Biology subjects

Goringer, H. U.

Publications and source records attributed to Goringer, H. U..

3 recordsLinked to original sources

bioRxiv2023

Nanopore-based direct RNA sequencing of the Trypanosoma brucei transcriptome identifies novel lncRNAs

Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression posttranscriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example, by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized today. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known because of the inherent cDNA recoding and DNA amplification limitations of short-read RNA sequencing. Here we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome T. brucei with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 109 of which are stage-specifically expressed. We also present insights into the complexity of the T. brucei transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms to provide a bias-free understanding of the intricate RNA landscape in T. brucei.

molecular biology↗

bioRxiv2017

Surface-driven RNA-refolding by the OB-fold proteins of the Trypanosoma brucei editosome

RNA editing in African trypanosomes represents an RNA-processing reaction that generates functional mitochondrial transcripts from sequence-deficient pre-mRNAs. The reaction is catalyzed by a macromolecular protein complex known as the editosome. Editosomes have been demonstrated to execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis of this activity is unknown. Here we test five OB-fold proteins of the editosome as potential candidates. We show that the different proteins interact by hetero-oligomerization and we demonstrate that all proteins execute RNA-chaperone activity. Activity differences correlate with the surface areas of the proteins and map predominantly to the intrinsically disordered subdomains of the polypeptides. To provide a structural context for our findings we present a coarse-grained model of the editosome. The model suggests that an inner core of catalytically active editosome components is separated from an outer shell of IDP-domains that act as RNA-remodeling sites.

molecular biology↗

bioRxiv2017

The 2D-structure of the T. brucei pre-edited RPS12 mRNA is not affected by macromolecular crowding

Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert nucleotide-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D-folds, however, it is not known whether these structures resemble the in vivo folds given the extreme \"crowding\" conditions within the mitochondrion. Here we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution. We demonstrate that crowding has no impact on the 2D-fold and we conclude that the MFE-structure in dilute solvent conditions represents a good proxy for the folding of the pre-mRNA in its mitochondrial solvent context.

molecular biology↗