RNA-seq transcriptome of Staphylococcus aureus at stationary phase in Tryptic Soy Broth

A commensal of the human body, Gram-positive <i>Staphylococcus aureus</i> is also an opportunistic pathogen of increasing concern across the world. Able to grow without oxygen, the bacterium is capable of infecting many types of wounds on different parts of the body. But, chief amongst concerns about the bacterium is its increasing ability to resist a variety of antibiotics. Understanding the physiology of <i>S. aureus</i> provides one avenue for the discovery of drugs able to combat this pathogen, and more fundamentally, provides a glimpse into the biology of this bacterium that has a shared evolution history with humans. In particular, understanding how <i>S. aureus</i> has transformed from a commensal into an opportunistic pathogen with the acquisition of new genetic and physiological repertoire is a fascinating question yet to be fully answered. This contribution hopes to provide some fundamental information that could illuminate the questions posted above. Chiefly, the RNA-seq transcriptome of <i>S. aureus</i> at stationary phase (16 hrs) in Tryptic Soy Broth at 37 ^oC (ArrayExpress accession number: E-GEOD-77242) was analysed by an in-house MATLAB algorithm to yield a transcriptional picture that revealed the importance of DNA and chromosomal maintenance to the cell. Specifically, an ensemble of 0.5 million reads indicated that highly expressed genes were: chromosomal replication initiation protein, lipase, delta-hemolysin, quinol oxidase subunit I, clumping factor, accessory gene regulator protein A, accessory gene regulator protein C, DNA polymerase III subunit beta, quinol oxidase AA3 subunit II, and elongation factor Tu. Overall, understanding the stationary phase gene expression pattern of <i>S. aureus</i> could potentially point us to therapeutic strategies to combat this increasing important human pathogen, that, in some cases, have resisted treatment with our front-line antibiotics. <br><br>作为人体共生菌群的一员，革兰氏阳性（Gram-positive）的金黄色葡萄球菌（*Staphylococcus aureus*）亦是全球范围内日益受到关注的机会致病菌。该菌可在无氧环境中存活并增殖，能够感染人体不同部位的各类伤口。但该菌最受学界关注的特征之一，是其对多种抗生素的耐药性持续攀升。解析金黄色葡萄球菌的生理学特性，不仅可为开发对抗该病原菌的药物提供可行路径，更从基础层面帮助我们窥探这一与人类共享演化历程的细菌的生物学本质。具体而言，阐明金黄色葡萄球菌如何通过获取全新的遗传与生理功能谱，从共生菌转变为机会致病菌，仍是一个尚未得到完整解答的关键科学问题。本数据集旨在为解答上述问题提供基础信息。本次分析通过自研MATLAB算法，对在37℃胰蛋白胨大豆肉汤（Tryptic Soy Broth）中培养至稳定期（16小时）的金黄色葡萄球菌进行RNA测序转录组分析，所得转录组图谱揭示了DNA与染色体维持机制在该菌中的关键作用，该数据集的ArrayExpress数据库收录号为E-GEOD-77242。具体而言，基于总计50万条测序读段的分析结果显示，该菌在稳定期高表达的基因包括：染色体复制起始蛋白、脂肪酶、δ-溶血素、醌氧化酶亚基I、聚集因子、辅助基因调节蛋白A、辅助基因调节蛋白C、DNA聚合酶III亚基β、醌氧化酶AA3亚基II以及延伸因子Tu。综上，解析金黄色葡萄球菌稳定期的基因表达模式，有望为对抗这一日益重要的人类病原菌提供全新治疗策略——在部分临床病例中，该菌已对一线抗生素产生耐药性。