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

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

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1180194

DOI=10.3389/fcimb.2023.1180194

ISSN=2235-2988

ABSTRACT=<sec><title>Introduction</title><p><italic>Pseudomonas aeruginosa</italic> (<italic>P.aeruginosa</italic>) 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.</p></sec><sec><title>Methods</title><p>This study applied SMRT technology to sequence a clinical strain <italic>P. aeruginosa</italic> PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.</p></sec><sec><title>Results</title><p>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 <italic>P. aeruginosa</italic> strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to <italic>P. aeruginosa</italic> 60503 and <italic>P. aeruginosa</italic> 8380. <italic>P. aeruginosa</italic>'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, <italic>purH</italic>, <italic>phaZ</italic>, and <italic>lexA</italic> 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.</p></sec><sec><title>Disucssion</title><p>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 <italic>P. aeruginosa</italic> pathogenicity.</p></sec>