三硝基甲苯之毒理機制及生物降解暨多氯乙烯汙染模場生物整治

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：18

、訪客IP：3.145.186.173

姓名

廖弘玉(Hung-Yu Liao) 查詢紙本館藏

畢業系所

生命科學系

論文名稱

三硝基甲苯之毒理機制及生物降解暨多氯乙烯汙染模場生物整治

相關論文

★ 利用斑馬魚研究肝臟疾病和肝癌之發生：B型肝炎病毒X抗原，黃麴毒素，p53突變，src和edn1的致癌作用及其協同效應	★ 4-aminobiphenyl誘導HepG2細胞中的microRNAs表現並藉由microRNAs調控DNA修復機制
★ 研究Dicrotophos對HepG2細胞毒性之分子機制：CSA蛋白質在毒性扮演之角色	★ TNT經由ROS介導之內質網壓力及粒線體失衡誘導人類肝臟細胞凋亡
★ Pseudomonas sp. A46全基因組分析與重金屬復育基因工程菌開發	★ 4-Aminobiphenyl 調控 miR-630 抑制 RAD18 表現誘導 Hep3B 細胞產生氧化性 DNA 損傷
★ 探討人類肝癌細胞HepG2經4-氨基聯苯處理過後miRNA-630對於同源重組修復相關蛋白MCM8的調控機制	★ 假單胞菌Pseudomonas sp. A46之基因工程菌開發及重金屬之生物累積和生物吸附潛力探討
★ 開發新穎性包埋Dehalococcoides mccartyi及Clostridium butyricum之長效脫氯膠體	★ 探討DNA損傷反應與慢性暴露4-胺基聯苯產生之肝臟毒性
★ 以Lpp-OmpA工法建構新穎性基因工程菌強化鎘生物復育能力	★ 建構脫鹵球菌與固氮菌共培養系統促進氮源缺乏環境下的還原脫氯作用
★ 硒代胱氨酸通過誘導人肝細胞癌中的 DNA 損傷和抑制 DNA 修復途徑來增強順鉑敏感性	★ 轉錄體分析 Acetobacterium woodii 降解1,1,1-三氯乙烷機制並用以協助 Dehalococcoides進行還原脫氯
★ 以宏觀基因體分析新穎 Candidatus Dehalobacterium strain DLY 降解二氯甲烷機制	★ 研究雙特松對HepG2細胞之DNA修復的影響

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

至系統瀏覽論文 ( 永不開放)

摘要(中)

三硝基甲苯常被使用在軍事或名間爆破用途，已經有許多研究證明三硝基甲苯會殘留在土地或地下水中，由於三硝基甲苯具有毒性，而其毒性機制尚未澄清，本研究第一部分，使用人類肝癌細胞HepG2和Hep3B，證明三硝基甲苯會誘導自由基產生，造成DNA的損傷，如果長期有此壓力存在可能導致癌症，進一步我們發現在高濃度的三硝基甲苯培養條件下會導致細胞內質網壓力及粒線體的破壞，造成細胞死亡；第二部分，由於上述我們證實三硝基甲苯對細胞會造成毒性，因此清除環境中三硝基甲苯的污染刻不容緩，我們於台灣南部受三硝基甲苯汙染之廠址篩選出一株可降解三硝基甲苯之本土菌株Citrobacter sp.，我們發現Citrobacter sp. 可以將三硝基甲苯轉化成4-amino-2,6-dinitrotoluene (4-ADNT)和2-amino-4,6-dinitrotoluene (2-ADNT)，並且我們利用轉錄體學結和蛋白質體學調查Citrobacter sp.在降解三硝基甲苯過程中的分子機制，發現在降解過程中中心代謝機制受到抑制，並且抵抗環境壓力相關基因(例如: chaperones, transport-related proteins, and membrane proteins)表現量增加，我們推測這些基因與Citrobacter sp. 的去毒性有關，最後我們純化降解三硝基甲苯的關鍵蛋白NemA，證實此蛋白質確實為降解三硝基甲苯之關鍵酵素;第三部分，我們將整治研究實際於一多氯乙烯污染場址施作，多氯乙烯是一種難以用化學或物理法去除的環境汙染物，我們於台南永康區一處多氯乙烯汙染模場，添加slow polycolloid releasing substrate (SPRS)，進行生物刺激法整治並在整治過程中利用次世代定序取代傳統變性析度凝膠電泳分析調查環境菌相變化，結果證實SPRS確實可刺激降解多氯乙烯菌株生長並增加降解。

摘要(英)

There have been several reports of widespread contamination of soil and groundwater resulting from explosives, such as 2,4,6- trinitrotoluene (TNT). The accumulation of TNT also presents potentially hazardous effects to both humans and animals. In chapter I, we examined TNT-induced apoptosis via ROS dependent mitochondrial dysfunction and ER stress in HepG2 and Hep3B cells. Chapter II, the bacterial strain Citrobacter sp. was isolated from 2,4,6-trinitrotoluene (TNT) contaminated soil. We investigated the transcriptomic and proteomic responses of Citrobacter sp. to TNT by comparing profiles at 0 h and 12 h to understand how Citrobacter sp. can survive and transform under TNT stress. Chapter III, Tetrachloroethene (PCE) and trichloroethene (TCE) are pollutants found in large quantities in industrial areas around the world. The slow polycolloid releasing substrate (SPRS) has been developed to continuously provide biodegradable substrates for the enhancement of TCE reductive dechlorination. We investigated microbial groundwater community before and after SPRS addition and proved that can be stimulated the dechlorinating.

關鍵字(中)

★ 生物降解

關鍵字(英)

★ Biodegradation

論文目次

Table of Contents
致謝 i
中文摘要 ii
ABSTRACT iii
Chapter I-2,4,6-Trinitrotoluene Induces Apoptosis via ROS-Regulated Mitochondrial Dysfunction and Endoplasmic Reticulum Stress in HepG2 and Hep3B Cells 1
ABSTRACT 2
INTRODUCTION 3
MATERIALS AND METHODS 5
RESULTS 11
DISCUSSION 16
Chapter II-Biodegradation of 2, 4, 6-Trinitrotoluene by Citrobacter sp. 20
ABSTRACT 21
INTRODUCTION 23
MATERIALS AND METHODS 25
RESULTS 32
DISCUSSION 38
Chapter Ⅲ-The Change of Microbial Community from Chlorinated Solvent-Contaminated Groundwater after Biostimulation using the Metagenome Analysis 44
ABSTRACT 45
INTRODUCTION 46
MATERIALS AND METHODS 49
RESULTS AND DISCUSSION 54
REFERENCES 59
?
List of Figures
Figure 1. TNT-induced cytotoxicity, DNA damage and apoptosis in HepG2 cells in a dose- and-time dependent manner... 70
Figure 2. TNT-induced ER stress in HepG2 cells. 72
Figure 3. TNT triggered the mitochondrial dysfunction and apoptosis pathways. 73
Figure 4. TNT induced the generation of ROS. 74
Figure 5. ROS-dependent ER stress was involved in the TNT-mediated ROS production. 75
Figure 6. Effects of CHOP siRNA on TNT-induced ER stress in HepG2 cells. 76
Figure 7. The schematic representation of proposed mechanisms according to TNT-induced apoptosis in HepG2 cells. 77
Figure 8. Growth curve of Citrobacter sp.in TNT-NFG medium. 78
Figure 9. TNT biodegradation by Citrobacter sp.. 79
Figure 10. Representative two-dimensional gel electrophoresis (2-DE) gel images (pH 4-7) of whole cell lysates of Citrobacter sp. 80
Figure 11. Identification of differential abundances of proteins of Citrobacter sp. in TNT-NFG medium at different time. 81
Figure 12. Functional classification of 42 protein spots 82
Figure 13. Proteins with significant differential abundances sorted by COG categories. 83
Figure 14. Venn diagram showing differentially expressed genes and proteins of Citrobacter sp. 84
Figure 15. Plasmid drawing of pET21b-NemA and SDS-PAGE of His6-NemA. 85
Figure 16. Time course of contamination levels of PCE,TCE,DCE,VC and ethene in monitoring well. 86
Figure 17. The graph showed the most abundant genera according to the RDP classification for V1-V3 region, in 16S rRNA sequences. 87
Figure 18. Metagenome reads were mapped on genomes of bacteria using LCA classification approach. 88
Figure 19. The predicted enzymes were mapped on the TCE biodegradation pathways
89

?
List of Supplementary Figures
Supplementary Figure S1. ROS-dependent ER stress was involved in the TNT-mediated ROS production.... 97
Supplementary Figure S2. HepG2 cells were transfected with CHOP siRNA for 24h, and analysis by western blot. 98
Supplementary Figure S3. Differentially expressed gene profile, according to clusters of orthologous groups of proteins (COG) analysis.. 99
Supplementary Figure S4. The predicted genes were mapped on the glycolysis/gluconeogenesis pathways. 100
Supplementary Figure S5. The predicted genes were mapped on the oxidative phosphorylation pathways. 101
Supplementary Figure S6. Site map showing the groundwater flow direction 102
?
List of Tables
Table 1. Draft genome assembly statistics of Citrobacter sp.... 90
Table 2. Summary of reads generation. 90
Table 3. Functional categorization of differentially expressed proteins of Citrobacter sp. in TNT-NFG medium at different time.. 91
Table 4. A list of common differentially expressed genes between transcriptome and proteome.. 94
Table 5. Geochemical characteristics of groundwater in monitoring wells. 95
Table 6. Mapping of assembled reads on xenobiotic degradation pathways present in KEGG database. 96
?
List of Supplementary Tables
Supplementary Table S1. Primer list... 104
Supplementary Table S4. Comparison of RNA-seq results by quantitative PCR on differentially expressed genes. 105
Supplementary Table S5. Differential Pathway detected in TNT (30 μM). 106
Supplementary Table S6. Differential Pathway detected in TNT (80 μM). 108
Supplementary Table S8. Primer list 111
Supplementary Table S10. Comparison of RNA-seq results by quantitative PCR on differentially expressed genes. 112
Supplementary Table S14. The most abundant genera according to the RDP classification approach. 113

參考文獻

REFERENCES
1. Chien, C. C., Kao, C. M., Chen, D. Y., Chen, S. C. & Chen, C. C. Biotransformation of trinitrotoluene (TNT) by Pseudomonas spp. isolated from a TNT-contaminated environment. Environ Toxicol Chem 33, 1059-1063 (2014).
2. Berthe-Corti, L., Jacobi, H., Kleihauer, S. & Witte, I. Cytotoxicity and mutagenicity of a 2,4,6-trinitrotoluene (TNT) and hexogen contaminated soil in S. typhimurium and mammalian cells. Chemosphere 37, 209-218 (1998).
3. Honeycutt, M. E., Jarvis, A. S. & McFarland, V. A. Cytotoxicity and mutagenicity of 2,4,6-trinitrotoluene and its metabolites. Ecotoxicol Environ Saf 35, 282-287 (1996).
4. Ross, R. H. & Hartley, W. R. Comparison of water quality criteria and health advisories for 2,4,6-trinitrotoluene. Regul Toxicol Pharmacol 11, 114-117 (1990).
5. Bolt, H. M., Degen, G. H., Dorn, S. B., Plottner, S. & Harth, V. Genotoxicity and potential carcinogenicity of 2,4,6-TNT trinitrotoluene: structural and toxicological considerations. Rev Environ Health 21, 217-228 (2006).
6. Hathaway, J. A. Trinitrotoluene: A Review of Reported Dose-Related Effects Providing Documentation for a Workplace Standard. J Occup Med 19, 341-345 (1977).
7. Deng, Y. et al. Analysis of common and specific mechanisms of liver function affected by nitrotoluene compounds. PLoS One 6, e14662 (2011).
8. Yan, C. et al. The retrospective survey of malignant tumor in weapon workers exposed to 2,4,6-trinitrotoluene. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 20, 184-188 (2002).
9. Song, L. et al. Trinitrotoluene Induces Endoplasmic Reticulum Stress and Apoptosis in HepG2 Cells. Med Sci Monit 21, 3434-3441 (2015).
10. Glass, K. Y., Newsome, C. R. & Tchounwou, P. B. Cytotoxicity and expression of c-fos, HSP70, and GADD45/153 proteins in human liver carcinoma (HepG2) cells exposed to dinitrotoluenes. Int J Environ Res Public Health 2, 355-361 (2005).
11. Shi, Y. et al. ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis. Cell Death Differ 21, 612-623 (2014).
12. Zhou, L. et al. Miltirone exhibits antileukemic activity by ROS-mediated endoplasmic reticulum stress and mitochondrial dysfunction pathways. Sci Rep 6, 20585 (2016).
13. Romanov, V., Whyard, T. C., Waltzer, W. C., Grollman, A. P. & Rosenquist, T. Aristolochic acid-induced apoptosis and G2 cell cycle arrest depends on ROS generation and MAP kinases activation. Arch Toxicol 89, 47-56 (2015).
14. Cooke, M. S., Evans, M. D., Dizdaroglu, M. & Lunec, J. Oxidative DNA damage: mechanisms, mutation, and disease. Faseb j 17, 1195-1214 (2003).
15. Chen, Y. W., Yang, Y. T., Hung, D. Z., Su, C. C. & Chen, K. L. Paraquat induces lung alveolar epithelial cell apoptosis via Nrf-2-regulated mitochondrial dysfunction and ER stress. Arch Toxicol 86, 1547-1558 (2012).
16. Soboloff, J. & Berger, S. A. Sustained ER Ca2+ depletion suppresses protein synthesis and induces activation-enhanced cell death in mast cells. J Biol Chem 277, 13812-13820 (2002).
17. Csordas, G., Thomas, A. P. & Hajnoczky, G. Quasi-synaptic calcium signal transmission between endoplasmic reticulum and mitochondria. Embo j 18, 96-108 (1999).
18. Wu, J. C., Hseu, Y. C., Chen, C. H., Wang, S. H. & Chen, S. C. Comparative investigations of genotoxic activity of five nitriles in the comet assay and the Ames test. J Hazard Mater 169, 492-497 (2009).
19. Hsu, L. S., Chiou, B. H., Hsu, T. W., Wang, C. C. & Chen, S. C. The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon. Environ Toxicol 32, 217-226 (2017).
20. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008).
21. Audic, S. & Claverie, J. M. The significance of digital gene expression profiles. Genome Res 7, 986-995 (1997).
22. Huan, L. C. et al. MicroRNA regulation of DNA repair gene expression in 4-aminobiphenyl-treated HepG2 cells. Toxicology 322, 69-77 (2014).
23. Zhao, M., Howard, E. W., Guo, Z., Parris, A. B. & Yang, X. p53 pathway determines the cellular response to alcohol-induced DNA damage in MCF-7 breast cancer cells. PLoS One 12, e0175121 (2017).
24. Ozgur, R., Turkan, I., Uzilday, B. & Sekmen, A. H. Endoplasmic reticulum stress triggers ROS signalling, changes the redox state, and regulates the antioxidant defence of Arabidopsis thaliana. J Exp Bot 65, 1377-1390 (2014).
25. Jacobson, J. & Duchen, M. R. Mitochondrial oxidative stress and cell death in astrocytes--requirement for stored Ca2+ and sustained opening of the permeability transition pore. J Cell Sci 115, 1175-1188 (2002).
26. Tait, S. W. & Green, D. R. Mitochondria and cell death: outer membrane permeabilization and beyond. Nat Rev Mol Cell Biol 11, 621-632 (2010).
27. Petrosillo, G., Ruggiero, F. M., Pistolese, M. & Paradies, G. Ca2+-induced reactive oxygen species production promotes cytochrome c release from rat liver mitochondria via mitochondrial permeability transition (MPT)-dependent and MPT-independent mechanisms: role of cardiolipin. J Biol Chem 279, 53103-53108 (2004).
28. Wilkening, S., Stahl, F. & Bader, A. Comparison of primary human hepatocytes and hepatoma cell line HepG2 with regard to their biotransformation properties. Drug Metab Dispos 31, 1035-1042 (2003).
29. Qiu, G. H. et al. Distinctive pharmacological differences between liver cancer cell lines HepG2 and Hep3B. Cytotechnology 67, 1-12 (2015).
30. Knasmuller, S. et al. Use of metabolically competent human hepatoma cells for the detection of mutagens and antimutagens. Mutat Res 402, 185-202 (1998).
31. Mersch-Sundermann, V., Knasmuller, S., Wu, X. J., Darroudi, F. & Kassie, F. Use of a human-derived liver cell line for the detection of cytoprotective, antigenotoxic and cogenotoxic agents. Toxicology 198, 329-340 (2004).
32. Pirozzi, A. V., Stellavato, A., La Gatta, A., Lamberti, M. & Schiraldi, C. Mancozeb, a fungicide routinely used in agriculture, worsens nonalcoholic fatty liver disease in the human HepG2 cell model. Toxicol Lett 249, 1-4 (2016).
33. Medina-Diaz, I. M. et al. Downregulation of human paraoxonase 1 (PON1) by organophosphate pesticides in HepG2 cells. Environ Toxicol 32, 490-500 (2017).
34. Tchounwou, P. B., Wilson, B. A., Ishaque, A. B. & Schneider, J. Transcriptional activation of stress genes and cytotoxicity in human liver carcinoma cells (HepG2) exposed to 2,4,6-trinitrotoluene, 2,4-dinitrotoluene, and 2,6-dinitrotoluene. Environ Toxicol 16, 209-216 (2001).
35. Hseu, Y. C., Hsu, T. W., Lin, H. D., Chen, C. H. & Chen, S. C. Molecular mechanisms of discrotophos-induced toxicity in HepG2 cells: The role of CSA in oxidative stress. Food Chem Toxicol 103, 253-260 (2017).
36. Chen, L. C. et al. Molecular mechanisms of 3,3′-dichlorobenzidine-mediated toxicity in HepG2 cells. Environ Mol Mutagen 55, 407-420 (2014).
37. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10, 57-63 (2009).
38. Arun, S., Liu, L. & Donmez, G. Mitochondrial Biology and Neurological Diseases. Curr Neuropharmacol 14, 143-154 (2016).
39. Fang, J., Seki, T. & Maeda, H. Therapeutic strategies by modulating oxygen stress in cancer and inflammation. Adv Drug Deliv Rev 61, 290-302 (2009).
40. Sahin, E. & Depinho, R. A. Linking functional decline of telomeres, mitochondria and stem cells during ageing. Nature 464, 520-528 (2010).
41. Chung, T. W. et al. Sinularin induces DNA damage, G2/M phase arrest, and apoptosis in human hepatocellular carcinoma cells. BMC Complement Altern Med 17, 62 (2017).
42. Turrens, J. F. Superoxide production by the mitochondrial respiratory chain. Biosci Rep 17, 3-8 (1997).
43. Woo, I. S. et al. TMEM14A inhibits N-(4-hydroxyphenyl)retinamide-induced apoptosis through the stabilization of mitochondrial membrane potential. Cancer Lett 309, 190-198 (2011).
44. Fei, Q. & Ethell, D. W. Maneb potentiates paraquat neurotoxicity by inducing key Bcl-2 family members. J Neurochem 105, 2091-2097 (2008).
45. Ron, D. & Walter, P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol 8, 519-529 (2007).
46. Perri, E. R., Thomas, C. J., Parakh, S., Spencer, D. M. & Atkin, J. D. The Unfolded Protein Response and the Role of Protein Disulfide Isomerase in Neurodegeneration. Front Cell Dev Biol 3, 80 (2015).
47. Panayi, G. S. & Corrigall, V. M. Immunoglobulin heavy-chain-binding protein (BiP): a stress protein that has the potential to be a novel therapy for rheumatoid arthritis. Biochem Soc Trans 42, 1752-1755 (2014).
48. Mera, K. et al. ER signaling is activated to protect human HaCaT keratinocytes from ER stress induced by environmental doses of UVB. Biochem Biophys Res Commun 397, 350-354 (2010).
49. McCullough, K. D., Martindale, J. L., Klotz, L. O., Aw, T. Y. & Holbrook, N. J. Gadd153 sensitizes cells to endoplasmic reticulum stress by down-regulating Bcl2 and perturbing the cellular redox state. Mol Cell Biol 21, 1249-1259 (2001).
50. De Lorme, M. & Craig, M. Biotransformation of 2,4,6-trinitrotoluene by pure culture ruminal bacteria. Curr Microbiol 58, 81-86 (2009).
51. Mulla, S. I., Talwar, M. P., Bagewadi, Z. K., Hoskeri, R. S. & Ninnekar, H. Z. Enhanced degradation of 2-nitrotoluene by immobilized cells of Micrococcus sp. strain SMN-1. Chemosphere 90, 1920-1924 (2013).
52. Chien, C. C., Kao, C. M., Chen, D. Y., Chen, S. C. & Chen, C. C. Biotransformation of trinitrotoluene (TNT) by Pseudomonas spp. isolated from a TNT-contaminated environment. Environ Toxicol Chem 33, 1059-1063 (2014).
53. Rylott, E. L., Lorenz, A. & Bruce, N. C. Biodegradation and biotransformation of explosives. Curr Opin Biotechnol 22, 434-440 (2011).
54. Fahrenfeld, N., Zoeckler, J., Widdowson, M. A. & Pruden, A. Effect of biostimulants on 2,4,6-trinitrotoluene (TNT) degradation and bacterial community composition in contaminated aquifer sediment enrichments. Biodegradation 24, 179-190 (2013).
55. Hathaway, J. A. Trinitrotoluene: a review of reported dose-related effects providing documentation for a workplace standard. J Occup Med 19, 341-345 (1977).
56. Deng, Y. et al. Analysis of common and specific mechanisms of liver function affected by nitrotoluene compounds. PLoS One 6, e14662 (2011).
57. Liao, H. Y. et al. 2,4,6-Trinitrotoluene Induces Apoptosis via ROS-Regulated Mitochondrial Dysfunction and Endoplasmic Reticulum Stress in HepG2 and Hep3B Cells. Sci Rep 7, 8148 (2017).
58. Kalderis, D., Juhasz, A. L., Boopathy, R. & Comfort, S. Soils contaminated with explosives: environmental fate and. Pure and Applied Chemistry 83, 1407(1407) (2011).
59. Weisse, R. The Bioremediation of (2, 4, 6) Trinitrotoluene by Three Classes of Organisms. Basic Biotechnol eJ. 4, 66-71 (2008).
60. Johnson, R. L., Tratnyek, P. G., Miehr, R., Thoms, R. B. & Bandstra, J. Z. Reduction of hydraulic conductivity and reactivity in zero-valent iron columns by oxygen and TNT. Ground Water Monitoring & Remediation 25, 129-136 (2005).
61. Stenuit, B. A. & Agathos, S. N. Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa? Appl Microbiol Biotechnol 88, 1043-1064 (2010).
62. Oh, K. & Kim, Y. Degradation of explosive 2,4,6-trinitrotoluene by s-triazine degrading bacterium isolated from contaminated soil. Bull Environ Contam Toxicol 61, 702-708 (1998).
63. Montpas, S. et al. Degradation of 2,4,6-trinitrotoluene by Serratia marcescens. Biotechnol Lett 19, 291-294 (1997).
64. French, C. E., Nicklin, S. & Bruce, N. C. Aerobic degradation of 2,4,6-trinitrotoluene by Enterobacter cloacae PB2 and by pentaerythritol tetranitrate reductase. Appl Environ Microbiol 64, 2864-2868 (1998).
65. Mercimek, H. A., Dincer, S., Guzeldag, G., Ozsavli, A. & Matyar, F. Aerobic biodegradation of 2,4,6-trinitrotoluene (TNT) by Bacillus cereus isolated from contaminated soil. Microb Ecol 66, 512-521 (2013).
66. Nishino, S. F., Paoli, G. C. & Spain, J. C. Aerobic degradation of dinitrotoluenes and pathway for bacterial degradation of 2,6-dinitrotoluene. Appl Environ Microbiol 66, 2139-2147 (2000).
67. Tam le, T. et al. Differential gene expression in response to phenol and catechol reveals different metabolic activities for the degradation of aromatic compounds in Bacillus subtilis. Environ Microbiol 8, 1408-1427 (2006).
68. Molina-Santiago, C., Udaondo, Z., Gomez-Lozano, M., Molin, S. & Ramos, J. L. Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene. Environ Microbiol 19, 645-658 (2017).
69. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10, 57-63 (2009).
70. Hong, Y. H. et al. Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability. Gene 584, 185-194 (2016).
71. Fernandez, M. et al. Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene. Microb Biotechnol 2, 287-294 (2009).
72. Bhaganna, P., Bielecka, A., Molinari, G. & Hallsworth, J. E. Protective role of glycerol against benzene stress: insights from the Pseudomonas putida proteome. Curr Genet 62, 419-429 (2016).
73. Jungblut, P. R. et al. Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 36, 710-725 (2000).
74. Wei, K. et al. Characteristics and proteomic analysis of pyrene degradation by Brevibacillus brevis in liquid medium. Chemosphere 178, 80-87 (2017).
75. Lee, S. Y. et al. Proteomic Analysis of Polycyclic Aromatic Hydrocarbons (PAHs) Degradation and Detoxification in Sphingobium chungbukense DJ77. J Microbiol Biotechnol 26, 1943-1950 (2016).
76. Feng, X. et al. A proteomic-based investigation of potential copper-responsive biomarkers: Proteins, conceptual networks, and metabolic pathways featuring Penicillium janthinellum from a heavy metal-polluted ecological niche. Microbiologyopen 6 (2017).
77. Ho, E. M., Chang, H. W., Kim, S. I., Kahng, H. Y. & Oh, K. H. Analysis of TNT (2,4,6-trinitrotoluene)-inducible cellular responses and stress shock proteome in Stenotrophomonas sp. OK-5. Curr Microbiol 49, 346-352 (2004).
78. Lee, B. U., Park, S. C., Cho, Y. S. & Oh, K. H. Exopolymer biosynthesis and proteomic changes of Pseudomonas sp. HK-6 under stress of TNT (2,4,6-trinitrotoluene). Curr Microbiol 57, 477-483 (2008).
79. Zhao, B. & Poh, C. L. Insights into environmental bioremediation by microorganisms through functional genomics and proteomics. Proteomics 8, 874-881 (2008).
80. Dewhirst, F. E. et al. Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int J Syst Evol Microbiol 51, 1797-1804 (2001).
81. Kao, C. M. et al. The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis. J Hazard Mater 302, 144-150 (2016).
82. Hsu, L. S., Chiou, B. H., Hsu, T. W., Wang, C. C. & Chen, S. C. The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon. Environ Toxicol 32, 217-226 (2017).
83. Chen, S. C. et al. Biodegradation of methyl tert-butyl ether (MTBE) by Enterobacter sp. NKNU02. J Hazard Mater 186, 1744-1750 (2011).
84. Erdjument-Bromage, H. et al. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J Chromatogr A 826, 167-181 (1998).
85. Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35, 3100-3108 (2007).
86. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
87. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35, W182-185 (2007).
88. M. Mar Gonzalez-Perez, Pieter van Dillewijn,Rolf-M. Wittich and Juan L: Escherichia coli has multiple enzymes that attack TNT and release nitrogen for growth. Environ Microbiol 9, 1535-1540 (2007).
89. Rajkumari, J., Singha, L. P. & Pandey, P. Draft Genome Sequence of Klebsiella pneumoniae AWD5. Genome Announc 5 (2017).
90. Koh, H. Y. et al. Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures. Environ Microbiol 19, 628-644 (2017).
91. Miura, K. et al. Molecular cloning of the nemA gene encoding N-ethylmaleimide reductase from Escherichia coli. Biol Pharm Bull 20, 110-112 (1997).
92. Annous, B. A., Kozempel, M. F. & Kurantz, M. J. Changes in membrane fatty acid composition of Pediococcus sp. strain NRRL B-2354 in response to growth conditions and its effect on thermal resistance. Appl Environ Microbiol 65, 2857-2862 (1999).
93. Seo, J. S., Keum, Y. S. & Li, Q. X. Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates. Biodegradation 24, 795-811 (2013).
94. Ramos, J. L. et al. Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida. FEMS Microbiol Rev 39, 555-566 (2015).
95. Tomas, C. A., Welker, N. E. & Papoutsakis, E. T. Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell′s transcriptional program. Appl Environ Microbiol 69, 4951-4965 (2003).
96. Kumar, R. et al. Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium. mSystems 2 (2017).
97. Sirko, A., Zatyka, M., Sadowy, E. & Hulanicka, D. Sulfate and thiosulfate transport in Escherichia coli K-12: evidence for a functional overlapping of sulfate- and thiosulfate-binding proteins. J Bacteriol 177, 4134-4136 (1995).
98. Udaondo, Z. et al. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome. Microb Biotechnol 6, 598-611 (2013).
99. Wu, X., Gent, D. B., Davis, J. L. & Alshawabkeh, A. N. Lactate Injection by Electric Currents for Bioremediation of Tetrachloroethylene in Clay. Electrochim Acta 86, 157-163 (2012).
100. Davidson, A. L., Dassa, E., Orelle, C. & Chen, J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 72, 317-364, table of contents (2008).
101. Kang, Z. H. et al. Purification and cloning of nicosulfuron-degrading enzymes from Bacillus subtilis YB1. Prikl Biokhim Mikrobiol 50, 39-43 (2014).
102. Yung, M. C. et al. Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium. J Proteome Res 13, 1833-1847 (2014).
103. Koning, S. M., Albers, S. V., Konings, W. N. & Driessen, A. J. Sugar transport in (hyper)thermophilic archaea. Res Microbiol 153, 61-67 (2002).
104. Hua, F. & Wang, H. Q. Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms. Biotechnol Biotechnol Equip 28, 165-175 (2014).
105. Wu, X. B. et al. Outer membrane protein OmpW of Escherichia coli is required for resistance to phagocytosis. Res Microbiol 164, 848-855 (2013).
106. Nikaido, H. & Vaara, M. Molecular basis of bacterial outer membrane permeability. Microbiol Rev 49, 1-32 (1985).
107. Caballero, A. & Ramos, J. L. A double mutant of Pseudomonas putida JLR11 deficient in the synthesis of the nitroreductase PnrA and assimilatory nitrite reductase NasB is impaired for growth on 2,4,6-trinitrotoluene (TNT). Environ Microbiol 8, 1306-1310 (2006).
108. Johnson, G. R. & Spain, J. C. Evolution of catabolic pathways for synthetic compounds: bacterial pathways for degradation of 2,4-dinitrotoluene and nitrobenzene. Appl Microbiol Biotechnol 62, 110-123 (2003).
109. French, C. E., Nicklin, S. & Bruce, N. C. Sequence and properties of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2. J Bacteriol 178, 6623-6627 (1996).
110. Zenno, S. et al. Biochemical characterization of NfsA, the Escherichia coli major nitroreductase exhibiting a high amino acid sequence homology to Frp, a Vibrio harveyi flavin oxidoreductase. J Bacteriol 178, 4508-4514 (1996).
111. Zenno, S., Koike, H., Tanokura, M. & Saigo, K. Conversion of NfsB, a minor Escherichia coli nitroreductase, to a flavin reductase similar in biochemical properties to FRase I, the major flavin reductase in Vibrio fischeri, by a single amino acid substitution. J Bacteriol 178, 4731-4733 (1996).
112. Peres, C. M. & Agathos, S. N. Biodegradation of nitroaromatic pollutants: from pathways to remediation. Biotechnol Annu Rev 6, 197-220 (2000).
113. Purohit, V. & Basu, A. K. Mutagenicity of nitroaromatic compounds. Chem Res Toxicol 13, 673-692 (2000).
114. Kumagai, Y., Kikushima, M., Nakai, Y., Shimojo, N. & Kunimoto, M. Neuronal nitric oxide synthase (NNOS) catalyzes one-electron reduction of 2,4,6-trinitrotoluene, resulting in decreased nitric oxide production and increased nNOS gene expression: implication for oxidative stress. Free Radic Biol Med 37, 350-357 (2004).
115. Wever, R., Stroes, E. & Rabelink, T. J. Nitric oxide and hypercholesterolemia: a matter of oxidation and reduction? Atherosclerosis 137 Suppl, S51-60 (1998).
116. Maier, T., Guell, M. & Serrano, L. Correlation of mRNA and protein in complex biological samples. FEBS Lett 583, 3966-3973 (2009).
117. Vogel, C. & Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 13, 227-232 (2012).
118. David, M. M. et al. Microbial ecology of chlorinated solvent biodegradation. Environ Microbiol 17, 4835-4850 (2015).
119. Tiehm, A. & Schmidt, K. R. Sequential anaerobic/aerobic biodegradation of chloroethenes--aspects of field application. Curr Opin Biotechnol 22, 415-421 (2011).
120. Mattes, T. E., Alexander, A. K. & Coleman, N. V. Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution. FEMS Microbiol Rev 34, 445-475 (2010).
121. He, J. et al. Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ Sci Technol 36, 3945-3952 (2002).
122. Dugat-Bony, E. et al. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microb Biotechnol 5, 642-653 (2012).
123. Hendrickson, E. R. et al. Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl Environ Microbiol 68, 485-495 (2002).
124. Pfeiffer, P., Bielefeldt, A. R., Illangasekare, T. & Henry, B. Partitioning of dissolved chlorinated ethenes into vegetable oil. Water Res 39, 4521-4527 (2005).
125. Bedard, D. L., Ritalahti, K. M. & Loffler, F. E. The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. Appl Environ Microbiol 73, 2513-2521 (2007).
126. Cupples, A. M. Real-time PCR quantification of Dehalococcoides populations: methods and applications. J Microbiol Methods 72, 1-11 (2008).
127. Borden, R. C. Effective distribution of emulsified edible oil for enhanced anaerobic bioremediation. J Contam Hydrol 94, 1-12 (2007).
128. Tsai, T. T., Liu, J. K., Chang, Y. M., Chen, K. F. & Kao, C. M. Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study. J Hazard Mater 268, 92-101 (2014).
129. Desai, C., Pathak, H. & Madamwar, D. Advances in molecular and ”-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresour Technol 101, 1558-1569 (2010).
130. Conrad, M. E. et al. Field evidence for co-metabolism of trichloroethene stimulated by addition of electron donor to groundwater. Environ Sci Technol 44, 4697-4704 (2010).
131. Shah, V. et al. Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. Microb Ecol 66, 533-550 (2013).
132. Desai, C., Parikh, R. Y., Vaishnav, T., Shouche, Y. S. & Madamwar, D. Tracking the influence of long-term chromium pollution on soil bacterial community structures by comparative analyses of 16S rRNA gene phylotypes. Res Microbiol 160, 1-9 (2009).
133. Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68, 669-685 (2004).
134. Dhal, P. K. & Sar, P. Microbial communities in uranium mine tailings and mine water sediment from Jaduguda U mine, India: A culture independent analysis. J Environ Sci Health A Tox Hazard Subst Environ Eng 49, 694-709 (2014).
135. Fang, H., Cai, L., Yu, Y. & Zhang, T. Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge. Bioresour Technol 129, 209-218 (2013).
136. Kotik, M., Davidova, A., Voriskova, J. & Baldrian, P. Bacterial communities in tetrachloroethene-polluted groundwaters: a case study. Sci Total Environ 454-455, 517-527 (2013).
137. Huson, D. H., Mitra, S., Ruscheweyh, H. J., Weber, N. & Schuster, S. C. Integrative analysis of environmental sequences using MEGAN4. Genome Res 21, 1552-1560 (2011).
138. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261-5267 (2007).
139. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336 (2010).
140. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30 (2000).
141. Holmes, V. F., He, J., Lee, P. K. & Alvarez-Cohen, L. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol 72, 5877-5883 (2006).
142. Tas, N., van Eekert, M. H., de Vos, W. M. & Smidt, H. The little bacteria that can - diversity, genomics and ecophysiology of ′Dehalococcoides′ spp. in contaminated environments. Microb Biotechnol 3, 389-402 (2010).
143. Loffler, F. E., Sanford, R. A. & Ritalahti, K. M. Enrichment, cultivation, and detection of reductively dechlorinating bacteria. Methods Enzymol 397, 77-111 (2005).
144. Freeborn, R. A. et al. Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ Sci Technol 39, 8358-8368 (2005).
145. Shukla, A. K., Upadhyay, S. N. & Dubey, S. K. Current trends in trichloroethylene biodegradation: a review. Crit Rev Biotechnol 34, 101-114 (2014).
146. Wolterink, A. et al. Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1. Int J Syst Evol Microbiol 55, 2063-2068 (2005).
147. Kittelmann, S. & Friedrich, M. W. Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing. Environ Microbiol 10, 31-46 (2008).
148. Maness, A. D., Bowman, K. S., Yan, J., Rainey, F. A. & Moe, W. M. Dehalogenimonas spp. can Reductively Dehalogenate High Concentrations of 1,2-Dichloroethane, 1,2-Dichloropropane, and 1,1,2-Trichloroethane. AMB Express 2, 54 (2012).

指導教授

陳師慶、喻秋華(Ssu-Ching Chen Chiou-Hwa Yuh)

審核日期

2017-9-21

推文