Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii

Dmitrii K Konstantinov; Aleksei Menzorov; Olga Krivenko; Alexey V Doroshkov

doi:10.7717/peerj.12737

Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii

PeerJ. 2022 Mar 9:10:e12737. doi: 10.7717/peerj.12737. eCollection 2022.

Authors

Dmitrii K Konstantinov^#^{1

2}, Aleksei Menzorov^{1

2}, Olga Krivenko³, Alexey V Doroshkov^#^{1

2

4}

Affiliations

¹ Novosibirsk State University, Novosibirsk, Russia.
² Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
³ A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia.
⁴ Siberian Federal University, Krasnoyarsk, Russia.

^# Contributed equally.

Abstract

Background: Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology.

Methods: We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species.

Results: The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes.

Conclusion: Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.

Keywords: Fatty acids; Marine protists; RNA-seq; Thraustochytrium; Transcriptome assembly.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Black Sea
Ecosystem*
Gene Expression Profiling
Phylogeny
RNA, Ribosomal, 18S / genetics
Stramenopiles* / genetics

Substances

RNA, Ribosomal, 18S

Grants and funding

The study was supported by the Ministry of Education and Science of the Russian Federation, grant 2019-0546 (FSUS-2020-0040). Part of the work carried out by O.V. Krivenko was done at the Laboratory of Marine Biodiversity and Functional Genomics (created with the support of grant No. 14.W03.31.0015), and was funded by IBSS GA No. 121030100028-0. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.