RNA sequencing of Acinetobacter baylyi and E. coli while co-incubating on LB agar plates

The bacterial type VI secretion system is a widespread secretion mechanism important for competition in many Gram-negative bacteria. Killing and lysing of competing bacteria can provide advantages such as nutrients or acquisition of new genes by DNA uptake. Here, we show that T6SS-dependent lysis of prey cells by the naturally competent Acinetobacter baylyi results in extensive filamentation of a significant subpopulation of A. baylyi cells. This is dependent on the release of genomic DNA from the lysed prey cells and its uptake by the competence system of A. baylyi. Single-cell level analysis using live-cell imaging shows that filamentous A. baylyi cells appear at the interface between the species. The analysis of A. baylyi transcriptome and the response of transcriptional reporters suggest that the uptake of genomic DNA results in a highly upregulated SOS response, which often leads to the cell division arrest. Using competition experiments, we show that the parental strain is outcompeted by a strain lacking the DNA uptake machinery because such mutant shows no SOS response-dependent cell division arrest. Our data suggest that the cost of SOS-response may drive selection of decreased DNA uptake in T6SS positive bacteria. We analyzed expression profiles of A. baylyi in competition with E. coli. We deep-sequenced cDNA prepared from a mixture of E. coli with tae1-expressing (no other effectors present) and T6SS-deficient A. baylyi upon 10-30min of incubation.

细菌VI型分泌系统（Type VI Secretion System，T6SS）是一类广泛分布的分泌机制，对多种革兰氏阴性菌（Gram-negative bacteria）的竞争生存至关重要。杀伤并裂解竞争菌，可为宿主带来营养获取、通过DNA摄取获得新基因等竞争优势。本研究发现，具有自然感受态的拜氏不动杆菌（Acinetobacter baylyi）通过依赖T6SS的方式裂解猎物细胞，会导致该菌大量亚种群发生显著的丝状化现象。该现象依赖于裂解猎物细胞释放的基因组DNA，以及拜氏不动杆菌通过其感受态系统对该DNA的摄取过程。通过活细胞成像开展的单细胞水平分析显示，丝状化的拜氏不动杆菌细胞出现在两种菌的交界处。对拜氏不动杆菌转录组的分析以及转录报告基因的响应实验结果表明，摄取基因组DNA会引发强烈上调的SOS应答（SOS response），而该应答通常会导致细胞分裂停滞。通过竞争实验我们发现，亲本菌株会被缺失DNA摄取系统的菌株竞争性排斥，因为这类突变体不会出现依赖SOS应答的细胞分裂停滞现象。本研究数据表明，SOS应答带来的适应性代价可能会促使T6SS阳性细菌演化出降低DNA摄取能力的表型。我们还分析了拜氏不动杆菌与大肠杆菌（Escherichia coli，E. coli）共培养时的表达谱。我们对共培养10至30分钟的大肠杆菌与表达tae1（无其他效应因子）菌株、T6SS缺陷型拜氏不动杆菌的混合样本所制备的cDNA进行了深度测序。