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Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates.

Giovanna Cesaro1,2, Heloisa Tramontin da Soler1, Eloise Pavão Guerra-Slompo1

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The essential ribonuclease Rrp44/Dis3, crucial for RNA processing and degradation, has a crystal structure revealed. This study shows TbRRP44 can degrade structured RNAs, expanding its known function in RNA metabolism.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Rrp44/Dis3 is a vital eukaryotic ribonuclease with both endo- (PIN) and exo- (RNB) nuclease domains, essential for RNA processing and degradation.
  • Depletion of Rrp44 in model organisms, including Trypanosoma brucei (TbRRP44), disrupts RNA metabolism, ribosome synthesis, and cell proliferation.

Purpose of the Study:

  • To elucidate the structural and mechanistic details of the exoribonucleolytic (RNB) module of TbRRP44.
  • To investigate the substrate specificity and RNA degradation capabilities of TbRRP44 and its Saccharomyces cerevisiae homologue.

Main Methods:

  • Determined the crystal structure of the exoribonucleolytic module of TbRRP44 in an active conformation.
  • Performed in vitro degradation assays using structured and non-structured RNA substrates.
  • Investigated the role of the PIN domain in RNA binding through deletion studies.

Main Results:

  • Revealed novel structural insights into the catalytic mechanism of the RNB domain, including the position of the second magnesium ion in the two-metal-ion catalytic site.
  • Demonstrated that TbRRP44 preferentially degrades uridine-rich, non-structured RNAs but can also degrade structured RNAs lacking a 3'-end overhang.
  • Showed that deletion of the TbRRP44 PIN domain differentially impairs RNA binding depending on the substrate type.

Conclusions:

  • The findings provide a detailed structural understanding of the RNB domain's catalytic mechanism and expand the known substrate range for Rrp44/Dis3 ribonucleases.
  • TbRRP44's ability to degrade structured RNAs suggests a broader role in RNA turnover than previously appreciated.
  • The PIN domain plays a significant role in substrate recognition and binding for TbRRP44.