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Profiling of glucose-induced transcription in Sulfolobus acidocaldarius DSM 639

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Abstract

Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner–Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs between the S. acidocaldarius cells grown under sugar-rich (YT with glucose) and sugar-limited (YT only) conditions. The functions and pathways of the DEGs were examined using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time PCR (qRT-PCR) was performed to validate the DEGs. Transcriptome analysis of the DSM 639 strain grown on sugar-limited and sugar-rich media revealed that 853 genes were differentially expressed, among which 481 were upregulated and 372 were downregulated under the glucose-supplemented condition. In particular, 70 genes showed significant changes in expression levels of ≥ twofold. GO and KEGG enrichment analyses revealed that the genes encoding components of central carbon metabolism, the respiratory chain, and protein and amino acid biosynthetic machinery were upregulated under the glucose condition. RNA-seq and qRT-PCR analyses indicated that the sulfur assimilation genes (Saci_2197–2204) including phosphoadenosine phosphosulfate reductase and sulfite reductase were significantly upregulated in the presence of glucose. The present study revealed metabolic networks in S. acidocaldarius that are induced in a glucose-dependent manner, improving our understanding of biomass production under sugar-rich conditions.

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Acknowledgements

This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Science, ICT and Future Planning (NRF-2016R1A2B4011554) to J. Cha.

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Authors and Affiliations

  1. Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea

    Jungwook Park, Areum Lee, Hyun-Hee Lee, Young-Su Seo & Jaeho Cha

  2. Department of Oriental Culinary, Youngsan University, Busan, 48015, Republic of Korea

    Inmyoung Park

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  1. Jungwook Park
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Correspondence to Young-Su Seo or Jaeho Cha.

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Jungwook Park declares that he has no conflict of interest. Areum Lee declares that she has no conflict of interest. Hyun-Hee Lee declares that she has no conflict of interest. Inmyoung Park declares that she has no conflict of interest. Young-Su Seo declares that he has no conflict of interest. Jaeho Cha declares that he has no conflict of interest.

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Park, J., Lee, A., Lee, HH. et al. Profiling of glucose-induced transcription in Sulfolobus acidocaldarius DSM 639. Genes Genom 40, 1157–1167 (2018). https://doi.org/10.1007/s13258-018-0675-3

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