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Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases

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Abstract

Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.

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  • 01 October 2020

    [Original sentence on Page 560, Line 34–37] The present BacSET protein family might be a novel, diatom-specific family of methyltransferases that target unique substrates, such as cell wall formation-related proteins and LCPAs.

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Acknowledgments

Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics. This work was supported by the Program to Disseminate Tenure Tracking System from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, Grants-in-Aid for Scientific Research (C) (No. 18K05818), Asahi Glass Foundation to MN.

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  1. Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan

    Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki & Kiori Obuse

  2. Department of Biology, Tokyo Gakugei University, Tokyo, 184-8511, Japan

    Shigeki Mayama

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  1. Michiko Nemoto
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  2. Sayako Iwaki
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Nemoto, M., Iwaki, S., Moriya, H. et al. Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. Mar Biotechnol 22, 551–563 (2020). https://doi.org/10.1007/s10126-020-09976-1

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