Genomic and transcriptomic profiling of phoenix colonies.
Genomic and transcriptomic profiling of phoenix colonies.
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DOI：
10.1038/s41598-022-18059-1
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发表时间：
2022-08-12
影响因子：
4.6
通讯作者：
Stoodley, Paul
中科院分区：
文献类型：
--
作者：
Sindeldecker, Devin;Dunn, Matthew;Zimmer, Aubree;Anderson, Matthew;Alfonzo, Juan;Stoodley, Paul
铜绿假单胞菌是一种革兰氏阴性细菌，导致许多人类感染。以前，在高浓度氨基糖苷类药物的作用下，鉴定出了被称为凤凰菌落的新型抗生素耐受性变体以及与可存活但不可培养（VBNC）菌落相似的变体。在这项研究中，凤凰集落和VBNC样集落出现背后的机制，进一步探索使用全基因组测序和RNA测序。Phoenix菌落被发现在PA4673基因中具有单核苷酸多态性（SNP），该基因被预测编码GTP结合蛋白。与创始人群体相比，在VBNC样集落内未鉴定出SNP。RNA测序没有检测到PA4673表达的变化，但揭示了多个差异表达的基因，可能在凤凰集落出现中发挥作用。这些差异表达的基因之一，PA3626，编码tRNA假尿苷合酶，当敲除时导致完全缺乏凤凰菌落。虽然目前还不清楚这项研究中确定的基因是否可能存在尚未被认识到的相互作用，但它们可能有助于了解凤凰群落如何在抗生素暴露的情况下出现和生存。
Pseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind phoenix colony and VBNC-like colony emergence were further explored using both whole genome sequencing and RNA sequencing. Phoenix colonies were found to have a single nucleotide polymorphism (SNP) in the PA4673 gene, which is predicted to encode a GTP-binding protein. No SNPs were identified within VBNC-like colonies compared to the founder population. RNA sequencing did not detect change in expression of PA4673 but revealed multiple differentially expressed genes that may play a role in phoenix colony emergence. One of these differentially expressed genes, PA3626, encodes for a tRNA pseudouridine synthase which when knocked out led to a complete lack of phoenix colonies. Although not immediately clear whether the identified genes in this study may have interactions which have not yet been recognized, they may contribute to the understanding of how phoenix colonies are able to emerge and survive in the presence of antibiotic exposure.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.8
作者：
Kelley LA;Mezulis S;Yates CM;Wass MN;Sternberg MJ
通讯作者：
Sternberg MJ
影响因子：
3
作者：
McCurtain, Jennifer L.;Gilbertsen, Adam J.;Hunter, Ryan C.
通讯作者：
Hunter, Ryan C.
影响因子：
4.9
作者：
Howlin, R. P.;Brayford, M. J.;Stoodley, P.
通讯作者：
Stoodley, P.