Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae

Hong Liao; Qian Li; Yulei Chen; Jiaye Tang; Borui Mou; Fujia Lu; Peng Feng; Wei Li; Jialian Li; Chun Fu; Wencong Long; Ximeng Xiao; Xuebing Han; Wenli Xin; Fengxuan Yang; Menggen Ma; Beidong Liu; Yaojun Yang; Hanyu Wang

doi:10.3389/fmicb.2024.1364425

Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae

Front Microbiol. 2024 Feb 21:15:1364425. doi: 10.3389/fmicb.2024.1364425. eCollection 2024.

Authors

Hong Liao^#¹, Qian Li^#^{1

2}, Yulei Chen^#^{1

2}, Jiaye Tang^#^{1

2}, Borui Mou¹, Fujia Lu¹, Peng Feng¹, Wei Li³, Jialian Li¹, Chun Fu¹, Wencong Long¹, Ximeng Xiao¹, Xuebing Han⁴, Wenli Xin¹, Fengxuan Yang¹, Menggen Ma², Beidong Liu^{5

6}, Yaojun Yang¹, Hanyu Wang¹

Affiliations

¹ Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China.
² College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China.
³ Aba Prefecture Ecological Protection and Development Research Institute, Wenchuan, Sichuan, China.
⁴ College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China.
⁵ State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China.
⁶ Department of Chemistry and Molecular Biology, University of Gothenburg Medicinaregatan, Gothenburg, Sweden.

^# Contributed equally.

Abstract

Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6Δ) is the most sensitive to CA. Based on the omics analysis of ERG6Δ under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP⁺ were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6Δ. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.

Keywords: Saccharomyces cerevisiae; catechol; genome-wide identification; omics analysis; response mechanism.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was financially supported by the National Natural Science Foundation of China (No. 32200044), the Key Project of Science and Technology Bureau of LeShan Town (No. 22ZDYJ0089), the Talent Research Startup Projects of Leshan Normal University (No. RC2022003), and the Scientific Research and Cultivation Plan of Leshan Normal University (No. 2022SSDJS010). The specific information pertains to the Leshan Normal University High-Level Talent Project (RC2021013).