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Ribozymes02:47

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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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Crenarchaeota, a prominent phylum of Archaea, is remarkable for its ability to thrive in extreme environments characterized by high temperatures and acidity. These microorganisms inhabit sulfuric hot springs, volcanic systems, and submarine hydrothermal vents, where temperatures often exceed 100°C. The unique adaptations of Crenarchaeota not only allow survival under such extreme conditions but also provide insights into the mechanisms of life in primordial Earth-like...
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Hammerhead Ribozymes in Archaeal Genomes: A Computational Hunt.

Angela Gupta1, D Swati2,3

  • 1Department of Bioinformatics, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India.

Interdisciplinary Sciences, Computational Life Sciences
|January 14, 2016
PubMed
Summary

This study identified four hammerhead ribozymes (HHRs) in Archaea, specifically in Thaumarchaeota and Euryarchaeota. The research highlights a scarce presence of HHRs in Archaea, suggesting alternative regulatory mechanisms.

Keywords:
Catalytic RNACatalytic coreHammerhead ribozymesRibozyme

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Area of Science:

  • * Molecular Biology
  • * Bioinformatics
  • * Genomics

Background:

  • * Hammerhead ribozymes (HHRs) are self-cleaving RNA molecules with a conserved catalytic core and three helical domains.
  • * Initially discovered in plant viruses, HHR sequences are now recognized across diverse taxa, including eukaryotes and prokaryotes, where they regulate various cellular functions.
  • * The Archaeal domain, a distinct domain of life, has been less explored for the presence and function of HHRs.

Purpose of the Study:

  • * To identify and characterize hammerhead ribozymes (HHRs) within the Archaeal domain using comprehensive bioinformatics approaches.
  • * To investigate the structural and functional conservation of identified Archaeal HHRs, particularly their catalytic core.
  • * To assess the prevalence of HHRs across different archaeal phyla and infer potential roles in gene regulation.

Main Methods:

  • * Employed three distinct bioinformatics strategies to screen Archaeal genomes for HHR sequences.
  • * Conducted 3-D structure analysis and free energy calculations to validate putative HHR candidates.
  • * Analyzed the conservation of catalytic core motifs and identified variations in identified HHR instances.

Main Results:

  • * Discovered four putative hammerhead ribozymes (HHRs) of type I and type II within the Thaumarchaeota and Euryarchaeota phyla.
  • * Confirmed the similarity of these Archaeal HHRs to known HHRs, with conserved catalytic cores essential for cleavage activity.
  • * Observed compensatory variations within the catalytic cores of some identified HHRs.
  • * Found no instances of HHRs in the Crenarchaeota phylum.

Conclusions:

  • * Hammerhead ribozymes (HHRs) are present but scarce in the Archaeal domain, with identified instances in Thaumarchaeota and Euryarchaeota.
  • * The identified Archaeal HHRs possess conserved catalytic cores, suggesting retained functionality, though variations exist.
  • * The limited occurrence of HHRs in Archaea implies that other non-coding RNA elements, such as RNase P, may play more prominent roles in gene regulation within this domain.