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RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

  • Sze-Wan Poong
  • Kok-Keong Lee
  • Phaik-Eem Lim
  • Tun-Wen Pai
  • Chiew-Yen Wong
  • Siew-Moi Phang
  • Chien-Ming Chen
  • Cing-Han Yang
  • Chun-Cheng Liu
8th Asian Pacific Phycological Forum

Abstract

The current outlook on mitigation of global warming does not appear promising, with figures in the reduction of anthropogenic greenhouse gas emissions lagging far behind climate goals. A recent environmental report even postulated a high possibility of temperature increase of at least 3 °C by 2100. Despite the low number of human inhabitants in Antarctica, the Antarctic Peninsula was reported as one of the most rapidly warming locations on earth. Many studies have shown that heat stress modulates physiological performance in many species of microalgae; however, studies to elucidate the molecular mechanisms of high-temperature thermotolerance are generally focused on the model species, i.e. Chlamydomonas reinhardtii. Furthermore, previous transcriptomic work in this aspect generally employed the microarray technique and/or involved the tropical or temperate strains, and few were conducted on the polar strains. In this study, RNA-Seq-mediated transcriptomic analysis was undertaken to compare the whole transcriptome profile of an Antarctic Chlorella sp. grown at ambient (4 °C) versus stress-inducing high (33 °C) temperatures and harvested at the 120-h time point. The findings of this study indicated a coordinated response to fine tune balance between energy production and utilisation for biosynthesis by redirecting carbon provision, and the arrest of cell division as a coping mechanism for an intense and relatively long period of stress. The strategies undertaken by this alga in acclimation to heat stress are somewhat similar to the heat stress response of the model species.

Keywords

Antarctic Energy metabolism Gene expression Global warming Temperature 

Notes

Acknowledgements

This study was supported by a Higher Institution Centre of Excellence (HICoE) grant (IOES-2014H) from the Ministry of Higher Education, Malaysia; the Antarctic Flagship Project (FP0712E012, PV002-2015) by the Ministry of Science, Technology & Innovation (MOSTI), Malaysia; University of Malaya Research Grant (RP002C-13SUS); University of Malaya Postgraduate Research Fund (PG121-2015A); and the Ministry of Science and Technology, Taiwan, R.O.C. (MOST 104-2627-B-019-003).

Supplementary material

10811_2018_1455_Fig5_ESM.gif (87 kb)
Fig. S1

Citrate cycle pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 87 kb)

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High resolution image (TIFF 758 kb)
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Fig. S2

Pyruvate metabolism pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 125 kb)

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High resolution image (TIFF 1031 kb)
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Fig. S3

Fatty acid biosynthesis pathway. Red box: Significantly upregulated gene mapped to at least one of the reference species. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 203 kb)

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High resolution image (TIFF 1632 kb)
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Fig. S4

Fatty acid degradation pathway. Red box: Significantly upregulated gene mapped to at least one of the reference species. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 144 kb)

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High resolution image (TIFF 1335 kb)
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Fig. S5

Pentose phosphate pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 111 kb)

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High resolution image (TIFF 3139 kb)
10811_2018_1455_Fig10_ESM.gif (252 kb)
Fig. S6

Purine metabolism pathway. Red boxes: Significantly upregulated genes mapped to at least one of the reference species. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 251 kb)

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High resolution image (TIFF 21855 kb)
10811_2018_1455_Fig11_ESM.gif (143 kb)
Fig. S7

Valine, leucine and isoleucine degradation pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 142 kb)

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High resolution image (TIFF 1206 kb)
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Fig. S8

Photosynthesis pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 154 kb)

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High resolution image (TIFF 15872 kb)
10811_2018_1455_Fig13_ESM.gif (105 kb)
Fig. S9

Carbon fixation pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 104 kb)

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High resolution image (TIFF 2592 kb)
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Fig. S10

Glyoxylate and dicarboxylate metabolism pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 170 kb)

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High resolution image (TIFF 4323 kb)
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Fig. S11

Porphyrin and chlorophyll metabolism pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 271 kb)

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High resolution image (TIFF 27983 kb)
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Fig. S12

Protein processing in endoplasmic reticulum pathway. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 157 kb)

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High resolution image (TIFF 13685 kb)
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Fig. S13

Peroxisome pathway. Red box: Significantly upregulated gene mapped to at least one of the reference species. Green boxes: Significantly downregulated genes mapped to at least one of the reference species. Grey boxes: Genes mapped to the reference species but are not significantly differentially expressed. (GIF 112 kb)

10811_2018_1455_MOESM13_ESM.tif (1 mb)
High resolution image (TIFF 1055 kb)
10811_2018_1455_MOESM14_ESM.doc (32 kb)
Table S1 Photosynthetic parameters of the cells prior to RNA isolation at 120 h. Data are presented as means ± S. D. (n = 3). The asterisk indicates significant difference (p < 0.05) between the means. (DOC 31 kb)
10811_2018_1455_MOESM15_ESM.xls (111 kb)
Table S2 List showing the number of genes annotated in each KEGG pathway for Chlorella variabilis NC64A (cvr), genes of Chlorella sp. mapped against cvr, and the number of DEGs. (XLS 111 kb)

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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Sze-Wan Poong
    • 1
  • Kok-Keong Lee
    • 1
    • 2
  • Phaik-Eem Lim
    • 1
  • Tun-Wen Pai
    • 3
  • Chiew-Yen Wong
    • 4
    • 5
  • Siew-Moi Phang
    • 1
    • 6
  • Chien-Ming Chen
    • 3
  • Cing-Han Yang
    • 3
  • Chun-Cheng Liu
    • 3
  1. 1.Institute of Ocean and Earth SciencesUniversity of MalayaKuala LumpurMalaysia
  2. 2.Institute of Graduate StudiesUniversity of MalayaKuala LumpurMalaysia
  3. 3.Department of Computer Science and EngineeringNational Taiwan Ocean UniversityKeelungRepublic of China
  4. 4.School of Health SciencesInternational Medical UniversityKuala LumpurMalaysia
  5. 5.National Antarctic Research CentreUniversity of MalayaKuala LumpurMalaysia
  6. 6.Institute of Biological Sciences, Faculty of ScienceUniversity of MalayaKuala LumpurMalaysia

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