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Insights into 6S RNA in lactic acid bacteria (LAB)
BMC Genetics ( IF 2.9 ) Pub Date : 2021-09-03 , DOI: 10.1186/s12863-021-00983-2
Pablo Gabriel Cataldo 1 , Paul Klemm 2 , Marietta Thüring 2 , Lucila Saavedra 1 , Elvira Maria Hebert 1 , Roland K Hartmann 2 , Marcus Lechner 2, 3
Affiliation  

6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.

中文翻译:

深入了解乳酸菌 (LAB) 中的 6S RNA

6S RNA 是细胞转录的调节剂,可调节细胞的新陈代谢。这种小的非编码 RNA 几乎存在于所有细菌中,并且是最丰富的转录本。乳酸菌 (LAB) 是一组具有很强生物技术相关性的微生物,通常通过发酵作为工业产品的起始培养物。一些菌株被用作益生菌,而另一些则代表潜在的病原体。该组中 6S RNA 的偶然报道已经表明了惊人的代谢影响。一个可以想象的想法是,具有 6S RNA 缺陷的 LAB 可能更快地代谢营养物质,正如对大肠杆菌的研究所推断的那样。这可以加速发酵过程,并有可能降低生产成本。同样,可能会产生更高水平的次生代谢物。这种可能性的证据来自关于枯草芽孢杆菌中产生表面活性素的初步发现,其功能类似于细菌素。其潜在的生物技术应用的先决条件是 6S RNA 在 LAB 中的一般表征。我们在整个乳酸杆菌目中提供了 6S RNA 的基因组注释。它为常见 6S RNA 特征的生物信息学表征奠定了基础。这包括二级结构、同线性、系统发育和产物 RNA 起始位点。典型的 6S RNA 结构由两侧为螺旋臂的中央凸起和用于产物 RNA 合成的模板位点形成。6S RNA 表现出强烈的同线保守性。它的两侧通常是复制相关重组蛋白 A 和通用应激蛋白 A。在超过三分之一的所有 6S RNA 基因中鉴定出分解代谢物反应元件。已知基于可用碳源调节基因表达。无法将反义转录物的存在作为 LAB 6S RNA 的一般特征来验证。尽管有大量的物种和 LAB 的异质性,但从结构和同线的角度来看,压力调节因子 6S RNA 都得到了很好的保护。这是第一种描述单一物种之外的 6S RNA 和短 6S RNA 衍生转录本的方法,涵盖了涵盖多个科的大型分类群。它产生了对该调节器的普遍见解,并补充了从其他细菌模式生物中得出的发现。无法将反义转录物的存在作为 LAB 6S RNA 的一般特征来验证。尽管有大量的物种和 LAB 的异质性,但从结构和同线的角度来看,压力调节因子 6S RNA 都得到了很好的保护。这是第一种描述单一物种之外的 6S RNA 和短 6S RNA 衍生转录本的方法,涵盖了涵盖多个科的大型分类群。它产生了对该调节器的普遍见解,并补充了从其他细菌模式生物中得出的发现。无法将反义转录物的存在作为 LAB 6S RNA 的一般特征来验证。尽管有大量的物种和 LAB 的异质性,但从结构和同线的角度来看,压力调节因子 6S RNA 都得到了很好的保护。这是第一种描述单一物种之外的 6S RNA 和短 6S RNA 衍生转录本的方法,涵盖了涵盖多个科的大型分类群。它产生了对该调节器的普遍见解,并补充了从其他细菌模式生物中得出的发现。这是第一种描述单一物种之外的 6S RNA 和短 6S RNA 衍生转录本的方法,涵盖了涵盖多个科的大型分类群。它产生了对该调节器的普遍见解,并补充了从其他细菌模式生物中得出的发现。这是第一种描述单一物种之外的 6S RNA 和短 6S RNA 衍生转录本的方法,涵盖了涵盖多个科的大型分类群。它产生了对该调节器的普遍见解,并补充了从其他细菌模式生物中得出的发现。
更新日期:2021-09-03
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