原核生物转录组研究的现状与进展
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摘要
转录技术在原核生物转录组研究上的突破,已经显示出其在揭示原核生物生命过程的分子机制上独特的优势。对原核生物的转录组研究开始于致病菌,近年来,通过转录组学分析原核生物对污染物的降解机制已成为研究热点。通过多组学整合分析,对降解菌的代谢机理、作用机制及转录相关基因进行深入探究。综述了原核生物转录组研究的现状及进展,即介绍了响应重金属及芳香族化合物、石油烃等有机污染物的降解菌种类及其转录组特征;重点关注了致病菌的转录组研究,包括人类、动植物致病菌的种类、性质及其转录组特征;并对原核生物的转录组研究在未来的发展和应用进行了展望,旨在为原核生物在环境污染治理和致病菌引起的人类和动植物疾病的防控奠定重要理论基础。
The breakthrough of transcriptional technology in studying prokaryotes transcriptome has shown its unique advantage in revealing the molecular mechanism of prokaryotes' life process. The transcriptome study of prokaryotes began with pathogenic bacteria,and recently the transcriptome analysis of the degradation mechanism of pollutants by prokaryotes has become a research focus. The metabolic mechanism,mechanism of action and transcription-related genes of degrading bacteria were further explored through multi-histological integration analysis. In this paper,the status and progress of the study on prokaryotic transcriptome are reviewed,i.e.,the degradation bacteria and their transcriptome characteristics in response to heavy metals,aromatic compounds,petroleum hydrocarbons and other organic pollutants are introduced. The transcriptome study of pathogenic bacteria is also focused,including human,animal and plant pathogenic bacteria species,nature,and transcriptome characteristics. The future development and application of transcriptome research in prokaryotes are also prospected. It aims to lay an important theoretical foundation for prokaryotes in environmental pollution control as well as prevention and control of human and animal and plant diseases caused by pathogenic bacteria.
The breakthrough of transcriptional technology in studying prokaryotes transcriptome has shown its unique advantage in revealing the molecular mechanism of prokaryotes' life process. The transcriptome study of prokaryotes began with pathogenic bacteria,and recently the transcriptome analysis of the degradation mechanism of pollutants by prokaryotes has become a research focus. The metabolic mechanism,mechanism of action and transcription-related genes of degrading bacteria were further explored through multi-histological integration analysis. In this paper,the status and progress of the study on prokaryotic transcriptome are reviewed,i.e.,the degradation bacteria and their transcriptome characteristics in response to heavy metals,aromatic compounds,petroleum hydrocarbons and other organic pollutants are introduced. The transcriptome study of pathogenic bacteria is also focused,including human,animal and plant pathogenic bacteria species,nature,and transcriptome characteristics. The future development and application of transcriptome research in prokaryotes are also prospected. It aims to lay an important theoretical foundation for prokaryotes in environmental pollution control as well as prevention and control of human and animal and plant diseases caused by pathogenic bacteria.
引文
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[13]Gu W, Semrau JD. Copper and cerium-regulated gene expression in Methylosinus trichosporium OB3b[J]. Applied Microbiology&Biotechnology, 2017, 101(23-24):8499-8516.
[14]Marcus SA, Sidiropoulos SW, Steinberg H, et al. CsoR is essential for maintaining copper homeostasis in Mycobacterium tuberculosis[J]. PLoS One, 2016, 11(3):e0151816.
[15]Larsen?, Karlsen OA. Transcriptomic profiling of Methylococcus capsulatus(Bath)during growth with two different methane monooxygenases[J]. Microbiologyopen, 2016, 5(2):254-267.
[16]Quintana J, Novoaaponte L, Argüello JM. Copper homeostasis networks in the bacterium Pseudomonas aeruginosa[J]. Journal of Biological Chemistry, 2017, 292(38):15691-15704.
[17]Zhang H, Ma Y, Liu P, et al. Multidrug resistance operon emrAB contributes for chromate and ampicillin co-resistance in a Staphylococcus strain isolated from refinery polluted river bank[J]. Springerplus, 2016, 5(1):1648-1659.
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[19]Chen Y, Huang C, Bai C, et al. Benzo[α]pyrene repressed DNA mismatch repair in human breast cancer cells[J]. Toxicology,2013, 304:167-172.
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[25]Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants:An overview[J]. Biotechnology Research International, 2010, 2011(1):1-13.
[26]Wu XL, Yu SL, Gu J, et al. Filomicrobium insigne sp. nov. isolated from an oil-polluted saline soil[J]. International Journal of Systematic&Evolutionary Microbiology, 2009, 59(2):300-305.
[27]Van Beilen JB, Funhoff EG. Alkane hydroxylases involved in microbial alkane degradation[J]. Applied Microbiology&Biotechnology, 2007, 74(1):13-21.
[28]Kothari A, Charrier M, Wu YW, et al. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization[J]. FEMS Microbiology Letters, 2016, 363(20):fnw224.
[29]Jung J, Jang IA, Ahn S, et al. Molecular mechanisms of enhanced bacterial growth on hexadecane with red clay[J]. Microbial Ecology, 2015, 70(4):912-921.
[30]Hong YH, Deng MC, Xu XM, et al. Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability[J]. Gene, 2016, 584(2):185-194.
[31]Scoma A, Barbato M, Hernandez-Sanabria E, et al. Microbial oildegradation under mild hydrostatic pressure(10 MPa):which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?[J]. Scientific Reports, 2016, 6:23526.
[32]Jin HM, Jeong HI, Kim KH, et al. Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment[J]. Scientific Reports,2016, 6(1):21796.
[33]Cruz A, Rodrigues R, Pinheiro M, et al. Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin(TBT):Unravelling the effects from the molecular level to the organism[J]. Marine Environmental Research, 2015, 109:132-139.
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[35]Kun W, Hua Y, Hui P, et al. Bioremediation of triphenyl phosphate in river water microcosms:Proteome alteration of Brevibacillus brevis and cytotoxicity assessments[J]. Science of The Total Environment, 2019, 649:563-570.
[36]Patrauchan MA, Parnell JJ, Mcleod MP, et al. Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400[J]. Archives of Microbiology, 2011, 193(9):641-650.
[37]Peng X, Yamamoto S, Alain A. Vertès, et al. Global transcriptome analysis of the tetrachloroethene-dechlorinating bacterium Desulfito bacterium hafniense Y51 in the presence of various electron donors and terminal electron acceptors[J]. Journal of Industrial Microbiology&Biotechnology, 2012, 39(2):255-268.
[38]Johnson DR, Nemir A, Andersen GL, et al. Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195[J]. FEMS Microbiology Letters, 2010,294(2):198-206.
[39]Johnson DR, Brodie EL, Hubbard AE, et al. Temporal transcriptomic microarray analysis of Dehalococcoides ethenogenes strain 195 during the transition into stationary phase[J]. Applied&Environmental Microbiology, 2008, 74(9):2864-2872.
[40]Lee J, Hiibel SR, Reardon KF, et al. Identification of stressrelated proteins in Escherichia coli using the pollutant cisdichloroethylene[J]. J Appl Microbiol, 2010, 108(6):2088-2102.
[41]Hristova KR, Schmidt R, Chakicherla AY, et al. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol[J].Applied&Environmental Microbiology, 2007, 73(22):7347-7357.
[42]Fida TT, Moreno-Forero SK, Breugelmans P, et al. Physiological and transcriptome response of the polycyclic aromatic hydrocarbon degrading Novosphingobium sp. LH128 after inoculation in soil[J]. Environmental Science&Technology, 2017, 51(3):1570-1579.
[43]Guan X, Liu F, Wang J, et al. Mechanism of 1, 4-dioxane microbial degradation revealed by 16S rRNA and metatranscriptomic analyses[J]. Water Science&Technology A Journal of the International Association on Water Pollution Research, 2018, 77(1):123-133.
[44]Chen Q, Tu H, Luo X, et al. The regulation of para-nitrophenol degradation in Pseudomonas putida DLL-E4[J]. PLoS One,2016, 11(5):e0155485.
[45]Dubey SK, Tokashiki T, Suzuki S. Microarray-mediated transcriptome analysis of the tributyltin(TBT)-resistant bacterium Pseudomonas aeruginosa 25W in the presence of TBT[J]. Journal of Microbiology, 2006, 44(2):200-205.
[46]Muller JF, Stevens AM, Craig J, et al. Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress[J].Applied&Environmental Microbiology, 2007, 73(14):4550-4558.
[47]Yang X, Xi J. Transcriptomic and benzoate metabolic pathways of Rhodococcus sp. R04 cultured in biphenyl[J]. Acta Microbiologica Sinica, 2015, 55(7):851-862.
[48]Edmilson R. Gon?alves, Hara H, Miyazawa D, et al. Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp.strain RHA1[J]. Applied&Environmental Microbiology, 2006,72(9):6183-6193.
[49]Sharp JO, Sales CM, Leblanc JC, et al. An inducible propane monooxygenase is responsible for n-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1[J]. Applied and Environmental Microbiology, 2007, 73(21):6930-6938.
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