Elucidation of salt stress defense and tolerance mechanisms of marine red yeast Sporobolomyces pararoseus NGR using transcriptomic and metabolomic profiling
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Abstract
Background. Salinity stress is one of the most environmental stresses in agricultural regions worldwide. Salinity inhibits shoot and root growth of various crops, which culminate in reductions in the quality and yield. It is of crucial to understand the molecular biological mechanisms of salt stress responses and defenses in order to enhance crops salt-tolerance. Sporobolomyces pararoseus is a member of marine red yeasts. Since marine red yeast has been naturally selected for its long-term survival in high-salt marine ecosystems, some unique salt-tolerant mechanism has been developed. Little research has conducted so far by considering S. pararoseus as model microorganisms to study salt stress tolerance mechanisms. A better understanding of the mechanisms mediating salt stress of S. pararoseus NGR will provide valuable information for enhancing the crops salt-tolerant via genetic engineering. Methods. S. pararoseus NGR (CGMCC 2.5280) cultures were treated with initial NaCl concentrations of 0.75 M throughout 3 days of growth period. Transcriptome analysis was performed using RNA-seq to study the differentially expressed genes (DEGs) between the NaCl-treated cells and the control cells. Metabolome analysis was performed using the LC-MS/MS untargeted metabolic profiling to study the differentially accumulated metabolites between the NaCl-treated cells and the control cells. Co-expression network analysis was carried out using the screening parameters of correlation coefficient = 0.99 and p-value = 0.01. Transcriptome analysis results were confirmed by real-time quantitative PCR (RT-qPCR). Results. After sequencing, de novo assembly and quantitative assessment, 9,533 unigenes were finally generated with an average length of 1,538 bp. A total of 3,849 DGEs were identified in NaCl-treated cultures, including 2,019 up-regulated genes and 1,830 down-regulated genes. Screening of metabolite features with untargeted metabolic profiling of all samples in NaCl-treated and control group, we characterized 4,862 compounds from the LC–MS/MS-based dataset. An integrated analysis of transcriptome and metabolome indicated that amino acid metabolism, carbohydrate metabolism, and lipid metabolism is significantly enriched in response to salt stress. Co-expression network analysis showed that 28 genes and 8 metabolites played an important role in the response of S. pararoseus NGR and defense against salt stress, which provides valuable clues for subsequent validation. Together, our results suggested that the most primary salt-tolerant mechanism of the S. pararoseus NGR is the biosynthesis of carotenoids, and torulene showed the dominated effect among them. Moreover, amino acid metabolism, carbohydrate metabolism and lipid metabolism act as its secondary salt-tolerant mechanism.
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2019. Elucidation of salt stress defense and tolerance mechanisms of marine red yeast Sporobolomyces pararoseus NGR using transcriptomic and metabolomic profiling. PeerJ Preprints 7:e27823v1 https://doi.org/10.7287/peerj.preprints.27823v1Author comment
This is a submission to PeerJ for review.
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Supplemental Information
Table S1 Oligonucleotide primers used for qRT-PCR
Table S1 Oligonucleotide primers used for qRT-PCR.
The all identified compounds
The all identified compounds.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Chunji Li conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Die Zhao analyzed the data, approved the final draft.
Ning Zhang approved the final draft, funding.
Bingxue Li conceived and designed the experiments, approved the final draft.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
S. pararoseus NGR was isolated from strawberries. Its strain number is recorded in the China General Microbiological Culture Collection Center as CGMCC 2.5280.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The following information was supplied regarding data availability:
The raw data of RNA-seq are available at the National Center for Biotechnology Information Sequence Read Archive (SRA): accession number SRP131948.
Data Deposition
The following information was supplied regarding data availability:
The raw data of RNA-seq are available at the National Center for Biotechnology Information Sequence Read Archive (SRA): accession number SRP131948.
Funding
This work is supported by the National Natural Science Foundation of China (Grant No. 31271818), the National Key Research and Development Program of China (Project No. 2017YFD200807-3) and Natural Science Foundation of Liaoning Province of China (Grant No.2015020763) and the Shenyang Science and Technology Innovation in Agriculture Special Fund (Grant No. F17-150-3-00). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
