解数据库：以酶为重点。
Nucleic Acids Res. 2001 Jan 1;29(1):340-3. doi: 10.1093/nar/29.1.340.
8
Bioremediation and microbial metabolism of benzo(a)pyrene.生物修复与苯并(a)芘的微生物代谢。
Mol Microbiol. 2018 Aug;109(4):433-444. doi: 10.1111/mmi.14062. Epub 2018 Aug 3.
9
Degradation of chlorinated nitroaromatic compounds.氯代硝基芳香族化合物的降解。
Appl Microbiol Biotechnol. 2012 Mar;93(6):2265-77. doi: 10.1007/s00253-012-3927-1. Epub 2012 Feb 14.
10
Bioremediation of Hazardous Pollutants Using Enzyme-Immobilized Reactors.利用酶固定化反应器进行危险污染物的生物修复。
Molecules. 2024 Apr 27;29(9):2021. doi: 10.3390/molecules29092021.
引用本文的文献
1
Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation.昆虫真菌养殖的经验教训：从微生物生态学到塑料降解
Front Microbiol. 2022 May 24;13:812143. doi: 10.3389/fmicb.2022.812143. eCollection 2022.
2
Concomitant prediction of environmental fate and toxicity of chemical compounds.化学化合物环境归宿与毒性的伴随预测。
Biol Methods Protoc. 2020 Nov 13;5(1):bpaa025. doi: 10.1093/biomethods/bpaa025. eCollection 2020.
3
Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.分枝杆菌 PYR-1 中的多环芳烃代谢网络。
J Bacteriol. 2011 Sep;193(17):4326-37. doi: 10.1128/JB.00215-11. Epub 2011 Jul 1.
4
Bionemo: molecular information on biodegradation metabolism.Bionemo：关于生物降解代谢的分子信息。
Nucleic Acids Res. 2009 Jan;37(Database issue):D598-602. doi: 10.1093/nar/gkn864. Epub 2008 Nov 5.
5
Metagenomics and the niche concept.宏基因组学与生态位概念。
Theory Biosci. 2008 Aug;127(3):241-7. doi: 10.1007/s12064-008-0028-x. Epub 2008 Apr 18.
6
The environmental fate of organic pollutants through the global microbial metabolism.有机污染物在全球微生物代谢作用下的环境归宿。
Mol Syst Biol. 2007;3:114. doi: 10.1038/msb4100156. Epub 2007 Jun 5.
7
Method for assessment of viability and morphological changes of bacteria in the early stage of colony formation on a simulated natural environment.在模拟自然环境中评估菌落形成早期细菌活力和形态变化的方法。
Appl Environ Microbiol. 2006 Jul;72(7):5037-42. doi: 10.1128/AEM.00106-06.
8
MetaRouter: bioinformatics for bioremediation.MetaRouter：用于生物修复的生物信息学
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D588-92. doi: 10.1093/nar/gki068.
本文引用的文献
1
On the Evolution of Biochemical Syntheses.论生物化学合成的进化
Proc Natl Acad Sci U S A. 1945 Jun;31(6):153-7. doi: 10.1073/pnas.31.6.153.
2
Genomics. Tinker, tailor: can Venter stitch together a genome from scratch?基因组学。修补匠，裁缝：文特尔能从头开始拼接出一个基因组吗？
Science. 2003 Feb 14;299(5609):1006-7. doi: 10.1126/science.299.5609.1006.
3
Biodegradation, biotransformation, and biocatalysis (b3).生物降解、生物转化和生物催化（b3）
Appl Environ Microbiol. 2002 Oct;68(10):4699-709. doi: 10.1128/AEM.68.10.4699-4709.2002.
4
Plasmid promiscuity: meeting the challenge of DNA immigration control.质粒的混杂性：应对DNA迁移控制的挑战
Environ Microbiol. 2002 Sep;4(9):495-500. doi: 10.1046/j.1462-2920.2002.00332.x.
5
Hierarchical organization of modularity in metabolic networks.代谢网络中模块化的层次组织。
Science. 2002 Aug 30;297(5586):1551-5. doi: 10.1126/science.1073374.
6
Pathway evolution, structurally speaking.从结构角度来看的通路进化。
Curr Opin Struct Biol. 2002 Jun;12(3):374-82. doi: 10.1016/s0959-440x(02)00331-7.
7
Biotechnology and bioremediation: successes and limitations.生物技术与生物修复：成功与局限
Appl Microbiol Biotechnol. 2002 Jul;59(2-3):143-52. doi: 10.1007/s00253-002-1024-6. Epub 2002 Jun 1.
8
Atmospherc deposition of organochlorine compounds to remote high mountain lakes of Europe.欧洲偏远高山湖泊中有机氯化合物的大气沉降。
Environ Sci Technol. 2002 Jun 15;36(12):2581-8. doi: 10.1021/es0102585.
9
Estimating prokaryotic diversity and its limits.估算原核生物多样性及其限度。
Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10494-9. doi: 10.1073/pnas.142680199. Epub 2002 Jul 3.
10
Evolution of enzymes in metabolism: a network perspective.新陈代谢中酶的进化：网络视角
J Mol Biol. 2002 Jul 19;320(4):751-70. doi: 10.1016/s0022-2836(02)00546-6.
Zotero 插件