Laboratory of RNA Biology of Protists (Zdeněk Paris)
Head: RNDr. Zdeněk Paris, PhD.
Joined the BCAS: February 2014,
2011–2014: postdoctoral researcher at the Ohio State University, Columbus, Ohio, USA (Research topic: tRNA modification, editing and splicing in Trypanosoma brucei, Supervisor: Dr. Juan D. Alfonzo)
Mission of the lab: Our group studies various aspects of RNA biology of protozoan parasite Trypanosoma brucei and related flagellates. In those early evolved unicellular organisms most genes are post-transcriptionally regulated. Consequently, posttranscriptional processing of RNA becomes of a great importance in order to regulate complex life cycles of these pathogens. We are mainly interested in processes such as tRNA modifications, nuclear tRNA export and role of the only intron containing tRNA in trypanosomes. Our long term goal is an identification of unique mechanisms of RNA metabolism. We believe this will help us to reveal new drug targets to combat diseases caused by trypanosomatid parasites.
P JAC Project - RNA4T: RNA for therapy
RNA-based drugs could overcome the limits of conventional small-molecule drugs modulating protein functions by targeting their active sites, which are restricted by the druggability of protein targets, which harbors less than 30% of the 2500 disease-related proteins. RNA therapies might have a number of other inherent advantages, such as low immunogenicity, rapid design and adaptivity, fast and efficient production, long-term effect, and usefulness for rare diseases. Most RNA therapeutics rely on base-pairing of RNA analogs in various antisense mechanisms or, alternatively, the mRNA-based drugs are transiently translated. However, the full potential of this modern and safe technology remains unexplored as there are less than a dozen FDA-approved RNA therapeutics.
The project brings together 14 research groups working on several disease models and mastering different methodological approaches in organic chemistry, biochemistry and cell and molecular biology with a common denominator in RNA biology. It thus gives us a unique opportunity to conduct highly interdisciplinary research that will strengthen our efforts to firmly establish the Czech Republic on the map of RNA therapeutics development and thus significantly increase its scientific prestige.
About the project
Project RNA for therapy is funded by Programme Johannes Amos Comenius managed by the Ministry of Education, Youth and Sports of the Czech Republic.
Registration number: CZ.02.01.01/00/22_008/0004575
Implementation date: 1. 1. 2024 – 31. 10. 2028
Budget: CZK 499 640 882, 63
Main Beneficiary: Institute of Organic Chemistry and Biochemistry of CAS
Scientific manager: Prof. Ing. Michal Hocek, CSc. DSc.
Project goals
The overall goal of the project is to build an RNA-focused innovation ecosystem where excellent labs will realize strong research programs in RNA biology and RNA therapeutics in cooperation with industrial partners and qualified intellectual property and technology transfer management to make the Czech Republic a recognized player in RNA therapeutics and strengthen its competitiveness in the pharmaceutical industry.
Link: https://www.uochb.cz/en/rna4t
PhD and postdoc position in Molecular Parasitology 2024
Research projects
Queuosine: The role of an essential tRNA modification in parasitic protist Trypanosoma brucei
Transfer RNAs are typical for the large number of posttranscriptional modifications. Most of the tRNA modifications are present in the anticodon loop, which have crucial role in proper translation of proteins. Queuosine is one of the most complex tRNA modifications. Despite its omnipresence among bacteria and eukaryotes, role of queuosine tRNA modification is not clear. The main aim of this project is to evaluate the function and subunit composition of the enzyme responsible for queuosine formation in T. brucei. Using the RNAi knock-down strategy we want to address the principal question regarding the role of queuosine tRNA modification with respect to biology and physiology of this protozoan parasite.
Role of the only tRNA intron in trypanosomatids
In yeast Saccharomyces cerevisiae and other model organisms, 20% of all tRNAs contain introns. Their removal is an essential step in the maturation of tRNA precursors. In T. brucei, there is only one intron containing tRNA: tRNATyrGUA. Since this tRNA is responsible for decoding all tyrosine codons, intron removal is essential for viability. Using molecular and biochemical approaches, several non-canonical editing events were identified within the intron-containing tRNATyrGUA. The RNA editing involves guanosine-to-adenosine transitions (G to A) and an adenosine-to-uridine transversion (A to U), which are both necessary for proper processing of the intron. We have been obtaining tRNA intron sequences from our collection of newly identified trypanosomatid species. We hope this will help us to understand the process of RNA editing and ultimately identify biological function for the presence of the only intron containing tRNA in these organisms.
Nuclear export of tRNAs in trypanosomes
Regulation of tRNA export from the nucleus to the cytoplasm might be an additional post-transcriptional event involved in gene regulation. However, our knowledge about tRNA export in trypanosomes is very limited. Although export factors of higher eukaryotes are reported to be conserved; only a few orthologs can be easily identified in the genome of T. brucei. Thus, we are going to employ methods of molecular biology and biochemistry to identify and characterize the tRNA export machinery in trypanosomes.
Euglena gracilis as a new model organism
Euglena gracilisis the evolutionarily closest free-living photosynthetic relative of the kinetoplastid parasites that cause serious diseases including African sleeping sickness, leishmaniasis and Chagas disease. Hence, this protist provides an evolutionary link to understand the emergence of several unique molecular processes in kinetoplastids. Moreover, Euglena spp. is also an ecologically significant, yet severely understudied protist. Despite the efforts of several laboratories, the Euglena genome project has not yet been assembled and the lack of tools for forward and reverse genetics makes Euglena refractory for molecular studies. It was shown recently that electroporation of dsRNA into its cells leads to specific degradation of the target sequence, although this process is only temporary, being lost after few generations. In our lab, we are going to analyze the genome project data with the emphasis on mitochondrial proteome, RNA editing and processing, and make a comparative analysis with the genomes of the parasitic groups within the phylum Euglenozoa. Moreover we will design and establish a transfection protocol of E. gracilis with the aim to achieve over-expression from a stably integrated construct. Provided this phase was successful, we will also generate cell line with T7-TR background, representing a tool for functional analysis of genes of interest using the RNAi approach.
