A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

RNA modification: A contemporary review of pseudouridine (Ψ) and its role in functional plant biology

Pseudouridine (Ψ) is a modified nucleoside present in diverse RNA species, including mRNA (messenger RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA) and tRNA (transfer RNA). In plants, Ψ serves a critical function in RNA modification, supporting the stability, structural integrity, and functionality of RNA molecules. This review provides the various roles that Ψ fulfils in the modification of plant RNA biology, encompassing effects on biosynthesis pathways, regulatory mechanisms, stability, and translation efficiency. Additionally, we discuss recent advancements in the dynamic regulation of Ψ deposition in response to environmental stimuli and stressors. Elucidating Ψ's roles contributes to the comprehension of plant biology and may facilitate developments in biotechnology and crop improvement.

TblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei

The protozoan parasite Trypanosoma brucei undergoes a complex life cycle, moving between its mammalian host and the blood-feeding tsetse fly vector. The two major surface proteins expressed by procyclic forms in the insect midgut, EP and GPEET procyclin, are transcribed from a polycistronic transcription unit by RNA polymerase I. Here we identify a long non-coding RNA, TblncRNA-23, that is encoded between the two procyclin genes. TblncRNA-23 localizes to the nucleolus and also associates with polysomes. Overexpression of TblncRNA-23 and its down regulation by RNAi or knockout (KO) identify EP and GPEET mRNAs as targets, among other mRNAs that changed abundance in the transition from early to late procyclic forms and from procylic to the metacylic forms, suggesting its role in regulating gene expression which accomapines or dictates of the parasite transitions within in its insect host. TblncRNA-23 interacts with its substrates via base-pairing using different domains. Purification of TblncRNA-23-associated proteins by RaPID identifies hundreds of proteins, including proteins translated from its target mRNAs, suggesting its association with translating ribosomes. Early and late procyclic forms differ in their social motility (SoMo) capabilities, which is essential for migration away from the insect midgut to enable parasite transmission. Overexpression of TblncRNA-23 results in hypermotility, whereas KO compromises this capacity, suggesting a regulatory role in SoMo. Moreover, silencing of the RNA abrogates the ability of the parasite to transform from procylic to the metacyclic forms affecting the parasite's potential to cycle between its hosts.

Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger

Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding of multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, are not compatible with newer RNA chemistry flowcells and the latest generation of graphics processing units (GPUs). To overcome these limitations, we introduce SeqTagger, a rapid and robust method that can demultiplex DRS data sets with 99% precision and 95% recall. We demonstrate the applicability of SeqTagger in both RNA002/R9.4 and RNA004/RNA chemistries and show its robust performance both for long and short RNA libraries, including custom libraries that do not contain standard poly(A) tails, such as Nano-tRNAseq libraries. Finally, we demonstrate that increasing the multiplexing up to 96 barcodes yields highly accurate demultiplexing models. SeqTagger can be executed in a standalone manner or through the MasterOfPores NextFlow workflow. The availability of an efficient and simple multiplexing strategy improves the cost-effectiveness of this technology and facilitates the analysis of low-input biological samples.

Ribosomes: from conserved origin to functional/medical mobility and heterogeneity

Ribosomes, the molecular machines that translate the genetic code from mRNA into proteins in all living cells, are highly structurally conserved across all domains of life and hence are believed to have evolved from a structurally unified pocket. Initially perceived as uniform cellular factories for protein synthesis, currently, ribosomes have emerged as more complex entities. Structural, medical and biochemical studies, including ours, have revealed significant variability in their compositions across tissues, species, functions and developmental stages, highlighting their multifunctional potential. Moreover, the diversity of ribosomes, their components and their associated biological factors challenge the traditional perception of uniform interactions under various conditions, including stress, and expose their mobility and heterogeneity. Evidence for their functional diversity can be seen even in modifications of ribosomal genes, where minor changes may play critical roles under stress or may lead to diseases called ribosomopathies, including Diamond-Blackfan anaemia, some types of cancer and Alzheimer's disease. Thus, through in-depth structural explorations, we improve the understanding of the mechanisms regulating protein biosynthesis in response to various environmental stressors. These findings should potentially reshape the perceptions of the various ribosomal roles.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

The zebrafish (Danio rerio) snoRNAome

Small nucleolar RNAs (snoRNAs) are one of the most abundant and evolutionary ancient group of functional non-coding RNAs. They were originally described as guides of post-transcriptional rRNA modifications, but emerging evidence suggests that snoRNAs fulfil an impressive variety of cellular functions. To reveal the true complexity of snoRNA-dependent functions, we need to catalogue first the complete repertoire of snoRNAs in a given cellular context. While the systematic mapping and characterization of "snoRNAomes" for some species have been described recently, this has not been done hitherto for the zebrafish (Danio rerio). Using size-fractionated RNA sequencing data from adult zebrafish tissues, we created an interactive "snoRNAome" database for this species. Our custom-designed analysis pipeline allowed us to identify with high-confidence 67 previously unannotated snoRNAs in the zebrafish genome, resulting in the most complete set of snoRNAs to date in this species. Reanalyzing multiple previously published datasets, we also provide evidence for the dynamic expression of some snoRNAs during the early stages of zebrafish development and tissue-specific expression patterns for others in adults. To facilitate further investigations into the functions of snoRNAs in zebrafish, we created a novel interactive database, snoDanio, which can be used to explore small RNA expression from transcriptomic data.

Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote

BACKGROUND

In trypanosomatids, a group of unicellular eukaryotes that includes numerous important human parasites, cis-splicing has been previously reported for only two genes: a poly(A) polymerase and an RNA helicase. Conversely, trans-splicing, which involves the attachment of a spliced leader sequence, is observed for nearly every protein-coding transcript. So far, our understanding of splicing in this protistan group has stemmed from the analysis of only a few medically relevant species. In this study, we used an extensive dataset encompassing all described trypanosomatid genera to investigate the distribution of intron-containing genes and the evolution of splice sites.

RESULTS

We identified a new conserved intron-containing gene encoding an RNA-binding protein that is universally present in Kinetoplastea. We show that Perkinsela sp., a kinetoplastid endosymbiont of Amoebozoa, represents the first eukaryote completely devoid of cis-splicing, yet still preserving trans-splicing. We also provided evidence for reverse transcriptase-mediated intron loss in Kinetoplastea, extensive conservation of 5' splice sites, and the presence of non-coding RNAs within a subset of retained trypanosomatid introns.

CONCLUSIONS

All three intron-containing genes identified in Kinetoplastea encode RNA-interacting proteins, with a potential to fine-tune the expression of multiple genes, thus challenging the perception of cis-splicing in these protists as a mere evolutionary relic. We suggest that there is a selective pressure to retain cis-splicing in trypanosomatids and that this is likely associated with overall control of mRNA processing. Our study provides new insights into the evolution of introns and, consequently, the regulation of gene expression in eukaryotes.

Ribosome Structural Changes Dynamically Affect Ribosome Function

Ribosomes were known to be multicomponent complexes as early as the 1960s. Nonetheless, the prevailing view for decades considered active ribosomes to be a monolithic population, in which all ribosomes are identical in composition and function. This implied that ribosomes themselves did not actively contribute to the regulation of protein synthesis. In this perspective, I review evidence for a different model, based on results showing that ribosomes can harbor different types of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) and, furthermore, need not contain a complete set of r-proteins. I also summarize recent results favoring the notion that such distinct types of ribosomes have different affinities for specific messenger RNAs and may execute the translation process differently. Thus, ribosomes should be considered active contributors to the regulation of protein synthesis.

Exploring pseudouridylation: dysregulation in disease and therapeutic potential

Pseudouridine (Ψ), the most abundant RNA modification, plays a role in pre-mRNA splicing, RNA stability, protein translation efficiency, and cellular responses to environmental stress. Dysregulation of pseudouridylation is linked to human diseases. This review explores recent insights into the role of RNA pseudouridylation alterations in human disorders and the therapeutic potential of Ψ. We discuss the impact of the reduction of Ψ levels in ribosomal, messenger, and transfer RNA in RNA processing, protein translation, and consequently its role in neurodevelopmental diseases and cancer. Furthermore, we review the success of N1-methyl-Ψ messenger RNA vaccines against COVID-19 and the development of RNA-guided pseudouridylation enzymes for treating genetic diseases caused by premature stop codons.

Transcript tinkering: RNA modifications in protozoan parasites

Apicomplexan and trypanosomatid parasites have evolved a wide range of post-transcriptional processes that allow them to replicate, differentiate, and transmit within and among multiple different tissue, host, and vector environments. In this review, we highlight the recent advances that point toward the regulatory potential of RNA modifications in mediating these processes on the coding and noncoding transcriptome throughout the life cycle of protozoan parasites. We discuss the recent technical advancements enabling the study of the 'epitranscriptome' and how parasites evolved RNA modification-mediated mechanisms adapted to their unique lifestyles.

Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification

Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.

Emerging roles of the epitranscriptome in parasitic protozoan biology and pathogenesis

RNA modifications (epitranscriptome) - such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ) - modulate RNA processing, stability, interaction, and translation, thereby playing critical roles in the development, replication, virulence, metabolism, and life cycle adaptations of parasitic protozoa. Here, we summarize potential homologs of the major human RNA modification regulatory factors in parasites, outline current knowledge on how RNA modifications affect parasitic protozoa, highlight the regulation of RNA modifications and their crosstalk, and discuss current progress in exploring RNA modifications as potential drug targets. This review contributes to our understanding of epitranscriptomic regulation of parasitic protozoa biology and pathogenesis and provides new perspectives for the treatment of parasitic diseases.