SWATH-MS proteome of Actinobacillus pleuropneumoniae showing differential protein expression due to the ModP and ModQ phasevarions

Actinobacillus pleuropneumoniae is responsible for porcine pleuropneumoniae, a severe respiratory disease that causes major global financial losses to the swine industry every year. Phase variation is the random switching of gene expression, either ON-OFF switching of expression, or the expression of multiple allelic protein variants. A number of bacteria encode cytoplasmic DNA methyltransferases that are phase-variable. This variable methyltransferase expression leads to global gene expression differences mediated by epigenetic mechanisms. These systems are called phasevarions (phase-variable regulons). In all described cases, phasevarions control expression of current and putative vaccine candidates, and influence phenotypes relevant to pathobiology. We have discovered two new phase-variable Type III DNA methyltransferases in A. pleuropneumoniae, which we named modP and modQ. Sequence analysis of multiple strains showed modP was present as four allelic variants, but just a single allelic variant of modQ was present. Phase-variable expression of modP (modP1 or modP2) and modQ leads to differential protein expression. This SWATH-MS dataset demonstrates the resulting changes to protein expression as a result of the of ModP1, ModP2 and ModQ phasevarions. This dataset represents triplicate repeats from strains which express either ModP or ModQ (ON) and strains which do not (OFF).

胸膜肺炎放线杆菌（Actinobacillus pleuropneumoniae）可引发猪胸膜肺炎——一种每年给全球养猪业造成巨额经济损失的烈性呼吸道传染病。相变异（phase variation）指基因表达的随机切换，既包括表达的开-关切换，也涵盖多种等位蛋白变体的表达切换。诸多细菌编码具有相变特性的胞质DNA甲基转移酶，这类可变的甲基转移酶表达会通过表观遗传（epigenetic）机制介导全局基因表达差异，此类系统被称为相变调控子（phasevarions，即phase-variable regulons）。在所有已报道的案例中，相变调控子均会调控现有及潜在疫苗候选抗原的表达，并影响与病原生物学（pathobiology）相关的表型特征。本研究在胸膜肺炎放线杆菌中发现了两种新型相变III型DNA甲基转移酶，并将其命名为modP与modQ。对多株菌株的序列分析显示，modP存在4种等位基因变体，而modQ仅存在1种等位基因变体。modP（modP1或modP2）与modQ的相变表达会导致蛋白表达谱产生差异。本SWATH-MS（数据非依赖采集质谱）数据集展示了ModP1、ModP2与ModQ相变调控子所引发的蛋白表达变化。本数据集涵盖表达ModP或ModQ（开启状态）以及不表达这两种蛋白（关闭状态）的菌株的三次生物学重复样本。