FY2010 Evolutionary Systems Biology Unit

Evolutionary Systems Biology Unit

Independent New Investigator: Holger Jenke-Kodama
Research Theme: Molecular analysis of microbial secondary metabolites and their evolution and biotechnological potential



The overall aim of the Evolutionary Systems Biology Unit is to elucidate the evolutionary processes shaping secondary metabolism in microorganisms. Secondary metabolites are small compounds that belong to diverse chemical substance classes and show a taxonomically inhomogeneous distribution. Many of these substances have pharmaceutically important bioactivities like antiobiotic, cytotoxic and antifungal activities, and some of them are classified as toxins. The last years, however, have seen an increasing interest in the biological functions of those compounds. From an evolutionary perspective, the key questions are: How is the plethora of compounds created, and how does natural selection influence secondary metabolism? To answer these questions we need information about the chemical structures of metabolites, biosynthesis schemes, gene cluster organisation and gene expression patterns. To understand the evolution of secondary metabolite pathways we need to combine the data at the systems level using both experimental and computational approaches. Furthermore, we are interested in  biotechnological applications of those compounds. Currently, the unit is working on bacterial model organisms, toxin producing dinoflagellates and environmental microbial communities that are associated to marine invertebrates. Moreover, we are studying a green microalgal species in order to improve its biotechnological potential as a biofuel source. The latter topic mirrors one important objective of OIST, namely to combine basic research and applied approaches in order to work also on the development of new technologies.

1. Staff

  • Dr. Kugako Sugimoto, Researcher  
  • Dr. Maiko Tamura, Researcher
  • Mr. David Richter, Technical Staff
  • Mr. Yosuke Taira, Technical Staff
  • Ms. Ryoko Uchida, Research Administrator / Secretary

2. Collaborations

  • Theme: Botryococcene biosynthesis in the green microalga Botryococcus  braunii
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Shigeki Matsunaga, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
      • Dr. Shigeru Okada, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan

  • Theme: Microbial communities associated to Palythoa tuberculosa and toxin production in marine dinoflagellates
    • Type of collaboration: Joint research
    • Researchers:
      • Dr. James D. Reimer, Department of Biology, University of the Ryukyus 

3. Activities and Findings

In the course of the last fiscal year, we continued our work on secondary metabolites in the cyanobacterium Nostoc punctiforme, which was initiated in May 2010 after lab space had become available at the new campus site. Moreover, the research unit has tried to adapt itself to the special OIST environment. Okinawa is obviously a perfect location for performing marine studies, and our interest in secondary metabolites fits extremely well to the opportunity of creating marine research focuses, as the ocean is well known to be a rich source of those compounds. Furthermore, marine biochemistry and related biotechnology approaches are part of the 21st century vision formulated by the government of Okinawa prefecture in order to set targets for the industrial development of the prefecture. Therefore, we started new projects that have a clear focus on marine topics.

3.1 Secondary metabolite gene clusters of the cyanobacterium Nostoc punctiforme

Nostoc punctiforme is a multicellular, filament-forming cyanobacterium. The choice as one of our bacterial model organisms is based on the the following reasons: (1) The genome of N. punctiforme has been sequenced completely, (2) it shows complex physiological and ecological features including nitrogen fixation, cell differentiation and symbiotic interactions with various plants and fungi, and (3) this bacterium has the genetic potential to biosynthesise several polyketides made by polyketide synthases (PKSs), nonribosomal peptides made by nonribosomal peptide synthetases (NRPSs) and hybrid structures thereof, which are produced by hybrid PKS/NRPS enzyme systems. We have identified 10 gene clusters of the PKS and NRPS type in the genome of N. punctiforme, but so far only two metabolites produced by N. punctiforme have been partially characterised, namely nostopeptolide and a glycolipid. However, even for nostopeptolide, whose structure is known, the physiological function remains unclear.

This project aims to identify and characterise the other secondary metabolites, study their biosynthesis and clarify their biological roles. We have initiated the construction of knock-out mutants for selected gene clusters. As soon as these mutants are available, we can compare their LC/MS profiles with the wild type strain in order to identify the relevant peaks. Furthermore we are culturing N. punctiforme cells under various conditions simulating environmental stress to study gene expression patterns by microarray analysis.

3.2 Toxin biosynthesis in marine dinoflagellates

Dinoflagellates are microalgae that are assumed to produce a variety of marine toxins. These toxins are of high socioeconomic relevance, as they can posion fish, other marine animals and humans. Dinoflagellate-associated poisoning of humans include ciguatera fish poisoning, paralytic shellfish poisoning and neurotoxic shellfish poisoning. We have recently started a new project on elucidating the biosynthesis pathways of palytoxin and other compounds belonging to the palytoxin family. The concept is to perform comparative studies with producing and non-producing strains of the genus Ostreopsis, which were sampled in Okinawa prefecture.  

3.3 Microbial communities associated with Palythoa tuberculosa

(Collaborative project with Dr. James D. Reimer, Ryukyus University)

The zoanthid Palythoa tuberculosa is a benthic cnidarian that belongs to the subclass Hexacorallia within the class Anthozoa. It is common in both deep and shallow coral reef ecosystems and grows in colonies. It is known that there is a variety of microorganisms living in association with Palythoa species. The idea of this project is to study the microbial communities in P. tuberculosa and their dependence on the environmental conditions along a human impact gradient at the west coast of the Okinawa main island. In the project, we decided on the sampling locations and did test samplings. We are now establishing the procedures for collection of microorganisms by filtration and DNA extraction for sequencing. 

3.4 Biofuel production using green microalgae

 (Collaborative project with Dr. Shigeru Okada, The University of Tokyo)

 The research unit has established a co-operation with the University of Tokyo within the CREST research area “Creation of basic technology for improved bioenergy production through functional analysis and regulation of algae and other aquatic microorganisms”, which was created in 2010. CREST stands for “Core Research of Evolutional Science and Technology” and gives public funding to research areas that have been identified to have substantial impact on the economy and lives in Japan. We collaborate with Dr. Shigeru Okada, who is Associate Professor at the Graduate School of Agricultural and Life Sciences and the Research Director of the newly started CREST project “Characterisation of hydrocarbon biosynthesis and secretion mechanisms by the green microalgae Botryococcus braunii to control biofuel production”. In this research project, we aim to understand “why and how” hydrocarbons are produced and secreted by this alga at both the cellular and molecular level. We identified and characterised biochemically the enzymes of the first two steps of the MEP (2-C-methylerythritol 4-phosphate) pathway in B. braunii. The MEP pathway provides the five-carbon units that are used for hydrocarbon biosynthesis and thus, is an important target for future genetic engineering approaches. The data about the recently identified enzymes will serve as the basis for comprehensive gene expression studies to get insight into regulation mechanisms and the dependence of hydrocarbon production on environmental conditions.

4. Publications

4.1 Journals

Nothing to report

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Maiko Tamura & Holger Jenke-Kodama. Evolutionary relationships of fatty acid and polyketide synthases spanning all domains of life, BMB 2010 (33rd Annual Meeting of the Molecular Biology Society of Japan and 83rd Meeting of the Japanese Biochemical Society), Kobe, Japan, Dec 7-10, 2010
  2. Maiko Tamura & Holger Jenke-Kodama. Evolutionary analysis of the distribution of fatty acid synthase types in protists, 18th Meeting of the International Society for Evolutionary Protistology, Kanazawa, Japan, Jul 2-7, 2010

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report 

6. Meetings and Events

6.1 Quantitative Evolutionary and Comparative Genomics (Summer School and Workshop)

  • Date: 24th May - 4th June 2010
  • Venue: Seaside House, OIST
  • Co-organizers:
    • Jonathan Miller, OIST
    • Alexander Mikheyev, OIST
    • Byrappa Venkatesh, IMCB Singapore
    • Oleg Gusev, NAIST Tsukuba (poster sessions)
  • Speakers:
    • Nadav Ahituv, University of California, San Francisco
    • Peter Arndt, MPI Berlin
    • Gill Bejerano, Standford University
    • Emmanouil Dermitzakis, University of Geneva
    • Takashi Gojobori, National Institute of Genetics, Japan
    • Ueli Grossniklaus, University of Zurich
    • Jotun Hein, Oxford University
    • H. C. Paul Lee, NCU Taiwan
    • Jonathan Miller, OIST
    • Nancy Moran, University of Arizona
    • Erik van Nimwegen, University of Basel
    • Howard Ochman, University of Arizona
    • Anirvan Sengupta, Rutgers University
    • Gasper Tkacik, University of Pennsylvania
    • Byrappa Venkatesh, IMCB Singapore
    • Ting Wu, Harvard Medical School