通过细菌转录因子PdxRR对DNA识别机制的结构洞察
Ida Freda1, Cécile Exertier2, Anna Barile2
1Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.
Nucleic acids research
|June 28, 2023
概括
研究人员阐明了转录因子PdxR如何与DNA结合,以调节醇5'-酸盐 (PLP) 生物合成. 关键因素包括静电相互作用和DNA曲,指导全的识别过程.
科学领域:
- 分子生物学分子生物学
- 结构生物学 结构生物学
- 生物化学 生物化学
背景情况:
- 蛋白质-DNA识别对于细胞过程至关重要.
- 细菌的转录因子PdxR调节了pyridoxal 5 ext3d ext27 ext2dphosphate (PLP) 的生物合成.
- 了解PdxR的DNA结合机制,可以了解MocR家族的转录因子.
研究的目的:
- 解读驱动细菌转录因子PdxR.DNA识别和结合的相互作用.
- 阐明PdxR-DNA复合体的结构和动态方面.
- 澄清holo-PdxR的DNA结合模式和MocR家族的调控特征.
主要方法:
- 单颗粒冷电子显微镜 (cryo-EM) 用于捕获PdxR-DNA复合体对应物.
- 进行X射线晶体学以了解决apo-PdxR结构.
- 使用突变DNA序列和PdxR变异的结合分析.
主要成果:
- 通过冷EM分离了PLP-PdxR-DNA复合体的三个不同的符合者.
- 一个晶体结构揭示了在PLP结合时的效应域过渡.
- 电静电相互作用和DNA曲被确定为PdxR-DNA全质识别的关键.
结论:
- 该研究详细介绍了PdxR-DNA复合体的结构和动态.
- 澄清了Holo-PdxRDNA结合和MocR家族调节的机制.
- 静电力和DNA的内在不对称性在指导PdxR结合中起着关键作用.
相关概念视频
Bacterial RNA Polymerase
29.7K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.7K
Transcription in Prokaryotes
102
Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.Initiation of TranscriptionIn bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow...
102
Bacterial Transcription
28.6K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.6K
Cooperative Binding of Transcription Regulators
6.5K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.5K
DNA Bacteriophages
61
Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
61
Prokaryotic Transcriptional Activators and Repressors
21.2K
The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
Transcription of prokaryotic...
21.2K


