反Shine-Dalgarno序列驱动了细菌的转化暂停和编码子选择
Gene-Wei Li1, Eugene Oh, Jonathan S Weissman
1Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA.
Nature
|March 30, 2012
概括
令人惊的是,细菌的翻译速度受到编码区域内的Shine-Dalgarno (SD) 序列的影响,而不是罕见的转移RNA. 这一发现揭示了内部SD类序列如何通过影响蛋白质合成率来驱动基因组进化.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 微生物学 微生物学
背景情况:
- 蛋白质合成期间的核糖体暂停会影响蛋白质折叠和准等共同翻译过程.
- 遗传密码的冗余性允许可变的翻译速率,但体内暂停机制仍然不太了解.
- 使者RNA序列显著影响核糖体暂停,影响蛋白质合成速度.
研究的目的:
- 为了研究基因组范围的景观和细菌中转化暂停的机制.
- 在体内确定核糖体暂停的序列特异性决定因素.
- 了解暂停对细菌基因组进化和蛋白质合成的影响.
主要方法:
- 采用全基因组的核糖体分析 (核糖体保护的mRNA片段的深度测序).
- 在大多数细菌转录中测量了高分辨率的核糖体密度概况.
- 一个直角的核糖体系统与改变的反-闪光-达尔加诺序列被用来探测暂停机制.
主要成果:
- 与预期相反,由罕见转移RNA解码的子在富含营养的条件下没有引起显著的转化暂停.
- 在编码区域内的类似Shine-Dalgarno (SD) 的序列被确定为普遍的核糖体暂停的主要原因.
- 有证据表明,mRNA与翻译核糖体的16S核糖体RNA之间的杂交导致暂停结果.
结论:
- 内部的SD类序列,而不是罕见的tRNA使用,是细菌转化率的关键决定因素.
- 细菌基因组表现出偏向的编码子使用,以避免内部SD站点,表明它们在编码序列进化中的驱动力.
- 这一发现为蛋白质合成的调节及其在细菌中的进化影响提供了新的视角.
相关概念视频
Translation in Prokaryotes
Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
Coordination of Gene Expression Processes in Bacteria
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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,...
Initiation of Translation
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
Initiation of Translation
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
Leaky Scanning
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...


