Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature.

Rui Guo,Xiuling Ji,Xiaoqing Zhang,Meixia He,Qi-Lin Zhang,Qi Zhang,Yunlin Wei

doi:10.3389/fmicb.2021.727105

Rui Guo, Xiuling Ji + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2021.727105

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Abstract

Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

Highlights

One of the crucial ecological factors associated with abiotic stress is low temperatures, which can disrupt microbial homeostasis and affect the biological functions of cells (García-Ríos et al, 2017; Wang et al, 2020)
The terms associated with metabolism were overrepresented (77, 71.96% of all terms) among the enriched KEGG pathways and adjustment of metabolism function due to gene expression changes primarily contributed to the low temperature response of R. kratochvilovae strain YM25235
Significant enrichment of the MAPK pathway in this study indicated the implication of MAPKs in transmitting stress signals from the environment to the cell nucleus in R. kratochvilovae strain YM25235 at low temperature

Summary

Introduction

One of the crucial ecological factors associated with abiotic stress is low temperatures, which can disrupt microbial homeostasis and affect the biological functions of cells (García-Ríos et al, 2017; Wang et al, 2020). The understanding of the molecular mechanisms of response in fungus to low temperature stress has been explored. Several fungal genera adapt to low temperature by changing the expression of different genes as part of the process known as the cold-shock response that has been investigated in Saccharomyces cerevisiae (Aguilera et al, 2007). Studies in Neurospora crassa have demonstrated a high accumulation of mRNAs of carotenoid genes to reduce oxidative stress under low temperature (Castrillo et al, 2018). These results suggest that differentially expressed genes (DEGs) play a key role under low temperature stress in fungi. The identification of genes associated with low temperature response and intensive exploration for molecular mechanisms in response to low temperature at the level of gene expression in fungi are necessary

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