超转录组学揭示了海洋水柱中独特的微生物小RNA
Yanmei Shi1, Gene W Tyson, Edward F DeLong
1Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Nature
|May 16, 2009
概括
超转录学研究表明,许多微生物RNA序列都是小RNA (sRNA),包括新型RNA. 这些sRNA在微生物适应和环境相关的过程中发挥作用,例如营养获取.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 甲基转录学研究分析微生物基因表达直接从环境样本.
- 之前的分析发现了许多未知的RNA序列,表明未表征的蛋白质.
研究的目的:
- 调查微生物转录基因数据中发现的以前未被描述的互补DNA序列的性质.
- 识别和描述新型小RNA (sRNA) 和它们在自然微生物群落中的潜在功能.
主要方法:
- 来自自然微生物组合的总RNA的热测序对补充DNA序列的分析.
- 将假定sRNAs (psRNAs) 映射到微生物基因组的基因间区域.
- 对调节功能指标的二次结构和侧边基因的评估.
- 检查深度依赖变异和psRNAs的基因组特异映射.
主要成果:
- 在元转录基因数据集中的cDNA序列中有很大一部分是已知的小RNA和小RNAs (sRNAs).
- 新的psRNA映射到基因间区域,具有保存的二次结构,并且靠近潜在的调节基因.
- psRNA变异与分类学分布相关,并表明在利基适应中的作用.
- 对Pelagibacter的分析揭示了psRNA中已知的和新的调节元素.
结论:
- 超转录组学是发现微生物群体中sRNA的多样性,分布和丰富性的强大工具.
- 已识别的sRNA参与了关键的环境过程,包括碳代谢和营养获取.
- 这项研究扩大了我们对微生物调节网络和适应策略的理解.
相关概念视频
Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Translational Regulation
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
Deep Sea Microbial Ecology
The deep ocean and its underlying sediments represent vast, largely unexplored microbial habitats that extend far beyond the sunlit photic zone. The photic (euphotic) zone typically spans the upper ~100–200 meters of pelagic waters in the open ocean, but its depth varies geographically and seasonally, where sufficient light supports photosynthetic life. Below this lies the deep sea, spanning roughly 1000–6000 meters (bathypelagic to abyssal zones), with deeper hadal trenches extending beyond...


