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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Substrate-dependent effects of quaternary structure on RNase E activity.

Christopher J Moore1, Hayoung Go1,2, Eunkyoung Shin2

  • 1Department of Genetics, Stanford University, Stanford, California 94305, USA.

Genes & Development
|January 15, 2021
PubMed
Summary

RNase E enzyme activity on long RNA is regulated by its quaternary structure. A mutation and AmiC protein enhance multimerization, affecting specific activity independently of RNA 5' end phosphorylation.

Keywords:
AmiCRNA stabilityRnedegradosomemultimerquaternary structure

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Area of Science:

  • Molecular Biology
  • Enzymology
  • Bacterial Genetics

Background:

  • RNase E (encoded by the rne gene) is a crucial multifunctional ribonuclease in E. coli.
  • Its catalytic activity arises from dimerized polypeptide chains forming a tetrameric quaternary structure.
  • Regulation of RNase E activity is essential for cellular processes.

Purpose of the Study:

  • To investigate the role of RNase E quaternary structure in substrate-specific activity.
  • To identify factors that modulate RNase E multimerization and function.
  • To understand the mechanism of substrate length-dependent regulation.

Main Methods:

  • Site-directed mutagenesis to create the E429G catalytic region mutation.
  • Biochemical assays to measure RNase E activity on various RNA substrates.
  • Analysis of RNase E interaction with Amidase C (AmiC).

Main Results:

  • The E429G mutation and AmiC protein enhance RNase E multimerization.
  • Enhanced multimerization selectively increases specific activity on long RNA substrates, not short oligonucleotides.
  • This regulation is independent of the RNA substrate's 5' terminus phosphorylation state.

Conclusions:

  • RNase E quaternary structure plays a critical role in substrate length-dependent regulation.
  • Both cis-acting (mutation) and trans-acting (AmiC) factors can modulate RNase E activity through altered multimerization.
  • These findings reveal novel regulatory mechanisms for essential bacterial enzymes.