Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

doi:10.1016/j.cjche.2021.01.009

Chinese Journal of Chemical Engineering ›› 2021, Vol. 39 ›› Issue (11): 205-210.DOI: 10.1016/j.cjche.2021.01.009

• Biotechnology and Bioengineering • Previous Articles Next Articles

Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

Yuting Huang¹, Liyang Wang², Xue Zhang³, Nan Su¹, Heping Li⁴, Yoshimitsu Oda⁵, Xinhui Xing^1,6,7,8

1 Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China;
2 Biobreeding Research Center, Wuxi Research Institute of Applied Technologies, Tsinghua University, Wuxi 214072, China;
3 Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
4 Department of Engineering Physics, Tsinghua University, Beijing 100084, China;
5 Institute of Life and Environmental Sciences, Osaka Shin-Ai College, Tsurumi, Tsurumi-ku, Osaka 5380052, Japan;
6 Centre for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China;
7 Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China;
8 Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518055, China

Received:2020-09-28 Revised:2021-01-22 Online:2021-12-27 Published:2021-11-28
Contact: Xinhui Xing
Supported by:
This work was supported by National Key Research and Development Project of China (2016YFD0102106) and National Key Scientific Instrument and Equipment Project of National Natural Science Foundation of China (21627812).

Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

Yuting Huang¹, Liyang Wang², Xue Zhang³, Nan Su¹, Heping Li⁴, Yoshimitsu Oda⁵, Xinhui Xing^1,6,7,8

1 Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China;
2 Biobreeding Research Center, Wuxi Research Institute of Applied Technologies, Tsinghua University, Wuxi 214072, China;
3 Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
4 Department of Engineering Physics, Tsinghua University, Beijing 100084, China;
5 Institute of Life and Environmental Sciences, Osaka Shin-Ai College, Tsurumi, Tsurumi-ku, Osaka 5380052, Japan;
6 Centre for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China;
7 Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China;
8 Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518055, China

通讯作者: Xinhui Xing
基金资助:
This work was supported by National Key Research and Development Project of China (2016YFD0102106) and National Key Scientific Instrument and Equipment Project of National Natural Science Foundation of China (21627812).

Abstract

Abstract: Mutagenesis is an important technique for microbial mutation breeding. As the source of mutations, DNA damage extent is a key indicator for the effectiveness of mutagenesis. Therefore, a rapid and easy DNA damage quantification method is required for the comparison of mutagenesis effects and development of mutagenesis tools. Here, we used the umu-microplate test system to quantitatively compare the DNA damage strength caused by atmospheric and room-temperature plasma (ARTP) and other traditional mutagenesis methods including:ultraviolet radiation (UV), diethyl sulfate (DES) and 4-nitroquinoline-1-oxide (4-NQO). The test strain of Salmonella typhimurium TA1535/pSK1002 was used to monitor the time-course profile of β-galactosidase activity induced by DNA damage caused by different mutagenesis methods using a microplate reader. The umu-microplate test results showed that ARTP caused higher extent of DNA damage than UV and chemical mutagens, which agrees well with the result obtained by SOS-FACS-based quantification method as reported previously. This umu-microplate test is accessible for broad researchers who are lack of the expensive FACS instruments and allows the quick quantitative evaluation of DNA damage among living cells for different mutagenesis methods in the study of the microbial mutation breeding.

Key words: ARTP mutagenesis, umu-Microplate test, Biological engineering, Cell engineering, Biotechnology

摘要： Mutagenesis is an important technique for microbial mutation breeding. As the source of mutations, DNA damage extent is a key indicator for the effectiveness of mutagenesis. Therefore, a rapid and easy DNA damage quantification method is required for the comparison of mutagenesis effects and development of mutagenesis tools. Here, we used the umu-microplate test system to quantitatively compare the DNA damage strength caused by atmospheric and room-temperature plasma (ARTP) and other traditional mutagenesis methods including:ultraviolet radiation (UV), diethyl sulfate (DES) and 4-nitroquinoline-1-oxide (4-NQO). The test strain of Salmonella typhimurium TA1535/pSK1002 was used to monitor the time-course profile of β-galactosidase activity induced by DNA damage caused by different mutagenesis methods using a microplate reader. The umu-microplate test results showed that ARTP caused higher extent of DNA damage than UV and chemical mutagens, which agrees well with the result obtained by SOS-FACS-based quantification method as reported previously. This umu-microplate test is accessible for broad researchers who are lack of the expensive FACS instruments and allows the quick quantitative evaluation of DNA damage among living cells for different mutagenesis methods in the study of the microbial mutation breeding.

关键词: ARTP mutagenesis, umu-Microplate test, Biological engineering, Cell engineering, Biotechnology

Yuting Huang, Liyang Wang, Xue Zhang, Nan Su, Heping Li, Yoshimitsu Oda, Xinhui Xing. Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding[J]. Chinese Journal of Chemical Engineering, 2021, 39(11): 205-210.

References

[1] R.D. Brock, Prospects and perspectives in mutation breeding, Basic Life Sci. 8(1976) 117-132.
[2] M.H. Liang, Y.J. Liang, J.Y. Chai, S.S. Zhou, J.G. Jiang, Reduction of methanol in brewed wine by the use of atmospheric and room-temperature plasma method and the combination optimization of malt with different adjuncts, J. Food Sci. 79(11) (2014) M2308-M2314.
[3] X.Y. Wu, Y.Q. Wei, Z.M. Xu, L.P. Liu, Z.L. Tan, S.R. Jia, Evaluation of an ethanoltolerant acetobacter pasteurianus mutant generated by a new atmospheric and room temperature plasma (ARTP) In:Advances In:Applied Biotechnology, Springer, Berlin (2015) 277-286.
[4] A. Bhattacharya, P. Leprohon, S. Bigot, P.K. Padmanabhan, A. Mukherjee, G. Roy, H. Gingras, A. Mestdagh, B. Papadopoulou, M. Ouellette, Coupling chemical mutagenesis to next generation sequencing for the identification of drug resistance mutations in Leishmania, Nat. Commun. 10(1) (2019) 1-14.
[5] P.D. Sniegowski, P.J. Gerrish, T. Johnson, A. Shaver, The evolution of mutation rates:Separating causes from consequences, BioEssays 22(12) (2000) 1057- 1066.
[6] Y.Z. Song, G.H. Li, S.F. Thornton, I.P. Thompson, S.A. Banwart, D.N. Lerner, W.E. Huang, Optimization of bacterial whole cell bioreporters for toxicity assay of environmental samples, Environ. Sci. Technol. 43(20) (2009) 7931-7938.
[7] B.N. Ames, J. McCann, E. Yamasaki, Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test, Mutat. Res. 31(6) (1975) 347-364.
[8] Y. Oda, S. Nakamura, I. Oki, T. Kato, H. Shinagawa, Evaluation of the new system (umu-test) for the detection of environmental mutagens and carcinogens, Mutat. Res. 147(5) (1985) 219-229.
[9] P. Quillardet, O. Huisman, R. D'Ari, M. Hofnung, SOS chromotest, a direct assay of induction of an SOS function in Escherichia coli K-12 to measure genotoxicity, PNAS 79(19) (1982) 5971-5975.
[10] K. Yasunaga, A. Kiyonari, T. Oikawa, N. Abe, K. Yoshikawa, Evaluation of the Salmonella umu test with 83 NTP chemicals, Environ. Mol. Mutagen. 44(4) (2004) 329-345.
[11] K. Yasunaga, A. Kiyonari, M. Nakagawa, K. Yoshikawa, Investigation into the ability of the Salmonella umu test to detect DNA damage using antitumor drugs, Toxicol. In Vitro 20(5) (2006) 712-728.
[12] T. Shimada, S. Nakamura, Cytochrome P-450-mediated activation of procarcinogens and promutagens to DNA-damaging products by measuring expression of umu gene in Salmonella typhimurium TA1535/pSK1002, Biochem. Pharmacol. 36(12) (1987) 1979-1987.
[13] S.I. Nakamura, Y. Oda, T. Shimada, I. Oki, K. Sugimoto, SOS-inducing activity of chemical carcinogens and mutagens in Salmonella typhimurium TA1535/pSK1002:examination with 151 chemicals, Mutat. Res. Lett. 192(4) (1987) 239-246.
[14] G. Reifferscheid, J. Heil, Validation of the SOS/umu test using test results of 486 chemicals and comparison with the Ames test and carcinogenicity data, Mutat. Res. 369(3-4) (1996) 129-145.
[15] F.R. de Gruijl, H.J. van Kranen, L.H.F. Mullenders, UV-induced DNA damage, repair, mutations and oncogenic pathways in skin cancer, J Photochem Photobiol B:Biol 63(1-3) (2001) 19-27.
[16] C. Lu, R.H. Scheuermann, H. Echols, Capacity of RecA protein to bind preferentially to UV lesions and inhibit the editing subunit (epsilon) of DNA polymerase III:A possible mechanism for SOS-induced targeted mutagenesis, PNAS 83(3) (1986) 619-623.
[17] Y. Oda, H. Yamazaki, M. Watanabe, T. Nohmi, T. Shimada, Development of high sensitive umu test system:Rapid detection of genotoxicity of promutagenic aromatic amines by Salmonella typhimurium strain NM2009 possessing high Oacetyltransferase activity, Mutat Res Mutagen Relat Subj 334(2) (1995) 145- 156.
[18] Y. Oda, K. Funasaka, M. Kitano, A. Nakama, T. Yoshikura, Use of a highthroughput umu-microplate test system for rapid detection of genotoxicity produced by mutagenic carcinogens and airborne particulate matter, Environ. Mol. Mutagen. 43(1) (2004) 10-19.
[19] X. Zhang, C. Zhang, Q.Q. Zhou, X.F. Zhang, L.Y. Wang, H.B. Chang, H.P. Li, Y. Oda, X.H. Xing, Quantitative evaluation of DNA damage and mutation rate by atmospheric and room-temperature plasma (ARTP) and conventional mutagenesis, Appl. Microbiol. Biotechnol. 99(13) (2015) 5639-5646.
[20] H.P. Li, Z.B. Wang, N. Ge, P.S. Le, H. Wu, Y. Lu, L.Y. Wang, C. Zhang, C.Y. Bao, X.H. Xing, Studies on the physical characteristics of the radio-frequency atmospheric-pressure glow discharge plasmas for the genome mutation of methylosinus trichosporium, IEEE Trans. Plasma Sci. 40(11) (2012) 2853-2860.
[21] X. Zhang, X.F. Zhang, H.P. Li, L.Y. Wang, C. Zhang, X.H. Xing, C.Y. Bao, Atmospheric and room temperature plasma (ARTP) as a new powerful mutagenesis tool, Appl. Microbiol. Biotechnol. 98(12) (2014) 5387-5396.
[22] M.Y. Fang, L.H. Jin, C. Zhang, Y. Tan, P.X. Jiang, N. Ge, H.P. Li, X.H. Xing, Rapid mutation of spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP) and generation of a mutant library with diverse phenotypes, PLoS ONE 8(10) (2013) e77046.
[23] X.F. Hua, J. Wang, Z.J. Wu, H.X. Zhang, H.P. Li, X.H. Xing, Z. Liu, A salt tolerant Enterobacter cloacae mutant for bioaugmentation of petroleum- and saltcontaminated soil, Biochem. Eng. J. 49(2) (2010) 201-206.
[24] M. Jiang, Q. Wan, R.M. Liu, L.Y. Liang, X. Chen, M.K. Wu, H.W. Zhang, K.Q. Chen, J.F. Ma, P. Wei, P.K. Ouyang, Succinic acid production from corn stalk hydrolysate in an E. coli mutant generated by atmospheric and roomtemperature plasmas and metabolic evolution strategies, J. Ind. Microbiol. Biotechnol. 41(1) (2014) 115-123.
[25] S.D. Liu, Y.N. Wu, T.M. Wang, C. Zhang, X.H. Xing, Maltose utilization as a novel selection strategy for continuous evolution of microbes with enhanced metabolite production, ACS Synth. Biol. 6(12) (2017) 2326-2338.
[26] G.P. Nolan, S. Fiering, J.F. Nicolas, L.A. Herzenberg, Fluorescence-activated cell analysis and sorting of viable mammalian cells based on beta-D-galactosidase activity after transduction of Escherichia coli lacZ, PNAS 85(8) (1988) 2603- 2607.
[27] S.N. Fiering, M. Roederer, G.P. Nolan, D.R. Micklem, D.R. Parks, L.A. Herzenberg, Improved FACS-Gal:Flow cytometric analysis and sorting of viable eukaryotic cells expressing reporter gene constructs, Cytometry 12(4) (1991) 291-301.
[28] M. El Mzibri, H. Guiraud-Dauriac, M. Laget, C. Beudot, M. De Méo, G. Duménil, Use of flow cytometry to detect genotoxins by the Salmonella sulA-test, Biotechnol Tech 11(1997) 467-470.
[29] G. Reifferscheid, J. Heil, Y. Oda, R.K. Zahn, A microplate version of the SOS/umutest for rapid detection of genotoxins and genotoxic potentials of environmental samples, Mutat. Res. 253(3) (1991) 215-222.
[30] B. Hamer, N. Bihari, G. Reifferscheid, R.K. Zahn, W.E. Müller, R. Batel, Evaluation of the SOS/umu-test post-treatment assay for the detection of genotoxic activities of pure compounds and complex environmental mixtures, Mutat. Res. 466(2) (2000) 161-171.
[31] Y. Oda, H. Yamazaki, M. Watanabe, T. Nohmi, T. Shimada, Highly sensitive umu test system for the detection of mutagenic nitroarenes in Salmonella typhimurium NM3009 having high O-acetyltransferase and nitroreductase activities, Environ. Mol. Mutagen. 21(4) (1993) 357-364.
[32] M.S. Cooke, M.D. Evans, M. Dizdaroglu, J. Lunec, Oxidative DNA damage:mechanisms, mutation, and disease, FASEB J. 17(10) (2003) 1195-1214.
[33] H.X. Chen, F.W. Bai, Z.L. Xiu, Oxidative stress induced in saccharomyces cerevisiae exposed to dielectric barrier discharge plasma in air at atmospheric pressure, IEEE Trans. Plasma Sci. 38(8) (2010) 1885-1891.
[34] A. Schutze, J.Y. Jeong, S.E. Babayan, J. Park, G.S. Selwyn, R.F. Hicks, The atmospheric-pressure plasma jet:A review and comparison to other plasma sources, IEEE Trans. Plasma Sci. 26(6) (1998) 1685-1694.
[35] G. Li, H.P. Li, L.Y. Wang, S. Wang, H.X. Zhao, W.T. Sun, X.H. Xing, C.Y. Bao, Genetic effects of radio-frequency, atmospheric-pressure glow discharges with helium, Appl. Phys. Lett. 92(22) (2008) 221504.
[36] L.Y. Wang, H.X. Zhao, D. He, Y.N. Wu, L.H. Jin, G. Li, N. Su, H.P. Li, X.H. Xing, Insights into the molecular-level effects of atmospheric and roomtemperature plasma on mononucleotides and single-stranded homo- and hetero-oligonucleotides, Sci. Rep. 10(1) (2020) 14298.

Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 9

Recommended Articles

Metrics

Comments

[1]	Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. Current advances of biocontainment strategy in synthetic biology [J]. Chinese Journal of Chemical Engineering, 2023, 56(4): 141-151.
[2]	Dahai Jiang, Zhidi Min, Jing Leng, Huanqing Niu, Yong Chen, Dong Liu, Chenjie Zhu, Ming Li, Wei Zhuang, Hanjie Ying. Characterization of two halophilic adenylate cyclases from Thermobifida halotolerans and Haloactinopolyspora alba [J]. Chinese Journal of Chemical Engineering, 2023, 53(1): 56-62.
[3]	Xiaoyan Zhuang, Qian Wu, Aihui Zhang, Langxing Liao, Baishan Fang. Single-molecule biotechnology for protein researches [J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 212-224.
[4]	Yu Kiat Lin, Hui Yi Leong, Tau Chuan Ling, Dong-Qiang Lin, Shan-Jing Yao. Raman spectroscopy as process analytical tool in downstream processing of biotechnology [J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 204-211.
[5]	Huiling Wei, Mengyue Wu, Aili Fan, Haijia Su. Recombinant protein production in the filamentous fungus Trichoderma [J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 74-81.
[6]	Yanfeng Liu, Xiaomin Dong, Bin Wang, Rongzhen Tian, Jianghua Li, Long Liu, Guocheng Du, Jian Chen. Food synthetic biology-driven protein supply transition: From animal-derived production to microbial fermentation [J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 29-36.
[7]	Mengmeng Wang, Gang Cao, Naixian Feng, Yongzhang Pan. Bioaugmentation of two-stage aerobic sequencing batch reactor with mixed strains for high nitrate nitrogen wastewater treatment [J]. Chinese Journal of Chemical Engineering, 2020, 28(12): 3103-3109.
[8]	Xiaojie Sui, Pengguang Chen, Chiyu Wen, Jing Yang, Qingsi Li, Lei Zhang. Exploring novel cell cryoprotectants based on neutral amino acids [J]. Chinese Journal of Chemical Engineering, 2020, 28(10): 2640-2649.
[9]	Huanru Ding, Weirui Zhao, Changjiang Lü, Jun Huang, Sheng Hu, Shanjing Yao, Lehe Mei, Jinbo Wang, Jiaqi Mei. Biosynthesis of 4-hydroxyphenylpyruvic acid from L-tyrosine using recombinant Escherichia coli cells expressing membrane bound L-amino acid deaminase [J]. Chin.J.Chem.Eng., 2018, 26(2): 380-385.