Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials

Zijiao Li; Xiang Zhou; Danxi Liao; Ruolan Liu; Xia Zhao; Jing Wang; Qiu Zhong; Zhuo Zeng; Yizhi Peng; Yinling Tan; Zichen Yang

doi:10.3389/fcimb.2023.1180194

Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials

Front Cell Infect Microbiol. 2023 Aug 18:13:1180194. doi: 10.3389/fcimb.2023.1180194. eCollection 2023.

Authors

Zijiao Li^{1

2}, Xiang Zhou^{1

2}, Danxi Liao¹, Ruolan Liu¹, Xia Zhao³, Jing Wang³, Qiu Zhong³, Zhuo Zeng⁴, Yizhi Peng⁴, Yinling Tan³, Zichen Yang^{1

3

4}

Affiliations

¹ Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China.
² Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China.
³ Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China.
⁴ Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China.

Abstract

Introduction: Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.

Methods: This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.

Results: General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.

Disucssion: This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.

Keywords: DNA methylation analysis; Pseudomonas aeruginosa; SMRT; antibacterial; comparative genome analysis; epigenetics.

Publication types

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

MeSH terms

Anti-Infective Agents*
DNA
DNA Methylation
Genomics
Phylogeny
Pseudomonas aeruginosa* / genetics

Substances

Anti-Infective Agents
DNA

Grants and funding

This work was supported by the National Natural Science Foundation of China (grant no. 82002051 and 81772073), the Natural Science Foundation of Chongqing CSTC (cstc2021jcyj-msxmX0655), and the Doctor Through Line Project of Chongqing CSTB (CSTB2022BSXM-JCX0019), the Foundation of Open Projects from State Key Laboratory of Trauma, Burns and Combined Injury (No. SKLKF201918), and the Young Talents Program of Army medical university.