Wehner Stefanie, Mannala Gopala K, Qing Xiaoxing, Madhugiri Ramakanth, Chakraborty Trinad, Mraheil Mobarak A, Hain Torsten, Marz Manja
Faculty of Mathematics and Computer Science, Friedrich-Schiller-University Jena, Jena, Germany.
Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.
PLoS One. 2014 Oct 6;9(10):e108639. doi: 10.1371/journal.pone.0108639. eCollection 2014.
The Gram-positive bacterium Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. L. monocytogenes causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. Listeriosis has one of the highest mortality rates (up to 30%) of all food-borne infections. This human pathogenic bacterium is an important model organism for biomedical research to investigate cell-mediated immunity. L. monocytogenes is also one of the best characterised bacterial systems for the molecular analysis of intracellular parasitism. Recently several transcriptomic studies have also made the ubiquitous distributed bacterium as a model to understand mechanisms of gene regulation from the environment to the infected host on the level of mRNA and non-coding RNAs (ncRNAs). We have used semiconductor sequencing technology for RNA-seq to investigate the repertoire of listerial ncRNAs under extra- and intracellular growth conditions. Furthermore, we applied a new bioinformatic analysis pipeline for detection, comparative genomics and structural conservation to identify ncRNAs. With this work, in total, 741 ncRNA locations of potential ncRNA candidates are now known for L. monocytogenes, of which 611 ncRNA candidates were identified by RNA-seq. 441 transcribed ncRNAs have never been described before. Among these, we identified novel long non-coding antisense RNAs with a length of up to 5,400 nt e.g. opposite to genes coding for internalins, methylases or a high-affinity potassium uptake system, namely the kdpABC operon, which were confirmed by qRT-PCR analysis. RNA-seq, comparative genomics and structural conservation of L. monocytogenes ncRNAs illustrate that this human pathogen uses a large number and repertoire of ncRNA including novel long antisense RNAs, which could be important for intracellular survival within the infected eukaryotic host.
革兰氏阳性菌单核细胞增生李斯特菌是李斯特菌病的病原体，李斯特菌病是一种严重的食源性感染，其特征为流产、败血症或脑膜脑炎。单核细胞增生李斯特菌可引发发热性肠胃炎疫情，并导致人类社区获得性细菌性脑膜炎。在所有食源性感染中，李斯特菌病的死亡率最高（可达30%）。这种人类致病细菌是用于研究细胞介导免疫的生物医学研究的重要模式生物。单核细胞增生李斯特菌也是用于细胞内寄生分子分析的特征最明确的细菌系统之一。最近，几项转录组学研究也将这种广泛分布的细菌作为模型，以在mRNA和非编码RNA（ncRNA）水平上了解从环境到受感染宿主的基因调控机制。我们使用半导体测序技术进行RNA测序，以研究单核细胞增生李斯特菌在细胞外和细胞内生长条件下的ncRNA库。此外，我们应用了一种新的生物信息学分析流程进行检测、比较基因组学和结构保守性分析，以鉴定ncRNA。通过这项工作，目前已知单核细胞增生李斯特菌共有741个潜在ncRNA候选位点，其中611个ncRNA候选物是通过RNA测序鉴定的。441个转录的ncRNA此前从未被描述过。在这些ncRNA中，我们鉴定出了长度达5400 nt的新型长链非编码反义RNA，例如与编码内化素、甲基化酶或高亲和力钾摄取系统（即kdpABC操纵子）的基因相对的反义RNA，这些通过定量逆转录聚合酶链反应分析得到了证实。单核细胞增生李斯特菌ncRNA的RNA测序、比较基因组学和结构保守性分析表明，这种人类病原体使用大量的ncRNA库，包括新型长链反义RNA，这可能对其在受感染真核宿主体内的细胞内存活很重要。
