PDF(Pubmed)
Abstract：
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.
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.
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.
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.
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.
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.
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.
摘要：
■铜绿假单胞菌（P.铜绿假单胞菌）是一种重要的机会致病菌，具有广泛的环境适应性和复杂的耐药性。单分子实时（SMRT）测序技术具有较长的读取长度序列，更准确,以及识别表观遗传DNA改变的能力。
■本研究应用SMRT技术对临床菌株铜绿假单胞菌PA3进行了测序，以获得其基因组序列和甲基化修饰信息。基因组，比较,泛基因组，并对PA3进行了表观遗传学分析。
■发现了PA3的一般基因组注释，以及有关毒力因子的信息，调节蛋白（RP），分泌的蛋白质，II型毒素-抗毒素（TA）对，和基因组岛。全基因组比较显示，PA3在身份方面与其他铜绿假单胞菌菌株相当，但在水平基因转移（HGT）领域有所不同。系统发育分析表明PA3与铜绿假单胞菌60503和铜绿假单胞菌8380密切相关。铜绿假单胞菌的全基因组由大约4,300个基因的核心基因组和至少5,500个基因的辅助基因组组成。表观遗传分析的结果确定了一个主要的甲基化位点，N6-甲基腺苷（m6A）和1基序（CATNNNNNNNTCCT/AGGANNNNNNNNATG）。挑选出16个有意义的甲基化位点。其中,purh,phaZ,LexA和LexA在PA3的耐药性和生物环境适应性中起着重要作用，这些基因的靶向作用可能有利于进一步的抗菌研究。
■这项研究提供了PA3基因组的详细可视化和DNA甲基化信息，并为后续研究DNA甲基转移酶控制的铜绿假单胞菌致病性的分子机制奠定了基础。
■本研究应用SMRT技术对临床菌株铜绿假单胞菌PA3进行了测序，以获得其基因组序列和甲基化修饰信息。基因组，比较,泛基因组，并对PA3进行了表观遗传学分析。
■发现了PA3的一般基因组注释，以及有关毒力因子的信息，调节蛋白（RP），分泌的蛋白质，II型毒素-抗毒素（TA）对，和基因组岛。全基因组比较显示，PA3在身份方面与其他铜绿假单胞菌菌株相当，但在水平基因转移（HGT）领域有所不同。系统发育分析表明PA3与铜绿假单胞菌60503和铜绿假单胞菌8380密切相关。铜绿假单胞菌的全基因组由大约4,300个基因的核心基因组和至少5,500个基因的辅助基因组组成。表观遗传分析的结果确定了一个主要的甲基化位点，N6-甲基腺苷（m6A）和1基序（CATNNNNNNNTCCT/AGGANNNNNNNNATG）。挑选出16个有意义的甲基化位点。其中,purh,phaZ,LexA和LexA在PA3的耐药性和生物环境适应性中起着重要作用，这些基因的靶向作用可能有利于进一步的抗菌研究。
■这项研究提供了PA3基因组的详细可视化和DNA甲基化信息，并为后续研究DNA甲基转移酶控制的铜绿假单胞菌致病性的分子机制奠定了基础。
