Quantitative Proteome and Transcriptome Analysis of the Archaeon <i>Thermoplasma acidophilum</i> Cultured under Aerobic and Anaerobic Conditions

A comparative proteome and transcriptome analysis of Thermoplasma acidophilum cultured under aerobic and anaerobic conditions has been performed. One-thousand twenty-five proteins were identified covering 88% of the cytosolic proteome. Using a label-free quantitation method, we found that approximately one-quarter of the identified proteome (263 proteins) were significantly induced (>2 fold) under anaerobic conditions. Thirty-nine macromolecular complexes were identified, of which 28 were quantified and 15 were regulated under anaerobiosis. In parallel, a whole genome cDNA microarray analysis was performed showing that the expression levels of 445 genes were influenced by the absence of oxygen. Interestingly, more than 40% of the membrane protein-encoding genes (145 out of 335 ORFs) were up- or down-regulated at the mRNA level. Many of these proteins are functionally associated with extracellular protein or peptide degradation or ion and amino acid transport. Comparison of the transcriptome and proteome showed only a weak positive correlation between mRNA and protein expression changes, which is indicative of extensive post-transcriptional regulatory mechanisms in T. acidophilum. Integration of transcriptomics and proteomics data generated hypotheses for physiological adaptations of the cells to anaerobiosis, and the quantitative proteomics data together with quantitative analysis of protein complexes provide a platform for correlation of MS-based proteomics studies with cryo-electron tomography-based visual proteomics approaches.本研究针对需氧与厌氧培养条件下的嗜酸热原体（Thermoplasma acidophilum）开展了比较蛋白质组学与转录组学联合分析。共鉴定得到1025种蛋白质，覆盖胞质蛋白质组的88%。采用无标记定量（label-free quantitation）方法分析后发现，约四分之一的鉴定蛋白质组（共263种蛋白质）在厌氧条件下显著上调，表达变化倍数≥2。本研究共鉴定得到39个大分子复合物，其中28个得以定量，15个在厌氧条件下呈现表达调控。 与此同时，本研究开展了全基因组cDNA微阵列（cDNA microarray）分析，结果显示445个基因的表达水平受氧缺失条件的调控。值得关注的是，超过40%的膜蛋白编码基因（335个开放阅读框（Open Reading Frame，ORF）中的145个）在mRNA水平呈现上调或下调表达。上述受调控基因编码的蛋白质中，多数功能与胞外蛋白质或肽类降解、离子及氨基酸转运相关。 对转录组与蛋白质组数据的比较分析显示，mRNA与蛋白质的表达变化仅存在微弱正相关，这表明嗜酸热原体中存在广泛的转录后调控机制。转录组学与蛋白质组学数据的整合，为阐释细胞对厌氧环境的生理适应性提供了假说；同时，定量蛋白质组数据与蛋白质复合物定量分析，为基于质谱（Mass Spectrometry，MS）的蛋白质组学研究与基于冷冻电子断层成像（cryo-electron tomography）的可视化蛋白质组学（visual proteomics）方法的关联分析搭建了研究平台。