一种通过结合黄素单核苷酸（FMN）来控制基因表达的信使核糖核酸（mRNA）结构。
An mRNA structure that controls gene expression by binding FMN.
作者信息
Winkler Wade C, Cohen-Chalamish Smadar, Breaker Ronald R
机构信息
Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.
出版信息
Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15908-13. doi: 10.1073/pnas.212628899. Epub 2002 Nov 27.
Abstract
The RFN element is a highly conserved domain that is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. We report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. Our results also indicate that in Bacillus subtilis, the riboswitch most likely controls gene expression by causing premature transcription termination of the ribDEAHT operon and precluding access to the ribosome-binding site of ypaA mRNA. Sequence and structural analyses indicate that the RFN element is a natural FMN-binding aptamer, the allosteric character of which is harnessed to control gene expression.
摘要
RFN元件是一个高度保守的结构域，常见于编码黄素单核苷酸（FMN）生物合成和转运蛋白的原核mRNA的5'非翻译区。我们报告称，该结构域作为一种代谢物依赖性核糖开关的受体，在没有蛋白质的情况下直接结合FMN。我们的结果还表明，在枯草芽孢杆菌中，该核糖开关很可能通过导致ribDEAHT操纵子的转录提前终止并阻止ypaA mRNA的核糖体结合位点被识别来控制基因表达。序列和结构分析表明，RFN元件是一种天然的FMN结合适体，其变构特性被用于控制基因表达。
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本文引用的文献
1
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Nature. 2002 Oct 31;419(6910):952-6. doi: 10.1038/nature01145. Epub 2002 Oct 16.
2
Genetic control by a metabolite binding mRNA.
Chem Biol. 2002 Sep;9(9):1043. doi: 10.1016/s1074-5521(02)00224-7.
3
Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions.
Bioessays. 2002 Aug;24(8):700-7. doi: 10.1002/bies.10125.
4
tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.
Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11121-6. doi: 10.1073/pnas.162366799. Epub 2002 Aug 6.
5
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
Nucleic Acids Res. 2002 Jul 15;30(14):3141-51. doi: 10.1093/nar/gkf433.
6
Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures.
Arch Microbiol. 2002 Jun;177(6):433-40. doi: 10.1007/s00203-002-0407-5. Epub 2002 Apr 3.
7
RNA expression analysis using an antisense Bacillus subtilis genome array.
J Bacteriol. 2001 Dec;183(24):7371-80. doi: 10.1128/JB.183.24.7371-7380.2001.
8
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Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9465-7. doi: 10.1073/pnas.181334498.
9
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10
Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes.
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