Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate

BMC Biology

Shinichi Yamasaki¹  Ross F. Waller²  Jun’ichi Kobayashi³  Koki Nishitsuji⁴  Eiichi Shoguchi⁴  Noriyuki Satoh⁴  Kanako Hisata⁴  Asuka Arimoto⁵  Girish Beedessee⁶  Takaaki Kubota⁷ 

[1] DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Okinawa, Japan;Department of Biochemistry, University of Cambridge, CB2 1QW, Cambridge, UK;Graduate School of Pharmaceutical Sciences, Hokkaido University, 060-0812, Sapporo, Japan;Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Okinawa, Japan;Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Okinawa, Japan;Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, 722-0073, Onomichi, Hiroshima, Japan;Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Okinawa, Japan;Present address: Department of Biochemistry, University of Cambridge, CB2 1QW, Cambridge, UK;Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, 194-8543, Tokyo, Japan;

关键词: Polyketide synthases;    Harmful algal blooms;    Dinoflagellates;    Iso-Seq;    Duplication;    Amphidinium;   

DOI  :  10.1186/s12915-020-00873-6

来源: Springer

【 摘 要 】

BackgroundSome dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been hampered by their unusually large genomes. To overcome this challenge, for the first time, we sequenced the genome, microRNAs, and mRNA isoforms of a basal dinoflagellate, Amphidinium gibbosum, and employed an integrated omics approach to understand its secondary metabolite biosynthesis.ResultsWe assembled the ~ 6.4-Gb A. gibbosum genome, and by probing decoded dinoflagellate genomes and transcriptomes, we identified the non-ribosomal peptide synthetase adenylation domain as essential for generation of specialized metabolites. Upon starving the cells of phosphate and nitrogen, we observed pronounced shifts in metabolite biosynthesis, suggestive of post-transcriptional regulation by microRNAs. Using Iso-Seq and RNA-seq data, we found that alternative splicing and polycistronic expression generate different transcripts for secondary metabolism.ConclusionsOur genomic findings suggest intricate integration of various metabolic enzymes that function iteratively to synthesize metabolites, providing mechanistic insights into how dinoflagellates synthesize secondary metabolites, depending upon nutrient availability. This study provides insights into toxin production associated with dinoflagellate blooms. The genome of this basal dinoflagellate provides important clues about dinoflagellate evolution and overcomes the large genome size, which has been a challenge previously.

【 授权许可】

CC BY