Cross-evolutionary dissection of the functional plasticity of the ribosomal epitranscriptome

Project Information

EpiRibo

Grant agreement ID: 101000970

DOI

10.3030/101000970

EC signature date 17 December 2020

Start date 1 May 2022

End date 30 April 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

WEIZMANN INSTITUTE OF SCIENCE
Israel

Periodic Reporting for period 2 - EpiRibo (Cross-evolutionary dissection of the functional plasticity of the ribosomal epitranscriptome)

Reporting period: 2023-11-01 to 2025-04-30

Summary of the context and overall objectives of the project

The grant proposal addresses the complex issue of ribosomal RNA (rRNA) modifications in ribosomes, the molecular machines responsible for protein synthesis in all living cells. These modifications are abundant and vary extensively across different species, yet their specific functions and the mechanisms by which they influence ribosomal activity remain largely unexplored. The key problem being addressed is the lack of a comprehensive understanding of how rRNA modifications affect the ribosome's ability to adapt to environmental changes and stress, and the implications of these modifications for cellular function and organismal adaptation.

The importance of this research for society is multifaceted. First, understanding rRNA modifications can significantly advance our knowledge of cellular biology and the fundamental processes of life, which is crucial for the medical, biotechnological, and pharmaceutical industries. Insights gained from studying these modifications could lead to novel approaches to enhance crop resilience, develop new antibiotics that target ribosomal functions, or even treat diseases related to protein synthesis dysfunctions. Additionally, by exploring the adaptive mechanisms of extremophiles like hyperthermophilic archaea, researchers can uncover strategies for bioengineering organisms or biomolecules that can withstand or perform in extreme conditions, potentially leading to new materials or industrial processes.

The overall objectives of the project are to systematically unravel the extent to which rRNA modifications can modulate the activity of the ribosome across evolutionary timescales and in response to cellular demands. The project aims to map these modifications comprehensively, understand their regulatory mechanisms, and identify the conditions under which these modifications are most impactful. This will be achieved through the development and application of advanced, sequencing-based methodologies designed to capture the dynamic landscape of rRNA modifications across a broad spectrum of life forms. By establishing a taxonomy of rRNA modifications along dimensions of evolutionary distribution, structural implications, and functional outcomes, the research seeks to illuminate the extent of regulatory potential within the ribosome, thereby offering a new layer of understanding to ribosomal biology and its applications in health and disease management.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In our project, we address the intricate dynamics of ribosomal RNA (rRNA) modifications and their roles in allowing organisms to adapt to extreme environmental conditions. We developed a new method called Pan-Mod-seq, which dramatically improves our ability to detect and analyze multiple rRNA modifications simultaneously across various species. This innovation has transformed our approach to studying how small changes in the ribosome's RNA can influence an organism's response to changes in its environment.

Using this method, we investigated rRNA modifications in 14 species from different domains of life, all of which thrive under extreme conditions. Our findings reveal that these species modify their rRNA in response to temperature changes, with these modifications playing a critical role in their survival at higher temperatures. For instance, we discovered that specific modifications in the rRNA of heat-loving microbes are essential for maintaining ribosomal stability and function in hot environments. These modifications are driven by enzymes that are themselves regulated by temperature, indicating a direct adaptation mechanism at the molecular level.

We also employed advanced imaging and biochemical tests to understand how these modifications impact the ribosome’s structure and function under thermal stress. Our experiments provide direct evidence of the molecular adaptations that enable survival in harsh conditions.

Overall, our work sheds light on the regulatory and adaptive significance of rRNA modifications. It sets the stage for further studies into how these modifications affect ribosomal function and organismal fitness across different environmental and evolutionary contexts.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In our project, we have made significant progress beyond the state of the art by developing and implementing Pan-Mod-seq, a groundbreaking method that has reshaped our ability to study rRNA modifications across a wide range of species and conditions. Before the advent of Pan-Mod-seq, research in this field was hampered by techniques that lacked the sensitivity, specificity, and throughput necessary to capture the full spectrum of rRNA modifications. Traditional methods were also not cost-effective for large-scale studies, limiting their usefulness in diverse and extensive environmental settings.

Pan-Mod-seq integrates various experimental approaches into a single, high-throughput pipeline that allows for the sensitive, specific, and simultaneous identification of multiple rRNA modifications. This method has enabled us to systematically identify and analyze 16 distinct rRNA modifications across multiple samples, transforming our understanding of the ribosomal epitranscriptome. By improving both the efficiency and the cost-effectiveness of rRNA modification studies, Pan-Mod-seq has opened up new avenues for research across different biological domains and conditions.

Looking forward to the expected results until the end of the project, we anticipate that Pan-Mod-seq will continue to play a pivotal role. We expect to expand our investigations to include a wider variety of organisms and environmental conditions, enhancing our understanding of the adaptive significance of rRNA modifications. This will likely lead to a comprehensive taxonomy of rRNA modifications, detailing their evolutionary distribution, structural implications, and functional roles. Such a taxonomy is crucial for understanding the extent of plasticity and regulatory potential inherent within the ribosome.

Furthermore, by continuing to leverage the capabilities of Pan-Mod-seq, we aim to uncover the underlying mechanisms of rRNA modification regulation and their impact on ribosome function under various stress conditions. This will not only advance our basic scientific understanding but also has the potential to inform the development of new therapeutic strategies targeting ribosomal functions in diseases. Through these efforts, our project will provide critical insights that could transform the fields of molecular biology, evolutionary biology, and biomedicine.