Altered Quorum Sensing and Physiology of Staphylococcus aureus During Spaceflight Detected by Multi-omics Data Analysis (BRIC-23: Secretomics)

Staphylococcus aureus colonizes the nares of approximately 30% of humans, a risk factor for opportunistic infections. Because of the potential threat of S. aureus to astronaut health, the effect of spaceflight conditions on this pathogen is of great interest. To gain insight into the virulence potential of S. aureus in the spaceflight environment, we performed differential expression (DE) analysis of RNA-Seq and cellular proteomics data from the “Biological Research in Canisters-23” (BRIC-23) GeneLab spaceflight experiment, a mission designed to measure the response of S. aureus to growth in low earth orbit (LEO) on the international space station (ISS). This experiment used Biological Research in Canisters-Petri Dish Fixation Units (BRIC-PDFUs) to grow asynchronous ground controls (GCs) and spaceflight cultures of S. aureus for 48 hours. Analysis of the RNA-Seq data revealed that RNAIII, the effector of the Accessory Gene Regulator (Agr) quorum sensing system, was the most highly upregulated gene in spaceflight cultures (~88-fold) relative to GCs. Genes of the agr operon (~14 fold) were also highly upregulated during spaceflight, followed by genes encoding secreted phenol-soluble modulins (PSMs) and secreted proteases, all of which are positively regulated by Agr. Upregulated spaceflight genes/proteins also had functions related to urease activity, Ess secretion, and copper transport. We also performed a secretome analysis of culture supernatant samples from BRIC-23. In line with the other BRIC-23 omics data, spaceflight supernatants displayed significantly increased abundance of several known secreted virulence factors, including Agr-regulated proteases (SspA, SspB), staphylococcal nuclease (Nuc), and EsxA, a small protein secreted by the type VII-like Ess secretion system. These data also suggested that S. aureus metabolism is altered in space flight conditions relative to the ground controls (increased amino acid metabolism, TCA cycle and PTS systems, and decreased glycolysis/fermentation and translation machinery). Collectively, these data suggest that S. aureus experiences increased quorum sensing and altered expression of virulence factors in response to the spaceflight environment that may impact its pathogenic potential.

金黄色葡萄球菌（Staphylococcus aureus）约定植于30%人类的鼻腔，是机会性感染的危险因素。鉴于金黄色葡萄球菌对宇航员健康存在潜在威胁，太空飞行环境对该病原体的影响备受学界关注。为深入解析太空飞行环境中金黄色葡萄球菌的致病潜力，我们针对“生物研究舱-23（Biological Research in Canisters-23，BRIC-23）”GeneLab太空飞行实验的RNA测序（RNA-Seq）及细胞蛋白质组学数据开展了差异表达（differential expression, DE）分析——该实验旨在探究国际空间站（International Space Station, ISS）低地球轨道（low earth orbit, LEO）环境下金黄色葡萄球菌的生长响应。本实验使用生物研究舱-培养皿固定单元（Biological Research in Canisters-Petri Dish Fixation Units，BRIC-PDFUs）培养金黄色葡萄球菌的异步地面对照组（ground controls, GCs）与太空飞行组培养物，培养时长为48小时。对RNA-Seq数据的分析显示，相较于地面对照组，辅助基因调节（Accessory Gene Regulator, Agr）群体感应系统的效应分子RNAIII在太空飞行组中上调幅度最高，达约88倍。agr操纵子相关基因（上调幅度约14倍）在太空飞行环境中也呈现显著上调，后续是编码分泌型酚可溶性调控蛋白（phenol-soluble modulins, PSMs）及分泌型蛋白酶的基因，上述基因均受Agr系统正向调控。上调的太空飞行相关基因/蛋白质还涉及脲酶活性、Ess分泌系统及铜转运相关功能。我们还对BRIC-23实验的培养上清样本进行了分泌组分析。结合其他BRIC-23组学数据，太空飞行组的培养上清中多种已知分泌型毒力因子的丰度显著升高，包括Agr调控的蛋白酶（SspA、SspB）、葡萄球菌核酸酶（Nuc）以及由VII型类似Ess分泌系统分泌的小分子蛋白EsxA。上述数据还表明，相较于地面对照组，太空飞行条件下金黄色葡萄球菌的代谢发生改变：氨基酸代谢、三羧酸（tricarboxylic acid, TCA）循环及磷酸转移酶系统（phosphotransferase system, PTS）活性上调，而糖酵解/发酵及翻译相关机制的表达则下调。综上，这些数据表明，金黄色葡萄球菌在太空飞行环境中会出现群体感应增强及毒力因子表达改变，这可能会影响其致病潜力。