Abstract:The research object was the Bacillus cereus sp. DQ01, a highly effective Polycyclic Aromatic Hydrocarbons degrading bacteria screened by the research group. Fluoranthene and Luria-Bertani medium (LB medium) were used as the target pollutant and the co-metabolic substrate, respectively. The whole protein expression result of bacteria degrading fluoranthene in Minimal Salt Medium (MSM) and MSM-LB culture environment was compared with the isobaric tags for relative and absolute quantity (iTRAQ) technology to reveal changes in molecular metabolism level of Bacillus cereus in the process of co-metabolism. In the results, a total of 64 differentially expressed proteins were detected, consisting of 28 up-regulated proteins and 36 down-regulated proteins. It was identified that the functions of differential proteins focused on metabolism, stress response, information transmission and regulation. At the same time, compared to the results from KEGG pathway enrichment analysis, the changes in bacterial pathways were thought to relate to energy metabolism, information transmission and regulation. Compared with the differential protein expression of bacteria under co-metabolism, the key link of bacteria in the process of degrading PAHs could be speculated to be the pathway of small molecule metabolism and adaptation to the external environment.
张银萍,王 芳,杨兴伦,等.土壤中高环多环芳烃微生物降解的研究进展 [J]. 微生物学通报, 2010,37(2):280-288. Zhang Y P, Wang F, Yang X L, et al. Recent Advances in Biodegradation of High-molecular Weight PAHs in Soil [J]. Microbiology China, 2010,37(2):280-288.
[2]
Fernando B L, Sanz R, Molina M C. et al. Effect of different non-ionic surfactants on the biodegradation of PAHs by diverse aerobic bacteria [J]. International Biodeterioration & Biodegradation, 2009,63(7):913-922.
[3]
Jiang R, Li Y, Wang H, et al. A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1based on iTRAQ [J]. Science of the Total Environment, 2020,737:140208.
[4]
Smułek W, Sydow M, Zabielska-Matejuk J, et al. Bacteria involved in biodegradation of creosote PAH – A case study of long-term contaminated industrial area [J]. Ecotoxicology and Environmental Safety, 2020,187(C):109843.
[5]
Bamforth S M, Singleton I. Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions [J]. Journal of Chemical Technology & Biotechnology Biotechnology, 2010,80(7): 723-736.
[6]
Liu Y L, Hu H Y, Giulio Z, et al. A Pseudomonas sp. strain uniquely degrades PAHs and heterocyclic derivatives via lateral dioxygenation pathways [J]. Journal of Hazardous Materials, 2021,403:123956.
[7]
Kolomytseva M P, Randazzo D, Baskunov B P, et al. Role of surfactants in optimizing fluorene assimilation and intermediate formation by Rhodococcus rhodochrous VKM B-2469. [J]. Bioresource Technology, 2009,99(2):839-844.
[8]
Reddy P V, Karegoudar T B, Monisha T R, et al. Biodegradation of fluoranthene by Paenibacillus sp. strain PRNK6: a pathway for complete mineralization [J]. Archives of Microbiology, 2018,200 (1):1-12.
[9]
Yang Y Y, Yang F Q, Gao J L. Differential proteomics for studying action mechanisms of traditional Chinese medicines [J]. Chinese Medicine, 2019,14(1):1.
[10]
Mukherjee A K, Bhagowati P, Biswa B B, et al. A comparative intracellular proteomic profiling of Pseudomonas aeruginosa strain ASP-53 grown on pyrene or glucose as sole source of carbon and identification of some key enzymes of pyrene biodegradation pathway [J]. Journal of Proteomics, 2017,167:25-35.
[11]
Yun S H, Choi C W, Lee S Y, et al. Proteomic characterization of plasmid pLA1for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, novosphingobium pentaromativorans US6-1 [J]. Plos One, 2014,9(3):e90812.
[12]
卢晓霞,李秀利,马 杰,等.焦化厂多环芳烃污染土壤的强化微生物修复研究 [J]. 环境科学, 2011,32(3):864-869. Lu X X, Li X L,Ma J, et al. Enhanced Bioremediation of Coking Plant Soils Contaminated with Polycyclic Aromatic Hydrocarbons. [J]. Environmental Science, 2011,32(3):864-869.
[13]
Kanaly R A, Harayama S. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. [J]. Journal of Bacteriology, 2000,182(8):2059-2067.
[14]
陶雪琴,党 志,卢桂宁,等.污染土壤中多环芳烃的微生物降解及其机理研究进展 [J]. 矿物岩石地球化学通报, 2003,22(4):356-360. Tao X Q, Dang Z, Lu G N, et al. Biodegradation Mechanism of Polycyclic Aromatic Hydrocarbons (PAHs) in Soil: A Review [J]. Bulletin of Mineralogy, Petrology and Geochemistry, 2003,22(4):356- 360.
[15]
Jensen H L. Carbon nutrition of some microorganisms decomposing halogen-substituted aliphatic acids [J]. Acta Agriculturae Scandinavica, 1963,13(4):404-412.
[16]
Leadbetter E R, Foster J W. Oxidation products formed from gaseous alkanes by the bacterium Pseudomonas methanica. [J]. Archives of biochemistry and biophysics, 1959,82(2):491-492.
[17]
Rentz J A, Alvarez P, Schnoor J L. Benzo[a]pyrene degradation by Sphingomonas yanoikuyae JAR02 [J]. Environmental Pollution, 2008, 151(3):669-677.
[18]
Juhasz A. Microbial degradation of high molecular weight polycyclic aromatic hydrocarbons [D]. Melbourne: Victoria University, 1998.
[19]
Wang G, Ji Z, Wang L, et al. Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax [J]. Brazilian Journal of Microbiology, 2010,41(2):431-438.
[20]
Chaudhary P, Sharma R, Singh S B, et al. Bioremediation of PAH by Streptomyces sp [J]. Bulletin of Environmental Contamination and Toxicology, 2011,86(3):268-271.
[21]
Zhao J Y, Chi Y L, Xu Y C, et al. Co-metabolic degradation of β-cypermethrin and 3-phenoxybenzoic acid by co-culture of bacillus licheniformis B-1and Aspergillus oryzae M-4 [J]. Plos One, 2016, 11(11):e166796.
[22]
Zhao J Y, Jia D Y, Du J, et al. Substrate regulation on co-metabolic degradation of β-cypermethrin by Bacillus licheniformis B-1 [J]. AMB Express, 2019,9(1):83.
[23]
Panikov N S, Sizova M V, Ros D, et al. Biodegradation kinetics of the nitramine explosive CL-20in soil and microbial cultures [J]. Biodegradation, 2007,18(3):317-332.
[24]
李 剑,谢春娟.废水中苯胺的好氧共代谢降解实验研究 [J]. 环境工程学报, 2007,01(6):51-55. Li J, Xie C J. Study on aerobic co-metabolism biodegradation of aniline in wastewater [J]. Chinese Journal of Environmental Engineering, 2007,1(6):51-55.
[25]
王文静,陈 海,李 博,等.以萘为共代谢的芘的好氧生物降解 [J]. 环境工程学报, 2016,10(11):6332-6336. Wang W J, Chen H, Li B, et al. Biodegradation of pyrene using naphthalene as cometabolism substrate [J]. Chinese Journal of Environmental Engineering, 2016,10(11):6332-6336.
[26]
许 洁,王红旗,孔德康.基于iTRAQ技术荧蒽降解菌的比较蛋白质组学分析 [J]. 中国环境科学, 2018,38(1):284-292. Xu J, Wang H Q, Kong D K. iTRAQ-based comparative proteomic analysis of a fluoranthene-degrading bacterium [J]. China Environmental Science, 2018,38(1):284-292.
[27]
Wisniewski J R, Zougman A, Nagaraj N, et al. Universal sample preparation method for proteome analysis [J]. Nature Methods, 2009,6(5):359-360.
[28]
Wurm J P, Sung S, Kneuttinger A C, et al. Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex [J]. Nature Communications, 2021,12(1):2748.
[29]
Zhang P, Wang J W, Shi Y G. Structure and mechanism of the S component of a bacterial ECF transporter [J]. Nature, 2010,468 (7324):717-720.
[30]
Xu L, Qi T, Xu L, et al. ChemInform abstract: Recent progress in the enzymatic glycosylation of phenolic compounds [J]. ChemInform, 2016,35(1):1-23.
[31]
Björn Z, Antje H, Boris G. Requirements for the phosphorylation of the Escherichia coli EIIANtr protein in vivo [J]. FEMS Microbiology Letters, 2008,286(1):96-102.
[32]
Jasinski M, Ducos E, Martinoia E, et al. The ATP-binding cassette transporters: Structure, function, and gene family comparison between rice and arabidopsis. [J]. Plant Physiology, 2003,131(3):1169-1177.
[33]
Liu S, Guo C, Dang Z, et al. Comparative proteomics reveal the mechanism of Tween80enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B [J]. Ecotoxicology & Environmental Safety, 2017,137:256-264.
[34]
Marques J C, Oh I K, Ly D C, et al. LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2 [J]. Proceedings of the National Academy of Sciences, 2014,111(39):14235-14240.
[35]
Nakagawa M, Kawano Y, Akasaka Y, et al. Resistance of bacillus endospores to extreme terrestrial and extraterrestrial environments [J]. Digestive Endoscopy, 2003,16(1):84-87.
[36]
冯 姗.一个新的家蚕转录相关锌带蛋白基因的克隆及其原核表达研究 [D]. 杭州:浙江大学, 2006. Feng S. Cloning and Prokaryotic Expression of a Novel Transcription-associated Zinc Ribbon Protein Gene from Silkworm, Bombyx Mori [D]. Hangzhou: Zhejiang University, 2006.
[37]
Lensbouer J J, Doyle R P. Secondary transport of metal-citrate complexes: the CitMHS family [J]. Critical Reviews in Biochemistry and Molecular Biology, 2010,45(5):453-462.
[38]
Hoa N T, Brannigan J A, Cutting S M. The Bacillus subtilis signaling protein SpoIVB defines a new family of serine peptidases [J]. Journal of Bacteriology, 2002,184(1):191.
[39]
Consortium G O. The Gene Ontology (GO) database and informatics resource [J]. Nucleic Acids Research, 2004,32(suppl_1):D258-D261.
[40]
Minoru K, Susumu G, Yoko S, et al. KEGG for integration and interpretation of large-scale molecular data sets [J]. Nucleic Acids Research, 2012,40(D1):D109-D114.
[41]
Kim S, Kwon C, Song G, et al. The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves [J]. Rice, 2018,11(1):1-15.
[42]
Sarantinopoulos P, Makras L, Vaningelgem F, et al. Growth and energy generation by Enterococcus faecium FAIR-E 198 during citrate metabolism [J]. International Journal of Food Microbiology, 2003,84(2):197-206.
[43]
Sauer D B, Song J, Wang B, et al. Structure and inhibition mechanism of the human citrate transporter NaCT [J]. Nature, 2021,591(7848): 157-161.
[44]
Dahl U, Jaeger T, Nguyen B T, et al. Identification of a phosphotransferase system of escherichia coli required for growth on N-acetylmuramic acid [J]. Journal of Bacteriology, 2004,186(8):2385.
[45]
Fujita Y. Carbon catabolite control of the metabolic network in bacillus subtilis [J]. Journal of the Agricultural Chemical Society of Japan, 2009,73(2):245-259.
[46]
Houot L, Chang S, Pickering B S, et al. The phosphoenolpyruvate phosphotransferase system regulates vibrio cholerae biofilm formation through multiple independent pathways [J]. Journal of Bacteriology, 2010,192(12):3055-3067.
[47]
陈孚江.乙酰辅酶A对酿酒酵母生理代谢的影响 [D]. 无锡:江南大学, 2010. Chen F J. Effects of Acetyl-CoA Synthetase Genes Overexpression on Physiological Functions of Saccharomyces Cerevisiae [D]. Wuxi: Jiangnan University, 2010.
[48]
Liu C E, Liu P Q, Ames F L. Characterization of the adenosine triphosphatase activity of the periplasmic histidine permease, a traffic ATPase (ABC Transporter) [J]. Journal of Biological Chemistry, 1997,272(35):21883-21891.
[49]
王镜岩,朱圣庚,徐长法.生物化学教程 [M]. 北京:高等教育出版社, 2008:16-29. Wang J Y, Zhu S G, Xu C F. Essential Biochemistry [M]. Beijing: Higher Education Press, 2008:16-29.
[50]
Hermann T. Antibiotic tricks a switch [J]. Nature, 2015,526(7575): 650-651.
[51]
Buesen R, Mock M, Seidel A, et al. Interaction between metabolism and transport of benzo[a]pyrene and its metabolites in enterocytes. [J]. Toxicology & Applied Pharmacology, 2002,183(3):168-178.
[52]
孔德康,李 艺,王红旗,等.红球菌跨膜运输荧蒽的差异膜蛋白分析 [J]. 中国环境科学, 2019,39(1):274-280. Kong D K, Li Y, Wang H Q, et al. Differential membrane protein analysis of Rhodococcus during the transmembrane-transport process of fluoranthene [J]. China Environmental Science, 2019,39(1): 274-280.
[53]
Kweon O, Kim S J, Jones R C, et al. A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1. [J]. Journal of Bacteriology, 2007,189(13):4635-4647.
[54]
Cao J, Lai Q, Yuan J, et al. Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T [J]. Scientific Reports, 2015,5(1):7741.
[55]
Qin W, Fan F, Zhu Y, et al. Comparative proteomic analysis and characterization of benzo(a)pyrene removal by Microbacterium sp. strain M.CSW3 under denitrifying conditions[J]. Bioprocess and Biosystems Engineering, 2017,40(12):1825-1838.
[56]
Li S W, Liu M Y, Yang R Q. Comparative genome characterization of a petroleum-degrading bacillus subtilis strain DM2 [J]. International Journal of Genomics, 2019,2019(3):1-16.
[57]
Goyal L, Jalan N K, Khanna S. Butanol tolerant bacteria: Isolation and characterization of butanol tolerant Staphylococcus sciuri sp [J]. Journal of Biotech Research, 2019,10:68-77.
[58]
Deng M, Li J, Liang F, et al. Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01from the crude oil-contaminated seawater at the Daya Bay, southern China [J]. Marine Pollution Bulletin, 2014,83(1):79-86.
[59]
Wang H, Yang Y, Xu J, et al. iTRAQ-based comparative proteomic analysis of differentially expressed proteins in Rhodococcus sp. BAP-1induced by fluoranthene [J]. Ecotoxicology and Environmental Safety, 2019,169:282-291.
[60]
Hong Y H, Deng M C, Xu X M, et al. Characterization of the transcriptome of Achromobacter sp. HZ01with the outstanding hydrocarbon-degrading ability [J]. Gene, 2016,584(2):185-194.
[61]
Buschiazzo A, Trajtenberg F. Two-component sensing and regulation: how do histidine kinases talk with response regulators at the molecular level? [J]. Annual Review of Microbiology, 2019,73(1):507-528.
[62]
汪国俊.双组分系统LisK/R通过调控鞭毛基因表达影响单增李斯特菌低温生长 [D]. 武汉:华中农业大学, 2021. Wang G J. TCS LisK/R plays a role in Listeria monocytogenes growth at cold temperatures by regulating the expression of flagellar genes [D]. Wuhan: Central China Agricultural University, 2021.
[63]
詹 清.新鞘氨醇杆菌US6-1降解BaP的群体感应调控系统的初步研究 [D]. 厦门:厦门大学, 2017. Zhan Q. Preliminary study on quorum sensing system in Novosphingobium pentaromativorans US6-1for BaP biodegradation [D]. Xiamen: Xiamen University, 2017.
[64]
Sampedro I, Parales R E, Krell T, et al. Pseudomonas chemotaxis. [J]. FEMS Microbiology Reviews, 2015,39(1):17-46.
[65]
Zaval'skii L Y, Marchenko A I, Borovik R V. The study of bacterial chemotaxis to naphthalene [J]. Microbiology, 2003,72(3):363-368.