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

被引：4
作者：
Wen, Su [1 ,2 ]
Yin, Fei [1 ,2 ]
Liu, Chunmao [1 ,2 ]
Dang, Yan [1 ,2 ]
Sun, Dezhi [1 ,2 ]
Li, Pengsong [1 ,2 ,3 ]
机构：
[1] Beijing Forestry Univ, Coll Environm Sci & Engn, Beijing Key Lab Source Control Technol Water Pollu, Beijing 100083, Peoples R China
[2] Beijing Forestry Univ, Coll Environm Sci & Engn, Engn Res Ctr Water Pollut Source Control & Ecoreme, Beijing 100083, Peoples R China
[3] Beijing Forestry Univ, Coll Environm Sci & Engn, 35 Tsinghua East Rd, Beijing 100083, Peoples R China
来源：
ENVIRONMENTAL RESEARCH | 2023年 / 218卷
基金：
国家重点研发计划;
关键词：
Geobacter sulfurreducens; Cadmium; RNA-seq; Protein-protein interaction network; Transcriptional regulator; SIGNAL-TRANSDUCTION PROTEINS; HEAVY-METAL RESISTANCE; FAMILY; TRANSPORT;
D O I：
10.1016/j.envres.2022.115063
中图分类号：
X [环境科学、安全科学];
学科分类号：
08 ; 0830 ;
摘要：
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-ParsR2 regulatory cir-cuit in Escherichia coli. This study provides new insight into Cd stress response in G. sulfurreducens, and identified a potential sensor element for Cd detection.
引用
收藏
页数：10
相关论文
共 52 条
[1]   SlyA Transcriptional Regulator Is Not Directly Affected by ppGpp Levels [J].
Bartoli, Julia ;
Viala, Julie Pamela ;
Bouveret, Emmanuelle .
FRONTIERS IN MICROBIOLOGY, 2020, 11
[2]   Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update [J].
Blair, Jessica M. A. ;
Piddock, Laura J. V. .
CURRENT OPINION IN MICROBIOLOGY, 2009, 12 (05) :512-519
[3]   Gene Ontology Consortium: going forward [J].
Blake, J. A. ;
Christie, K. R. ;
Dolan, M. E. ;
Drabkin, H. J. ;
Hill, D. P. ;
Ni, L. ;
Sitnikov, D. ;
Burgess, S. ;
Buza, T. ;
Gresham, C. ;
McCarthy, F. ;
Pillai, L. ;
Wang, H. ;
Carbon, S. ;
Dietze, H. ;
Lewis, S. E. ;
Mungall, C. J. ;
Munoz-Torres, M. C. ;
Feuermann, M. ;
Gaudet, P. ;
Basu, S. ;
Chisholm, R. L. ;
Dodson, R. J. ;
Fey, P. ;
Mi, H. ;
Thomas, P. D. ;
Muruganujan, A. ;
Poudel, S. ;
Hu, J. C. ;
Aleksander, S. A. ;
McIntosh, B. K. ;
Renfro, D. P. ;
Siegele, D. A. ;
Attrill, H. ;
Brown, N. H. ;
Tweedie, S. ;
Lomax, J. ;
Osumi-Sutherland, D. ;
Parkinson, H. ;
Roncaglia, P. ;
Lovering, R. C. ;
Talmud, P. J. ;
Humphries, S. E. ;
Denny, P. ;
Campbell, N. H. ;
Foulger, R. E. ;
Chibucos, M. C. ;
Giglio, M. Gwinn ;
Chang, H. Y. ;
Finn, R. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D1049-D1056
[4]   The in vivo and in vitro characterization of DnaK from Agrobacterium tumefaciens RUOR [J].
Boshoff, A ;
Hennessy, F ;
Blatch, GL .
PROTEIN EXPRESSION AND PURIFICATION, 2004, 38 (02) :161-169
[5]   Bacterial Transcription Factors: Regulation by Pick "N" Mix [J].
Browning, Douglas F. ;
Butala, Matej ;
Busby, Stephen J. W. .
JOURNAL OF MOLECULAR BIOLOGY, 2019, 431 (20) :4067-4077
[6]   The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance [J].
Busenlehner, LS ;
Pennella, MA ;
Giedroc, DP .
FEMS MICROBIOLOGY REVIEWS, 2003, 27 (2-3) :131-143
[7]   Biofilms Formed by Gram-Negative Bacteria Undergo Increased Lipid A Palmitoylation, Enhancing In Vivo Survival [J].
Chalabaev, Sabina ;
Chauhan, Ashwini ;
Novikov, Alexey ;
Iyer, Pavithra ;
Szczesny, Magdalena ;
Beloin, Christophe ;
Caroff, Martine ;
Ghigo, Jean-Marc .
MBIO, 2014, 5 (04)
[8]   fastp: an ultra-fast all-in-one FASTQ preprocessor [J].
Chen, Shifu ;
Zhou, Yanqing ;
Chen, Yaru ;
Gu, Jia .
BIOINFORMATICS, 2018, 34 (17) :884-890
[9]  
Chen T., 2022, IMETA, V1, P1, DOI DOI 10.1002/IMT2.5
[10]   cytoHubba: identifying hub objects and sub-networks from complex interactome [J].
Chin, Chia-Hao ;
Chen, Shu-Hwa ;
Wu, Hsin-Hung ;
Ho, Chin-Wen ;
Ko, Ming-Tat ;
Lin, Chung-Yen .
BMC SYSTEMS BIOLOGY, 2014, 8
123456