Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides

The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis. However, the mechanisms used by S. meliloti to resist antimicrobial activity of plant peptides are poorly understood. To address this, we applied a global genetic approach using transposon mutagenesis followed by high-throughput sequencing (Tn-seq) to identify S. meliloti genes and pathways that increase or decrease bacterial competitiveness during exposure to the well-studied cationic NCR247 peptide and also to the unrelated model antimicrobial peptide polymyxin B. We identified 78 genes and several diverse pathways whose interruption alters S. meliloti resistance to NCR247. These genes encode the following: (i) cell envelope polysaccharide biosynthesis and modification proteins, (ii) inner and outer membrane proteins, (iii) peptidoglycan (PG) effector proteins, and (iv) non-membrane-associated factors such as transcriptional regulators and ribosome-associated factors. We describe a previously uncharacterized yet highly conserved peptidase, which protects S. meliloti from NCR247 and increases competitiveness during symbiosis. Additionally, we highlight a considerable number of uncharacterized genes that provide the basis for future studies to investigate the molecular basis of symbiotic development as well as chronic pathogenic interactions.模式豆科植物蒺藜苜蓿（Medicago truncatula）可表达超过700种根瘤特异性富半胱氨酸（nodule-specific cysteine-rich, NCR）信号肽，这些肽能够介导苜蓿中华根瘤菌（Sinorhizobium meliloti）分化为固氮类菌体。NCR肽对于反向重复缺失演化支（inverted-repeat-lacking clade, IRLC）豆科植物的成功共生至关重要，且与哺乳动物防御素具有序列相似性。除信号传导功能外，多数NCR肽在体外及体内均表现出抗菌活性。细菌对这类抗菌活性的抗性对于共生过程可能具有重要意义。然而，苜蓿中华根瘤菌抵御植物源肽抗菌活性的分子机制目前仍不甚明确。为解析这一科学问题，本研究采用转座子诱变结合高通量测序（transposon sequencing, Tn-seq）的全局遗传学筛选策略，在苜蓿中华根瘤菌中鉴定出在暴露于研究较为透彻的阳离子NCR247肽以及非同源模式抗菌肽多粘菌素B时，可影响细菌竞争力的基因与通路。本研究共鉴定出78个基因以及多条不同的通路，其功能缺失会改变苜蓿中华根瘤菌对NCR247的抗性水平。这些基因编码的蛋白包括：(i) 细胞包膜多糖生物合成与修饰相关蛋白；(ii) 内膜与外膜蛋白；(iii) 肽聚糖（peptidoglycan, PG）效应蛋白；以及(iv) 非膜结合因子，如转录调控因子与核糖体结合因子。本研究报道了一种此前未被表征但高度保守的肽酶，该酶可保护苜蓿中华根瘤菌免受NCR247的侵害，并提升其在共生过程中的竞争力。此外，本研究还筛选得到大量未被表征的基因，为后续开展共生发育以及慢性致病互作的分子机制研究奠定了基础。