DNA Methyltransferase Regulates Nitric Oxide Homeostasis and Virulence in a Chronically Adapted Pseudomonas aeruginosa Strain

Han, Shuhong1,2; Liu, Jihong1,2; Li, Mianhuan2,3; Zhang, Yizhou1,2; Duan, Xiangke2; Zhang, Yingdan2; Chen, Hao2; Cai, Zhao2; Yang, Liang2,4,5; Liu, Yang1,2; Oliveira, Pedro H.1,2

2022-09-01

10.1128/msystems.00434-22

mSystems   影响因子和分区

2379-5077

["Opportunistic pathogens such as Pseudomonas aeruginosa adapt their genomes rapidly during chronic infections. Understanding their epigenetic regulation may provide biomarkers for diagnosis and reveal novel regulatory mechanisms. We performed single-molecule real-time sequencing (SMRT-seq) to characterize the methylome of a chronically adapted P. aeruginosa clinical strain, TBCF10839. Two N-6-methyladenine (6mA) methylation recognition motifs (RCCANNNNNNNTGAR and TRGANNNNNNTGC [modification sites are in bold]) were identified and predicted as new type I methylation sites using REBASE analysis. We confirmed that the motif TRGANNNNNNTGC was methylated by the methyltransferase (MTase) M.PaeTBCFII, according to methylation sensitivity assays in vivo and vitro. Transcriptomic analysis showed that a Delta paeTBCFIIM knockout mutant significantly downregulated nitric oxide reductase (NOR) regulation and expression of coding genes such as nosR and norB, which contain methylated motifs in their promoters or coding regions. The Delta paeTBCFIIM strain exhibited reduced intercellular survival capacity in NO-producing RAW264.7 macrophages and attenuated virulence in a Galleria mellonella infection model; the complemented strain recovered these defective phenotypes. Further phylogenetic analysis demonstrated that homologs of M.PaeTBCFII occur frequently in P. aeruginosa as well as other bacterial species. Our work therefore provided new insights into the relationship between DNA methylation, NO detoxification, and bacterial virulence, laying a foundation for further exploring the molecular mechanism of DNA methyltransferase in regulating the pathogenicity of P. aeruginosa.","IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed broad genome diversity among P. aeruginosa clinical strains and revealed their different regulatory traits compared to the laboratory strains. While current investigation of the epigenetics of P. aeruginosa is still lacking, understanding epigenetic regulation may provide biomarkers for diagnosis and facilitate development of novel therapies. Denitrification capability is critical for microbial versatility in response to different environmental stress conditions, including the bacterial infection process, where nitric oxide (NO) can be generated by phagocytic cells. The denitrification regulation mechanisms have been studied intensively at genetic and biochemical levels. However, there is very little evidence about the epigenetic regulation of bacterial denitrification mechanism. P. aeruginosa TBCF10839 is a chronically host-adapted strain isolated from a cystic fibrosis (CF) patient with special antiphagocytosis characteristics. Here, we investigated the regulatory effect of an orphan DNA MTase, M.PaeTBCFII, in P. aeruginosa TBCF10839. We demonstrated that the DNA MTase regulates the transcription of denitrification genes represented by NOR and affects antiphagocytic ability in bacteria. In silico analysis suggested that DNA methylation modification may enhance gene expression by affecting the binding of transacting factors such as DNR and RpoN. Our findings not only deepen the understanding of the role of DNA MTase in transcriptional regulation in P. aeruginosa but also provide a theoretical foundation for the in-depth study of the molecular mechanism of the epigenetic regulation on denitrification, virulence, and hostpathogen interaction."]

Pseudomonas aeruginosa DNA methyltransferase denitrification virulence bacterium-host interactions DNA methylation

SCI

英语

第一 ; 通讯

Guangdong Basic and Applied Basic Research Foundation[2020A1515010316] ; Guangdong Natural Science Foundation for Distinguished Young Scholar[2020B1515020003] ; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology[ZDSYS20200811144002008] ; Shenzhen Science and Technology Program[KQTD20200909113758004]

Microbiology

Microbiology

WOS:000855357100001

AMER SOC MICROBIOLOGY

Web of Science

1.Southern Univ Sci & Technol Hosp, Med Res Ctr, Shenzhen, Peoples R China
2.Southern Univ Sci & Technol, Sch Med, Shenzhen, Peoples R China
3.Southern Univ Sci & Techno, Shenzhen Peoples Hosp 3, Natl Clin Res Ctr Infect Dis, Dept Clin Lab,Hosp 2, Shenzhen, Guangdong, Peoples R China
4.Southern Univ Sci & Techno, Shenzhen Peoples Hosp 3, Natl Clin Res Ctr Infect Dis, Hosp 2, Shenzhen, Peoples R China
5.Southern Univ Sci & Technol, Shenzhen Key Lab Gene Regulat & Syst Biol, Shenzhen, Peoples R China

Han, Shuhong,Liu, Jihong,Li, Mianhuan,et al. DNA Methyltransferase Regulates Nitric Oxide Homeostasis and Virulence in a Chronically Adapted Pseudomonas aeruginosa Strain[J]. mSystems,2022.

Han, Shuhong.,Liu, Jihong.,Li, Mianhuan.,Zhang, Yizhou.,Duan, Xiangke.,...&Oliveira, Pedro H..(2022).DNA Methyltransferase Regulates Nitric Oxide Homeostasis and Virulence in a Chronically Adapted Pseudomonas aeruginosa Strain.mSystems.

Han, Shuhong,et al."DNA Methyltransferase Regulates Nitric Oxide Homeostasis and Virulence in a Chronically Adapted Pseudomonas aeruginosa Strain".mSystems (2022).