FY2022 Annual Report

Evolutionary and Synthetic Biology
Professor Fyodor Kondrashov

Abstract

This has been the first year of existence of our laboratory, which we have spent on capacity building. This capacity necessarily includes two things, the recruitment of talented individuals and the realization of their natural talents and interests to pursue interesting science. Our main success this year has been the recruitment of a substantial number of wonderful established and young scientists. Our laboratory is opportunistic by design and we strive to pursue projects that capture the interest of any members of the laboratory. Therefore, our recruitment has been focused on obtaining a wide diversity of talent - members of our lab include computational biologists, programers, field biologists, molecular biologist and biochemists. Together, we plan to pursue different directions of research, with a central focus on understanding evolutionary principles and using them to design synthetic biological constructs.

1. Staff

  • Dr. Shingo Miyauchi, Staff Scientist
  • Dr. Nikolai Iakushev, Staff Scientist
  • Arina Mazurova, Research Unit Technician
  • Anna Toidze, Research Unit Technician
  • Aygul Minnegalieva, Research Unit Technician
  • Fedor Gagarin, Research Unit Technician
  • Anton Kulikov, Visiting Researcher
  • Anastasiia Ishchenko, Research Intern
  • Liubov Shestakova, Research Intern
  • Milena Dobronos, Research Intern
  • Lada Isakova, Research Intern
  • Maria Gorshkova, Research Intern
  • Saori Chappell, Research Unit Administrator

2. Collaborations

2.1 Fungal genomics

  • Type of collaboration: Joint research
  • Researchers:
    • Emer. Prof. Francis Martin
      Dr. Annegret Kohler
      Université de Lorraine, l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, France (INRAE), France.
    • Dr. Igor V Grigoriev
      US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, US
    • Prof. Alga Zuccaro
      University of Cologne, Institute for Plant Sciences, Cologne, Germany
    • Prof. Paul Schulze-Lefert
      Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    • Dr. László G. Nagy
      Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, Hungary
    • Dr. Hirofumi Nakagami
      Max-Planck Institute for Plant Breeding Research, Cologne, Germany
    • Dr. Christoffer Bugge Harder
      University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
    • Elodie Drula
      INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
    • Dr. Yuriko Nagano
      Deep-Sea Biodiversity Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Japan
    • Assoc. Prof. Jonathan Plett
      Hawkesbury Institute for the Environment, Western Sydney University, Australia

3. Activities and Findings

Over the course of this year we were focused on building capacity. The quickest to mature were some computational projects. We performed comparative multi-omics of plant-microbe interactions. Our work contributed to nine research projects during the period of 2022, which include; Department of Energy, Joint Genome Institute (US) driven fungal sequencing projects with comparative analyses for various fungal taxa, including Morchellaceae, Mycenaceae, Pisolithus and Lactarious species, and deep-sea and marine fungi from Microascales. We also started research on the chitinase activity of ectomycorrhizal fungal species in the context of nutrition cycles in the forest ecosystem, transcriptomic changes of endophytic fungi living in plant hosts and fungal colonization effects on plant hosts, defense mechanisms of the liverwort Marchantia polymorpha against fungal pathogens and comparative genomics of commensal bacteria from the soil in Italy. We also continued to study topics in molecular evolution, including the extent of epistasis in proteins. Our experimental capacity is slower to build, but we are developing projects to assay the fitness landscapes of several proteins, to pursue experimental evolution, construct and study evolution of synthetic life forms, experimentally characterize the function of novel genes and continue to implement the headstarting program of the Spoon-billed sandpiper.

4. Publications

4.1 Journals

  1. Plett J.M., Miyauchi S., Morin E., Plett K., Wong-Bajracharya J., Maira de Freitas Pereira, Kuo A., Henrissat B., Drula E., Wojtalewicz D., Riley R., Pangilinan J., Andreopoulos W., LaButti K., Daum C., Yoshinaga Y., Fauchery L., Ng V., Lipzen A., Barry K., Singan V., Guo J., Lebel T., Dutra Costa M., Grigoriev I.V., Martin F., Anderson I.C., Kohler A. Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus. Molecular Biology and Evolution, doi:10.1093/molbev/msad045 (2023).
  2. Pak M.A., Markhieva, K.A., Novikova M.S., Petrov D.S., Vorobyev I.S., Maksimova E.S., Kondrashov F.A., Ivankov D.N. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS One, doi: 10.1371/journal.pone.0282689 (2023)

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Kondrashov, F., Attempting to understand fitness landscapes in the context of protein physics, BIOLOGY FOR PHYSICS NONEQUILIBRIUM PHYSICS: CLOSE ENCOUNTERS, Barcelona, Spain, July 3 - 7 July 2022
  2. Miyauchi, S., Visual integrative omics of fungi, International Conference on Mycorrhiza (ICOM11), Hybrid conference, 1- 4 Aug 2022
  3. Kondrashov, F., Experimental assays of GFP-based studies of the fitness landscapes, 24th EMBL PhD Symposium The spectra of life: dimensional breadth in biological research, EMBL Heidelberg, Germany, 7 - 9 Dec 2022
  4. Miyauchi, S., Visual integrative omics of fungi, International symposium on sustainable crop production and biosciences, Osaka, Japan, 22 Feb 2023

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminar

  • Visual integrative omics of fungi
  • Date: November 30, 2022
  • Venue: OIST Campus
  • Speaker: Dr. Shingo Miyauchi

7. Other

Nothing to report.