Department of Biology, Brooklyn College, City University of New York , Brooklyn, New York, USA.
Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York , New York, New York, USA.
mBio. 2023 Aug 31;14(4):e0057323. doi: 10.1128/mbio.00573-23. Epub 2023 Jun 23.
() is an opportunistic pathogen that is frequently isolated from urban water systems, posing a health risk to susceptible individuals. Despite its ability to cause tuberculosis-like pulmonary disease, very few studies have probed the genetics of this opportunistic pathogen. Here, we report a comprehensive essentiality analysis of the genome. Deep sequencing of a high-density library of transposon mutants revealed that 86.8% of the chromosomal thymine-adenine (TA) dinucleotide target sites were permissive to insertion, leaving 13.2% TA sites unoccupied. Our analysis identified 394 of the 5,350 annotated open reading frames (ORFs) as essential. The majority of these essential ORFs (84.8%) share essential mutual orthologs with (). A comparative genomics analysis identified 139 essential ORFs that share essential orthologs in four other species of mycobacteria. Thirteen essential ORFs share orthologs in all four species that were identified as being not essential, while only two essential ORFs are absent in all species compared. We used the essentiality data and a comparative genomics analysis reported here to highlight differences in essentiality between candidate drug targets and the corresponding orthologs. Our findings suggest that the genome encodes redundant or additional pathways that may confound validation of potential drugs and drug target candidates against the opportunistic pathogen. Additionally, we identified 57 intergenic regions containing four or more consecutive unoccupied TA sites. A disproportionally large number of these regions were located upstream of / genes. Finally, we present an essentiality and orthology analysis of the pRAW-like plasmid, pMK1248. IMPORTANCE is one of the most common nontuberculous mycobacterial pathogens associated with tuberculosis-like pulmonary disease. Drug resistance emergence is a threat to the control of infections, which already requires long-term, multidrug courses. A comprehensive understanding of biology is critical to facilitate the development of new and more efficacious therapeutics against . We combined transposon-based mutagenesis with analysis of insertion site identification data to uncover genes and other genomic regions required for growth. We also compared the gene essentiality data set of to those available for several other mycobacteria. This analysis highlighted key similarities and differences in the biology of compared to these other species. Altogether, the genome-wide essentiality information generated and the results of the cross-species comparative genomics analysis represent valuable resources to assist the process of identifying and prioritizing potential drug target candidates and to guide future studies on biology.
（）是一种机会性病原体，经常从城市水系中分离出来，对易感个体构成健康风险。尽管它能够引起类似肺结核的肺部疾病，但很少有研究探讨这种机会性病原体的遗传学。在这里，我们报告了对基因组的全面必需性分析。对转座子突变体高密度文库的深度测序显示，胸腺嘧啶-腺嘌呤（TA）二核苷酸靶位的 86.8%允许插入，留下 13.2%的 TA 位未被占据。我们的分析确定了 5350 个注释开放阅读框（ORF）中的 394 个为必需的。这些必需的 ORF 中的大多数（84.8%）与（）中的必需互同源物共享。比较基因组学分析鉴定出 139 个必需 ORF 在其他四种分枝杆菌中具有必需的直系同源物。在所有四个物种中，有 13 个必需 ORF 与被鉴定为非必需的所有四个物种中的直系同源物共享，而只有两个必需 ORF 在所有比较物种中都不存在。我们使用必需性数据和这里报告的比较基因组学分析来突出候选药物靶点和相应的之间的必需性差异。我们的研究结果表明，基因组编码冗余或额外的途径，这可能会使验证针对机会性病原体的潜在药物和药物靶标候选物复杂化。此外，我们鉴定了 57 个包含四个或更多连续未占据 TA 位的基因间区。这些区域中有很大一部分位于 / 基因的上游。最后，我们对 pRAW 样质粒 pMK1248 进行了必需性和直系同源性分析。重要性 是与肺结核样肺部疾病相关的最常见非结核分枝杆菌病原体之一。耐药性的出现对 感染的控制构成了威胁，这已经需要长期的、多药疗程。全面了解生物学对于促进针对 的新的和更有效的治疗方法的发展至关重要。我们结合转座子诱变和插入位点鉴定数据的分析，揭示了 生长所必需的基因和其他基因组区域。我们还比较了 与其他几种分枝杆菌的基因必需性数据集。这项分析突出了 与这些其他物种的生物学之间的关键相似性和差异。总的来说，生成的全基因组必需性信息和跨物种比较基因组学分析的结果代表了有价值的资源，可用于协助识别和优先考虑潜在的药物靶点候选物，并指导针对 生物学的未来研究。
