Identification and characterization of ethanol-inducible promoters of Zymomonas mobilis based on omics data and dual reporter-gene system.
Zymomonas mobilis
dual reporter-gene system
ethanol
inducible promoter
promoter strength
Journal
Biotechnology and applied biochemistry
ISSN: 1470-8744
Titre abrégé: Biotechnol Appl Biochem
Pays: United States
ID NLM: 8609465
Informations de publication
Date de publication:
Jan 2020
Jan 2020
Historique:
received:
19
08
2019
accepted:
13
10
2019
pubmed:
19
10
2019
medline:
15
12
2020
entrez:
19
10
2019
Statut:
ppublish
Résumé
Zymomonas mobilis is a model bacterial ethanologen and has been engineered to produce lignocellulosic biofuels and biochemicals such as 2,3-butanediol. We have previously identified promoters of different strengths using systems biology datasets and characterized them using the flow cytometry-based dual reporter-gene system. Here, we further demonstrated the capability of applying the dual reporter-gene system and omics datasets on discovering inducible promoters. Ten candidate ethanol-inducible promoters were identified through omics datasets mining and clustering. Using the dual reporter-gene system, these promoters were characterized under natural growth, ethanol stress, and ethanol-induced condition to investigate the transcriptional strength and ethanol inducibility. The results demonstrated that three promoters of P0405, P0435, and P0038 driving the expression of native genes of ZMO0405, ZMO0435, and ZMO0038, correspondingly, are potential ethanol-responsive promoters and may be growth related. This study not only identified and verified three ethanol-inducible promoters as biological parts, which can be used to synchronize the expression of heterologous pathway genes with the ethanol production process of Z. mobilis, but also demonstrated the power of combining omics datasets and dual reporter-gene system to identify biological parts for metabolic engineering and synthetic biology applications in Z. mobilis and related microorganisms.
Substances chimiques
Ethanol
3K9958V90M
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
158-165Subventions
Organisme : National Key Research and Development Program of China
ID : 2018YFA0900300
Organisme : National Key Research and Development Program of China
ID : 2018YFC1801200
Organisme : National Science Foundation of China
ID : 21978071
Organisme : National Science Foundation of China
ID : U1932141
Organisme : Technical Innovation Special Fund of Hubei Province
ID : 2019AHB055
Organisme : Technical Innovation Special Fund of Hubei Province
ID : 2018ACA149
Informations de copyright
© 2019 International Union of Biochemistry and Molecular Biology, Inc.
Références
Yu, T., Zhou, Y. J., Huang, M., Liu, Q., Pereira, R., David, F., and Nielsen, J. (2018) Cell 174(6), 1549-1558, e1514.
Deaner, M., and Alper, H. S. (2016) Adv. Biochem. Eng. Biotechnol. 162, 21-44.
Timerbaev, V., and Dolgov, S. (2019) Planta 250, 1307-1323.
Yang, Y., Hu, M., Tang, Y., Geng, B., Qiu, M., He, Q., Chen, S., Wang, X., and Yang, S. (2018) Bioresources Bioprocess 5, 6.
Gao, X., Gao, Q., and Bao, J. (2018) J. Biotechnol. 282, 32-37.
Yang, S., Fei, Q., Zhang, Y., Contreras, L. M., Utturkar, S. M., Brown, S. D., Himmel, M. E., and Zhang, M. (2016) Microbiol. Biotechnol. 9(6), 699-717.
He, M. X., Wu, B., Qin, H., Ruan, Z. Y., Tan, F. R., Wang, J. L., Shui, Z. X., Dai, L. C., Zhu, Q. L., Pan, K., Tang, X. Y., Wang, W. G., and Hu, Q. C (2014) Biotechnol. Biofuels 7(101), 101.
Zhang, M., Eddy, C., Deanda, K., Finkelstein, M., and Picataggio, S. (1995) Science 267(5195), 240-243.
Pandey, S. P., Singh, A. P., Srivastava, S., Chandrashekar, K., and Sane, A. P. (2019) Plant Biotechnol. J. 17(7), 1458-1470.
Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y. C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M. (2016) Biotechnol. Biofuels 9(1), 189.
Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J., and Voigt, C. A. (2019) Nat. Chem. Biol. 15, 196-204.
Fischer, S., Engstler, C., Procopio, S., and Becker, T. (2016) FEMS Yeast Res. 16(3), fow014. https://doi.org/10.1093/femsyr/fow014.
Xu, N., Wei, L., and Liu, J. (2019) World. J. Microbiol. Biotechnol. 35(2), 33.
Peebles, C. A., Gibson, S. I., Shanks, J. V., and San, K. Y. (2007) Biotechnol. Prog. 23(5), 1258-1260.
Dahl, R. H., Zhang, F., Alonso-Gutierrez, J., Baidoo, E., Batth, T. S., Redding-Johanson, A. M., Petzold, C. J., Mukhopadhyay, A., Lee, T. S., Adams, P. D., and Keasling, J. D. (2013) Nat. Biotechnol. 31(11), 1039-1046.
Wang, X., He, Q., Yang, Y., Wang, J., Haning, K., Hu, Y., Wu, B., He, M., Zhang, Y., Bao, J., Contreras, L. M., and Yang, S. (2018) Metab Eng. 50, 57-73.
Xia, J., Yang, Y., Liu, C.-G., Yang, S., and Bai, F.-W. (2019) Trends Biotechnol. 37, 960-972.
Yang, S., Vera, J. M., Grass, J., Savvakis, G., Moskvin, O. V., Yang, Y., McIlwain, S. J., Lyu, Y., Zinonos, I., Hebert, A. S., Coon, J. J., Bates, D. M., Sato, T. K., Brown, S. D., Himmel, M. E., Zhang, M., Landick, R., Pappas, KM, and Zhang Y (2018) Biotechnol. Biofuels 11, 125.
Yang, S., Pappas, K. M., Hauser, L. J., Land, M. L., Chen, G. L., Hurst, G. B., Pan, C., Kouvelis, V. N., Typas, M. A., Pelletier, D. A., Klingeman, D. M., Chang, Y. J., Samatova, N. F., and Brown SD (2009) Nat. Biotechnol. 27(10), 893-894.
Seo, J. S., Chong, H., Park, H. S., Yoon, K. O., Jung, C., Kim, J. J., Hong, J. H., Kim, H., Kim, J. H., Kil, J. I., Park, C. J., Oh, H. M., Lee, J. S., Jin, S. J., Um, H. W., Lee, H. J., Oh, S. J., Kim, J. Y., Kang, H.L., Lee SY, Lee KJ, and Kang HS (2005) Nat. Biotechnol. 23(1), 63-68.
Yi, X., Gu, H., Gao, Q., Liu, Z. L., and Bao, J. (2015) Biotechnol. Biofuels 8, 153.
Dunn, K. L., and Rao, C. V. (2015) Biotechnol. Bioeng. 112(11), 2228-2240.
Yang, S., Pan, C., Hurst, G. B., Dice, L., Davison, B. H., and Brown, S. D. (2014) Front. Microbiol 5, 246.
Yang, S., Franden, M. A., Brown, S. D., Chou, Y. C., Pienkos, P. T., and Zhang, M. (2014) Biotechnol. Biofuels 7(1), 140.
Yang, S., Pan, C., Tschaplinski, T. J., Hurst, G. B., Engle, N. L., Zhou, W., Dam, P., Xu, Y., Rodriguez, M., Jr., Dice, L., Johnson, C. M., Davison, B. H., and Brown, S.D. (2013) PLoS One 8(7), e68886.
He, M. X., Wu, B., Shui, Z. X., Hu, Q. C., Wang, W. G., Tan, F. R., Tang, X. Y., Zhu, Q. L., Pan, K., Li, Q., and Su, X. H. (2012) Biotechnol. Biofuels 5(1), 75.
He, M. X., Wu, B., Shui, Z. X., Hu, Q. C., Wang, W. G., Tan, F. R., Tang, X. Y., Zhu, Q. L., Pan, K., Li, Q., and Su, X. H. (2012) Appl. Microbiol. Biotechnol. 95(1), 189-199.
Yang, S., Land, M. L., Klingeman, D. M., Pelletier, D. A., Lu, T. Y., Martin, S. L., Guo, H. B., Smith, J. C., and Brown, S. D. (2010) Proc. Natl. Acad. Sci. U. S. A. 107(23), 10395-10400.
Yang, S., Tschaplinski, T. J., Engle, N. L., Carroll, S. L., Martin, S. L., Davison, B. H., Palumbo, A. V., Rodriguez, M., Jr., and Brown, S. D. (2009) BMC Genomics 10, 34.
Yang, Y., Shen, W., Huang, J., Li, R., Xiao, Y., Wei, H., Chou, Y. C., Zhang, M., Himmel, M. E., Chen, S., Yi, L., Ma, L., and Yang, S. (2019) Biotechnol. Biofuels 12, 52.
Solovyev, V., Salamov, A. (2011) In: Metagenomics and Its Applications in Agriculture (L. RW, ed). pp. 61-78, Nova Science Publishers, Hauppauge, NY.
Wu, J., Brandt, S., and Hyder, S. M. (2005) Mol. Endocrinol. 19(2), 312-326.
Schuettengruber, B., Simboeck, E., Khier, H., and Seiser, C. (2003) Mol. Cell. Biol. 23(19), 6993-7004.
Wilke, N., Sganga, M. W., Gayer, G. G., Hsieh, K. P., and Miles, M. F. (2000) J. Pharmacol. Exp. Ther. 292(1), 173-180.
Mazzoni, C., Santori, F., Saliola, M., and Falcone, C. (2000) Res. Microbiol. 151, 19-28.
Mao, F., Dam, P., Chou, J., Olman, V., and Xu, Y. (2009) Nucleic. Acids Res. 37(Database issue), D459-D463.