Groundbreaking study unveils unique roles of yeast protein complexes in cellular lifespan and environmental response by rationally engineering based on the predicted three-dimensional structures

Assistant Professor Takahiro Kosugi of Institute for Molecular Science, assistant Professor Yoshiaki Kamada at National Institute for Basic Biology, and colleagues have developed an advanced molecular cell biology approach by integrating computational redesigning of protein complexes based on the predicted three-dimensional structure into yeast genetics. They revealed that two types of protein complexes in yeast, which were thought to have the same function, play distinct roles in cellular environmental response and lifespan. Furthermore, they showed that two complexes function differently in response to stress and uncovered potential pathways for treating age-related diseases. This study offers promising insights for human health advancements.

Proteins, serving as cellular workhorses, often form complex structures to execute essential functions. One such vital protein complex is TORC1, which plays a pivotal role in orchestrating cellular responses to environmental stimuli such as nutrient availability. This complex is not only linked to various diseases but also plays a significantly role in lifespan regulation in a wide range of organisms, including human. Unlike many organisms, one of the yeast species, Saccharomyces cerevisiae, possesses two different types of TORC1 complexes, each incorporating either the Tor1 or Tor2 proteins. This research challenges the previous assumption that these complexes are functionally redundant, merely existing as backups for each other. The research team shows the distinct and non-redundant roles of the two complexes (Fig. 1).

The research team embarked on a mission to uncover the differences between the two types of yeast TORC1 complexes. By engineering a mutant version of the Tor2 protein, they effectively prevented it from forming TORC1 complex while allowing it to maintain the ability to form TORC2. This strategic alteration enabled the researchers to analyze the distinct functions of the two TORC1 complexes, particularly focusing on the one containing Tor2. The study showed that yeast cells lacking Tor2-containing TORC1 responded differently to various environmental stresses compared to wild-type cells or cells lacking Tor1-containing TORC1. For instance, cells without Tor2-TORC1 exhibited higher sensitivity to TORC1 inhibitors including rapamycin and caffeine.

Additionally, the research team examined the effects of the TORC1 alteration on the yeast's lifespan. The findings were compelling: the absence of Tor2-containing TORC1 resulted in unique lifespan characteristics, distinctly different from those observed in cells without Tor1-containing TORC1. These results provide new insights into molecular evolution of Tor complexes, cellular signaling pathways, and lifespan regulation. The study not only sheds light on the specific functions of Tor1- and Tor2-containing TORC1 in yeast but also opens avenues for further exploration in the context of human biology and disease.

Their advanced approach of using three-dimensional structure-based engineering of target protein complexes to address a biological question is a noteworthy point. Three-dimensional structures of target proteins were computationally generated and then the mutants were selected based on a robust rationale rooted in these model structures. Consequently, among a small number of candidates, one mutant was as designed. Also, the structures are model complex structures predicted computationally and not on the experimental structures. This approach has a potential to be a general method, because it can be applied to an extensive array of high-quality predicted protein structure models made available by recently developed high-accuracy structure prediction methods using deep learning. We could engineer native proteins based on their predicted structure and uncover their biological functions as this study has done.

The findings of this study hold profound implications for advancing our understanding of cellular aging and disease treatment. By distinguishing the non-redundant functions of the TORC1 complex variants in yeast, the research team has laid the groundwork for future medical interventions that could target these pathways more precisely. This could revolutionize therapeutic strategies for a variety of age-related diseases and conditions linked to cellular nutrient response. Furthermore, given the conservation of the TOR pathway through evolution, these yeast models could foreshadow similar breakthroughs in human health, potentially offering new avenues for treating complex diseases such as cancer, diabetes, and neurodegenerative disorders. This study not only provides insight into the specific roles of TORC1 in yeast but also underscores the potential for predicted protein structure-based genetic engineering to unveil the intricate workings of cellular life, potentially enhancing human health and longevity.

The research team includes Yoshiaki Kamada from the Interdisciplinary Research Unit at the National Institute for Basic Biology (NIBB), part of the National Institutes of Natural Sciences (NINS), and a member of the Basic Biology Program at The Graduate University for Advanced Studies, SOKENDAI. Joining him is Chiharu Umeda, along with Yukio Mukai, both from the Department of Frontier Bioscience at Nagahama Institute of Bio-Science and Technology. Hokuto Ohtsuka from the Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, brings his expertise to the team. Yoko Otsubo and Akira Yamashita, also from the Interdisciplinary Research Unit at NIBB, NINS, add to the group's interdisciplinary strength. Lastly, Takahiro Kosugi, representing the Research Center of Integrative Molecular Systems at Institute for Molecular Science (IMS), NINS, and a member of both The Exploratory Research Center on Life and Living Systems (ExCELLS), NINS, and the Molecular Science Program at SOKENDAI, completes this diverse and accomplished team.

▼Financial Supports
This research is funded the NINS program for cross-disciplinary study, the grant of Joint Research by the National Institutes of Natural Sciences (NINS), Japan Science and Technology Agency (JST) “Precursory Research for Embryonic Science and Technology (PRESTO)”, and a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

▼Information of the paper
Authors: Yoshiaki Kamada*, Chiharu Umeda, Yukio Mukai, Hokuto Ohtsuka, Yoko Otsubo, Akira Yamashita, and Takahiro Kosugi*
Journal Name: Journal of Cell Science
Journal Title: “Structure-based engineering of Tor complexes reveals that two types of yeast TORC1 produce distinct phenotypes”
DOI: 10.1242/jcs.261625

▼Contact Person
Takahiro Kosugi
TEL: +81-564-55-7379, +81-564-55-7382
E-mail: takahirokosugi_at_ims.ac.jp

Yoshiaki Kamada
TEL: +81-564-55-7536
E-mail: yoshikam_at_nibb.ac.jp

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