Biology subjects

Marinus, T.

Publications and source records attributed to Marinus, T..

4 recordsLinked to original sources

bioRxiv2026

Comparative analysis identifies a shared topological organisation among divergent intergenic RNAs

Biological function is often inferred from sequence conservation or structural similarity. However, many viral RNAs maintain regulatory functions despite extensive diversification of both sequence and structures. Using arenavirus intergenic regions (IGRs) as a model system, we investigated what level of RNA organization remains conserved when these conventional sequence-structure-function relationships break down. Combining cryogenic OrbiSIMS guided RNA structure determination with graph theory-based analysis of fifty-eight IGRs across phylogenetically diverse arenaviruses, we discovered that IGR topology, defined by the connectivity and relative integration of individual stem-loop elements, is consistently arranged around a highly connected helical core that persists across divergent IGR folds. Quantitative centrality analyses further revealed that topologically peripheral stem-loops are comparatively sparse and variable across the phylogenetic classes. Investigation of the functional consequence of the peripheral elements in Golden Gate virus (a reptile arenavirus) S-IGR revealed selective association with interferon-induced and antiviral RNA-binding proteins in human host cells infected with recombinant Lymphocytic Choriomeningitis virus (a distantly related human arenavirus). Taken together, these findings identify graph-defined topology as a recurrent organisational feature among divergent arenavirus IGRs that is not captured by sequence identity or global RNA-structure similarity. The data are consistent with a model in which a topologically central helical organisation may be associated with conserved regulatory capacity, whereas structurally variable peripheral elements may contribute to lineage- or segment-specific host-factor interaction profiles.

biophysics↗

bioRxiv2024

Alanine-scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure.

Yeast killer toxins (YKTs) are antimicrobial proteins secreted by yeast with potential applications ranging from food preservation to therapeutic agents in human health. However, the practical use of many YTKs is limited by specific pH requirements, low temperature stability, low production yields, and narrow target specificity. While protein engineering could potentially overcome these challenges, progress is hindered by a lack of detailed knowledge about sequence-function relationships and structural data for these often multi-step processed proteins. In this study, we focused on the YKT K2, encoded by the M2 dsRNA satellite virus in Saccharomyces cerevisiae. Using alanine scanning mutagenesis of the full open reading frame and structure predictions combined with molecular dynamics simulations, we generated a comprehensive sequence-function map, refined the model for the proteolytic processing of the K2 precursor, and predicted the mature toxin structure. Our findings also demonstrate that K2 can be engineered towards enhanced toxicity and altered target specificity through single-site mutations. Furthermore, we identified structural homology between K2 and the SMK toxin from the yeast Millerozyma farinosa. Our cost-effective workflow provides a platform to broadly map YKT sequence-structure-function relationships, facilitating the engineering towards toxin-based technologies. The workflow could also serve as a template to resolve the processing and conformations of other proteins within the secretory pathway - a dynamic multi-step process that is challenging to structurally capture by purification and solving structures of intermediates.

microbiology↗

bioRxiv2020

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art SHAPE reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.

biochemistry↗

bioRxiv2020

Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures

SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of [~]30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date. Here, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5' UTR, ribosomal frameshifting element, and 3' UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, [~]8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.

genetics↗