Molecular biology a genomics

The research programme consists of eight main activities

Main activity 1 Identification and characterisation of new or poorly studied viruses

Building on the research already started, viruses of selected protist groups, mainly trypanosomatids and unicellular algae, will be studied to elucidate their diversity, evolution and interaction with the hosts. We expect to discover entirely new viruses through the analysis of genomic data. Metagenomic data will also be analyzed to map the true diversity of selected viral groups and their gene repertoire, with special attention to Nucleocytoviricota and polinton-like viruses.

Specific activities and goals:

• Bioinformatic analysis of RNA diversity of viruses of trypanosomatids and unicellular algae in transcriptomic databases
• Detailed comparative and phylogenetic analyses of the identified candidate viral sequences
• Targeted search for selected viral groups in metagenomes and metatranscriptomes
• Targeted in vitro and in vivo studies of newly discovered viruses

Main activity 2 Identification and characterization of virulence factors of leishmaniases

Here, we will build on a very well-established research programme to advance our understanding of the molecular determinants of virulence of human pathogens of the genus Leishmania, particularly using the model species L. mexicana. Additional candidates for virulence factors will be tested using a wide arsenal of in vitro and in vivo functional genomics methods. This research line will include further study of the physiological function of the enzyme catalase in trypanosomatids to understand the role of the loss of this enzyme in the evolution of the dixenic life cycle of Leishmania.

Specific activities and goals:

• Bioinformatic analyses of potential virulence factors of leishmaniases
• Testing the effects of potential antiparasitics on leishmania physiology
• Functional analysis of leishmania virulence potentiation factors
• Study of the physiological function of the enzyme catalase in trypanosomatids

Main activity 3 Comprehensive research on protist endosymbionts

The biology of prokaryotic endosymbionts of selected groups of protists, mainly trypanosomatids and unicellular algae, will be studied using genomic and other methods. In the case of kinetoplastids it will be mainly the systems "Novymonas esmeraldas - Ca. Pandoraea novymonadis" and "Angomonas deanei - Ca. Kinetoplatobacterium sp." In particular, this research should reveal the molecular mechanisms behind the respective endosymbiotic relationships.

Specific activities and goals:

• Selection of promising host-endosymbiont model systems
• Basic characterization of hosts and their endosymbionts
• Taxonomic and phylogenetic characterization
• Morphological and ultrastructural characterization
• Genomic characterization of hosts and their endosymbionts
• Functional characterization of endosymbiont-host relationships

Main activity 4 Stablishing the possibility of targeted genetic manipulations in selected protist models

The introduction of targeted genetic manipulation techniques, primarily based on the CRISPR-Cas system, will substantially expand the possibilities of functional genomic research in selected important model unicellular eukaryotes. We will primarily focus on specific representatives of trypanosomatids, e.g. Vickermania ingenoplastis or Novymonas esmeraldas, characterized by unique biological features revealed by existing genomic and transcriptomic analyses. The unique translational system of trypanosomatids of the genus Blasthocrithidia with position-dependent meaning of certain codons will also be further studied within this research direction.  

Specific activities and goals:

• Optimisation of cultivation and selection conditions
• Development of protocols for the preparation of targeted knock-in mutants
• Development of protocols for regulatable expression of transgenes
• Subsequent experiments with the prepared mutants

Main activity 5 Characterization of unusual functional complexes and pathways of endosymbiotic organelles

Building on previous results, selected components of mitochondria and plastids of non-standard model systems will be studied in detail, representing new and previously unstudied functional aspects of these organelles. Examples include the newly discovered mitochondrial system based on the bacterial T2SS or a previously uncharacterized metabolic pathway encoded by a specific operon in the plastid genome of some eustigmatophyte algae.

Specific activities and goals:

• In silico characterization of organellar proteomes
• Experimental characterization of organellar proteomes
• Functional characterization of selected organellar components
• Evolutionary and phylogenetic analyses

Main activity 6 Genomic characterization of new organismal lineages

Genomic data will be obtained from organisms representing poorly studied groups of microbial eukaryotes, including previously unknown and newly described species. The results will improve understanding of the phylogenetic diversity of eukaryotes and the evolution of their gene repertoire.

Specific activities and goals:

• Isolation and cultivation of new eukaryotic microorganisms
• Basic biological characterization of the new organisms
• Generation of reference genomic data
• Phylogenomic analyses

Main activity 7 Comparative genomic analyses of novel genes

The history of the gene repertoire in selected groups of eukaryotes will be reconstructed in order to understand the role of gene duplications, horizontal gene transfer and de novo origin of genes in the evolution of these groups. Special attention will be paid to the reconstruction of metabolic pathways and the identification of candidate proteins with novel enzyme activities that can then be characterized by experimental approaches.

Specific activities and goals:

• Comparative genomic analysis of gene repertoire
• In silico reconstruction of metabolic and other functional maps
• Identification of new targets for experimental investigation using phylogenetic profiling methods
• Experimental characterization of newly defined target genes

Main activity 8 New study and academic programmes

We will get accreditation for a new specialisation in the existing NMgr. degree programme and for a new habilitation and professorship programme in the field related to the Research Programme "Molecular Biology and Genomics".

Specific activities and goals:

• Accreditation of the new specialization in the NMgr. degree programme “Biology”; working title "Genome Biology and Bioinformatics"
• Accreditation of a new habilitation and professorship program; working title "Molecular Biology and Genomics"

Cooperation with other VPs

Due to the very strong interdisciplinary links, the VP1 research team collaborates with other research teams of the LERCO project:

• VP2 on identification and quantification of selected metabolites, determination of enzyme activity and other analyses of biological specimens
• VP3 on simulation and modelling of biologically active macromolecules
• VP6 on the preparation of a new PhD programme with the working title “Biomedicine”