RNA landscape of the emerging cancer-bug Fusobacterium nucleatum

Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered much attention for its newly discovered prevalence in colorectal and breast cancer tissue. The growing interest in this emerging cancer-associated bacterium sharply contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. Post-transcriptional networks are also unknown, for fusobacteria lack all established small RNA-associated proteins. Here, we present high-resolution global RNA maps for two clinically relevant F. nucleatum subspecies for different growth conditions, and use these to uncover fundamental aspects of fusobacterial gene expression architecture and a previously unknown suite of noncoding RNAs. Developing a new vector for functional analysis of fusobacterial genes, we identify a conserved oxygen-induced small RNA as a post-transcriptional repressor of major porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum to colonize different compartments of the human body. Overall design: Samples of different growth stages were taken for RNA extraction. Isolated RNA was used for cDNA library generation following the dRNA-seq protocol.

核梭杆菌（Fusobacterium nucleatum）长期以来被认定为口腔微生物群（oral microflora）的组成组分，近期因在结直肠癌（colorectal cancer）与乳腺癌（breast cancer）组织中被发现广泛定植而受到广泛关注。学界对这一新兴癌症相关细菌的研究兴趣与日俱增，但与之形成鲜明反差的是，我们对其基础基因表达特征与生理响应的认知仍极为匮乏。鉴于梭杆菌缺乏所有已被确认的小RNA相关蛋白（small RNA-associated proteins），其转录后调控网络（post-transcriptional networks）同样尚未被阐明。本研究针对两种临床相关的核梭杆菌亚种（F. nucleatum subspecies），在不同生长条件下绘制了高分辨率全局RNA图谱（global RNA maps），并借此揭示了梭杆菌基因表达调控的核心架构，以及此前未被发现的一系列非编码RNA（noncoding RNAs）。我们开发了一款用于梭杆菌基因功能分析（functional analysis）的新型载体（vector），并借此鉴定出一种保守的氧诱导小RNA（oxygen-induced small RNA），其可作为主要孔蛋白（porin）FomA的转录后阻遏因子（post-transcriptional repressor）。本研究成果为阐明核梭杆菌定植于人体不同解剖部位的调控网络迈出了关键一步。实验设计：采集不同生长阶段的样本用于RNA提取，分离得到的RNA依照直接RNA测序（dRNA-seq）实验方案构建cDNA文库（cDNA library）。