LF82, an adherent-invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn's disease, an inflammatory bowel disease of unknown etiology. Although AIEC phenotypes differ from those of ‘commensal’ or pathogenic E. coli, work has failed to identify genetic features accounting for these differences. We have investigated a natural, but rare, single nucleotide polymorphism (SNP) in LF82 present within the highly conserved rpoD gene, encoding σ70 [primary sigma factor, RNA polymerase (RNAP)]. We demonstrate that σ70 D445V results in transcriptomic and phenotypic changes consistent with LF82 phenotypes, including increased antibiotic resistance and biofilm formation and increased capacity for methionine biosynthesis. RNA-seq analyses comparing σ70 V445 versus σ70 D445 identified 24 genes upregulated by σ70 V445 in both LF82 and the laboratory E. coli K-12 strain MG1655. Using in vitro transcription, we demonstrate that σ70 D445V directly increases transcription from promoters for several of the up-regulated genes and that the presence of a 16 bp spacer and -14 G:C is associated with this increase. The position of D445V within RNAP suggests that it could affect RNAP/spacer interaction. Our work represents the first identification of a distinguishing SNP for this pathobiont and suggests an underrecognized mechanism by which pathobionts and strain variants can emerge.

中文翻译：

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单个罕见的 σ70 变体在大肠杆菌致病菌 LF82 中建立了独特的基因表达模式


LF82 是一种粘附性侵袭性大肠埃希菌 （AIEC） 致病菌，与克罗恩病有关，克罗恩病是一种病因不明的炎症性肠病。尽管 AIEC 表型与“共生”或致病性大肠杆菌的表型不同，但工作未能确定导致这些差异的遗传特征。我们研究了 LF82 中一种天然但罕见的单核苷酸多态性 （SNP），存在于高度保守的 rpoD 基因中，编码 σ70 [初级 Sigma 因子，RNA 聚合酶 （RNAP）]。我们证明 σ70 D445V 导致与 LF82 表型一致的转录组和表型变化，包括增加抗生素耐药性和生物膜形成以及增加蛋氨酸生物合成能力。比较 σ70 V445 与 σ70 D445 的 RNA-seq 分析发现，在 LF82 和实验室大肠杆菌 K-12 菌株 MG1655 中，有 24 个基因被 σ70 V445 上调。使用体外转录，我们证明 σ70 D445V 直接增加了几个上调基因的启动子的转录，并且 16 bp 间隔区和 -14 G：C 的存在与这种增加有关。D445V 在 RNAP 中的位置表明它可能会影响 RNAP/间隔区相互作用。我们的工作代表了首次确定了该致病因子的区分 SNP，并提出了一种未被充分认识的机制，通过该机制可以出现致病因子和菌株变体。