FY2012 Annual Report

Microbiology and Biochemistry of Secondary Metabolites Unit

Assistant Professor Holger Jenke-Kodama

Abstract

This research unit works on bacterial model organisms, toxin-producing dinoflagellates and microbial communities associated to marine invertebrates. The common theme behind all projects is to gain a better understanding of the biological functions of secondary metabolites. In fiscal year 2012 (April 2012 - March 2013), we continued various projects, most of them being now in the stage of data analysis and interpretation. Therefore, we expect to get publishable results in the course of FY 2013. We also continued our collaborative projects with the University of the Ryukyus and thus could attain one of the important objectives of OIST, namely to become better integrated in the Okinawan research community. The staff of the unit changed considerably due to a relatively high fluctuation at the end of the fiscal year. We presented some research results at conferences, but we did not publish journal articles mainly based on research at OIST.

1. Staff

• Dr. Holger Jenke-Kodama, Assistant Professor
• Dr. Tomoko Yamazaki, Group Leader/Lab Manager (from January 2013)
• Dr. Maiko Tamura, Researcher (until March 2013)
• Dr. Aika Yamguchi, Researcher (until March 2013)
• Dr. Hiroshi Izumi, Researcher (from March 2013)
• Yosuke Taira, MSc, Technician
• Akiko Sato, MSc, Technician (from March 2013)
• David Richter, MSc, Technician (until March 2013)
• Ryoko Uchida, Research Administrator

2. Collaborations

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

• Theme: Microbial communities in Palythoa tuberculosa and palytoxin production
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. James D. Reimer, Associate Professor, Department of Chemistry, Biology and Marine Science, University of the Ryukyus

• Theme: Effects of the Kaichu-Doro causeway on biodiversity
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. James D. Reimer, Associate Professor, Department of Chemistry, Biology and Marine Science, University of the Ryukyus

3. Activities and Findings

3.1 Toxin production in marine dinoflagellates

The qualitative transcriptome sequencing data obtained from cultured ovatoxin-producing dinoflagellates are still in the process of being analysed. Database searches revealed a high number of secondary metabolite genes, some of which show unusual structural configurations (manuscripts in preparation). These data also form the basis for an ongoing comparative study using publicly available transcriptomes of other dinoflagellates. Furthermore, the data will be used for setting up quantitative transcriptome experiments, which will contribute to clarifying what genes are involved in the biosynthesis of the toxin.

3.2 Microbial communities of Palythoa tuberculosa and their relation to palytoxin production

(Collaboration with Dr. James D. Reimer, Associate Professor, University of the Ryukyus)

We concluded the first phase of environmental sampling, which had had its focus on Ishigaki island (Okinawa prefecture). The main aim of this first sampling phase was to identify geographical distribution patterns, whose analysis is now in the final stage (manuscript in preparation). We initiated a microbial community analysis using next-generation sequencing last year. The initial sequencing results, which we obtained by outsourcing, were promising and revealed some unexpected correlations between toxin content and the bacterial communities. We are now in the process of establishing the amplicon sequencing procedure at OIST in order to broaden the data basis for bacteria and complement the existing data with sequences of the eukaryotic microbial community, which has been neglected so far. With the help of Dr. J. D. Reimer of the University of the Ryukyus we were able to establish a new sampling site in Okinawa-honto (the main island of Okinawa prefecture where OIST is located). This will allow for more intense and more frequent sampling activities in the future.

3.3 Effects of the Kaichu-Doro causeway on biodiversity and environmental chemodiversity

(Collaboration with Dr. James D. Reimer, Associate Professor, University of the Ryukyus)

3.4 Secondary metabolites of the cyanobacterium Nostoc punctiforme

We have been creating knockout mutants for some of the gene clusters that encode enzyme complexes for secondary metabolite biosynthesis. This is ongoing work and will be continued in FY 2013 to provide materials for comparative microarray-based transcriptome analysis.

4. Publications

4.1 Journals

1. Nishimura, Y., S. Sato, H. Sakanari, K. Uehara, M. M. Rahman Shah, S. Suda, T. Yasumoto, Y. Taira, H. Yamaguchi and M. Adachi (2013). Genetic diversity and distribution of the ciguatera-causing dinoflagellate Gambierdiscus spp. (dinophyceae) in coastal areas of Japan. PLoS ONE (4): e60882. [Available online 11th March 2013, peer-reviewed]

Note: This article is co-authored by a unit member, but is based on work that was mainly performed at another institution.

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

1. A. Yamaguchi, M. Tamura, Y. Taira, D. Richter, S.-Y. Yang, J. D. Reimer, H. Jenke-Kodama. Toxin distribution patterns in Palythoa tuberculosa colonies from Ishigaki island and their microbial communities. International Symposium on Human Well-being and the Marine Environment in the Pacific Islands, April 2012, Ginowan, Okinawa. [Oral presentation]
2. D. Richter and H. Jenke-Kodama. A simple model system for detecting metabolic changes in symbiotic Nostoc punctiforme. XV. International Conference of Molecular Plant-Microbe Interactions, 29th July - 2nd August 2012, Kyoto. [Poster presentation] 
3. A. Yamaguchi, M. Tamura, H. Jenke-Kodama. Phylogeny and domain configuration of fatty acid synthases and polyketide synthase-like proteins in protists. Protist 2012, XIII. International Congress on Protistology, 29th July - 3rd August 2012, Oslo, Norway. [Poster presentation]
4. H. Jenke-Kodama. The Palytoxin Mystery - On the hunt for the producer of the strongest non-peptide poison. Invited talk, 18th March 2013, Akita University, Akita. [Oral presentation]

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report.

6. Meetings and Events

Nothing to report.