Transcriptomic response of an Antarctic yeast Rhodotorula sp. USM-PSY62 to  temperature changes

Mardani Abdul Halim; Cleo-nicole Chai; Hok-chai Yam; Nurlina Rosli; Azali Azlan; Faisal Mohamad; Ghows Azzam; Nazalan Najimudin

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Transcriptomic response of an Antarctic yeast Rhodotorula sp. USM-PSY62 to temperature changes

Author: Mardani Abdul Halim ¹ ; Cleo-Nicole Chai ² ; Hok-Chai Yam ³ ; Nurlina Rosli ² ; Azali Azlan ² ; Faisal Mohamad ² ; Ghows Azzam ^{2
,

4} ; Nazalan Najimudin ⁵
Author Information

1. Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
2. School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.&
3. Faculty of Applied Science, University College Sedaya International (UCSI), 56000 Kuala Lumpur, Malaysia.
4. Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.
5. School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
Publication Type:Journal Article
Keywords: Antarctica; cold shock; heat shock; Rhodotorula; transcriptome; yeast
From:Malaysian Journal of Microbiology 2023;19(no.5):458-471
CountryMalaysia
Language:English
Abstract: Aims:Rhodotorula sp. (USM-PSY62) is a psychrophilic yeast isolated from Antarctic sea ice that grows optimally at 15°C. The inevitable global warming poses many challenges to the microbial community in Antarctica. Therefore, this studywas conceptualized to observe how USM-PSY62 adapted to fluctuations in temperature.
Methodology and results :Rhodotorula sp. (USM-PSY62) was grown in YPD broth until the mid-log phase. Then, the culture was transferred to four different temperatures, specifically at 0 °C, 5 °C, 15 °C and 21 °C for 24 h. Then, the RNA was extracted, sequenced and analysed. During cold adaptation, an elevated transcription of the CorA magnesium transporter gene in USM-PSY62 indicated a higher requirement for magnesium ions to gain additional enzyme cofactors or maintain cytoplasmic fluidity. The HepA homologue coding for DNA/RNA helicase was also over-expressed with log fold change 2.89 in cold conditions possibly to reorganize secondary structures of DNA and RNA. An up-regulation of the catalase gene was also observed, reflecting an increment in the concentration of reactive oxygen species and fluctuations in the associated antioxidant system. The YOP1 gene, which encodes a membrane protein associated with protein transport and membrane traffic, was the most down-regulated, with log2 fold change values of -6.93 lower under cold shock conditions. The genes responsible for the structural maintenance of chromosome (SMC) have a -8.80 in expression log2 fold change, indicating the gene was down-regulated when the temperature was shifted to 0 °C. Upon cold shock, the gene for heat shock factor protein 1 (HSF1) was also down-regulated with a log2 fold change value of - 5.86. Hsf1 is a transcriptional regulator which regulates the heat shock responses.
Conclusion, significance and impact of study: :In conclusion, the transcriptomic responses demonstrated by Rhodotorula sp. USM-PSY62 characterized critical physiological and biochemical compensatory mechanisms especially cellular processes and signalling, information storage and processing, and metabolism to survive at low and high temperatures. This study provides valuable data for industry, especially in the usage of molecular chaperones.
Full text:20.2023my0049.pdf