Downregulation of the essential Rrp44 ribonuclease causes extensive ultra-structure cell modifications in Trypanosoma brucei

Abstract

AbstractRrp44 is a conserved eukaryotic protein showing endonuclease and exoribonuclease activity that plays essential functions in RNA maturation and degradation. In Trypanosoma brucei, depletion of Rrp44 (TbRrp44) blocks processing of large subunit ribosomal RNA precursors, leading to disruption of ribosome synthesis and inhibition of cell proliferation. We used a combination of molecular and chemical markers to investigate the fate of T. brucei cells upon knockdown of TbRrp44. In addition, synchrotron deep UV microscopy and cryo soft X-ray tomography were used to investigate cell morphology and ultra-structure modifications. Downregulation of TbRrp44 results in induction of autophagy, inactivation of mitochondria and expansion of acidic and lysosome-derived vacuoles in parallel with enlargement of cell size. Nuclei also increase in size without changes in DNA content. 3D tomographic reconstructions revealed extreme vacuolation of the cytoplasm of TbRrp44 knockdown cells and general alteration of organelles. Calcium-containing vesicles (acidocalcisomes) were identified by X-ray absorption near-edge structure spectra (XANES) of calcium L2,3 edges on fully hydrated cells. The volumes of acidocalcisomes and lipid droplet were quantified from 3D reconstructions. Both were found in higher number and with larger volumes in TbRrp44 knockdown cells. These multiple defects indicate that a combination of signals, starting from nucleolar stress and activation of autophagy, converge to induce lysosome expansion. With time, the cytoplasm is taken up by lysosome-derived vacuoles, which may be one of the final stages leading to cell death triggered by TbRrp44 depletion. These studies provide the first evidence on the ultra-structure cell modifications caused by Rrp44 ribonuclease deficiency.Author summaryTrypanosoma brucei is a parasitic protozoan belonging to the Kinetoplastidae Class, which displays distinct cellular, genomic and molecular features. These features include extra intervening sequences in the large subunit ribosomal RNA (rRNA) precursor that are not found in the homologous rRNA precursor of host cells. Genetic downregulation of the T. brucei Rrp44 (TbRrp44) ribonuclease shows that it is required for accurate excision of these intervening sequences to produce mature rRNA molecules. Here, we have used a multidisciplinary approach based on molecular and chemical markers, synchrotron deep UV microscopy and cryo soft X-ray tomography to show that downregulation of TbRrp44 leads to a series of cellular alterations that eventually result in cell death. Mitochondrial activity is particularly affected in parallel with induction of autophagy response, increase in size of the cell and of organelles such as acidocalcisomes and lipid droplets, and with a massive expansion of lysosome-derived vacuoles. The ultrastructural modifications that take place in T. brucei cells are nicely highlighted in the 3D reconstructions generated using cryo soft X-ray tomography images. This study provides new insights into the multiple cellular consequences of Rrp44 ribonuclease depletion in T. brucei parasites.