Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.
Present address: Public Health England, 61 Colindale Avenue, London, NW9 5EQ, England.
BMC Genomics. 2017 Nov 16;18(1):882. doi: 10.1186/s12864-017-4242-0.
Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens.
We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation.
Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria.
小调控 RNA（sRNAs）广泛存在于细菌中，在许多重要的生理和适应过程中发挥关键作用。研究它们的进化并筛选与其他基因组特征的共进化事件，是更好地了解它们的起源并评估它们之间普遍存在的功能或适应性关系的有力方法。然而，细菌病原体中 sRNA 与编码基因的进化和共进化研究还很少。
我们设计了一种稳健且通用的系统发生基因组学方法，该方法使用在一组注释基因组中观察到和推断的存在-缺失模式来检测 sRNA 和蛋白质编码基因之间的相关性进化。我们将此方法应用于 79 个李斯特菌属的完整基因组上，鉴定了 52 个辅助 sRNA，其中大多数存在于李斯特菌共同祖先中，并在李斯特菌进化过程中丢失。我们检测到 23 个 sRNA 和 52 个编码基因之间存在显著的共进化关系，并推断出李斯特菌 sRNA-编码基因共进化网络。我们对与细胞壁蛋白和毒力因子编码基因共进化的 12 个 sRNA 进行了特征描述，其中一个特定于李斯特菌属物种的 sRNA rli133 与参与致病性或与宿主细胞相互作用的基因共进化，可能作为直接的负转录后调控。
我们的方法能够识别潜在参与致病性和宿主相互作用的候选 sRNA，这与最近对已知致病性因子的发现一致。我们强调了四个与七个肠毒素基因共进化的 sRNA，其中一些是李斯特菌中的重要毒力因子。
