Integrated analysis of transcriptomic and protein-protein interaction data reveals cadmium stress response in Geobacter sulfurreducens

Su Wen; Fei Yin; Chunmao Liu; Yan Dang; Dezhi Sun; Pengsong Li

doi:10.1016/j.envres.2022.115063

Integrated analysis of transcriptomic and protein-protein interaction data reveals cadmium stress response in Geobacter sulfurreducens

Environ Res. 2023 Feb 1:218:115063. doi: 10.1016/j.envres.2022.115063. Epub 2022 Dec 14.

Authors

Su Wen¹, Fei Yin¹, Chunmao Liu¹, Yan Dang¹, Dezhi Sun¹, Pengsong Li²

Affiliations

¹ Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
² Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China. Electronic address: pengsongli@bjfu.edu.cn.

PMID: 36528045
DOI: 10.1016/j.envres.2022.115063

Abstract

Bacteria have evolved several mechanisms to resist Cd toxicity, which are crucial for Cd detoxication and have the potential to be used for bioremediation of Cd. Geobacter species are widely found in anaerobic environments and play important roles in natural biogeochemical cycles. However, the transcriptomic response of Geobacter sulfurreducens under Cd stress have not been fully elucidated. Through integrated analysis of transcriptomic and protein-protein interaction (PPI) data, we uncovered a global view of mRNA changes in Cd-induced cellular processes in this study. We identified 182 differentially expressed genes (|log₂(fold change)| > 1, adjusted P < 0.05) in G. sulfurreducens exposed to 0.1 mM CdCl₂ using RNA sequencing (RNA-seq). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that CdCl₂ significantly affected sulfur compound metabolic processes. In addition, through PPI network analysis, hub genes related to molecular chaperones were identified to play important role in Cd stress response. We also identified a Cd-responsive transcriptional regulator ArsR2 (coded by GSU2149) and verified the function of ArsR2-P_arsR2 regulatory circuit in Escherichia coli. This study provides new insight into Cd stress response in G. sulfurreducens, and identified a potential sensor element for Cd detection.

Keywords: Cadmium; Geobacter sulfurreducens; Protein-protein interaction network; RNA-seq; Transcriptional regulator.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cadmium / toxicity
Gene Expression Profiling
Geobacter* / genetics
Transcriptome*

Substances

Cadmium

Supplementary concepts

Geobacter sulfurreducens