Transcriptome Profiling of the Salt-Stress Response in the Halophytic Green Alga Dunaliella salina

Li, Liang; Zhang, Xiaochai; He, Ningfang; Wang, Xiaoyang; Zhu, Pengyue; Ji, Zhiyong

doi:10.1007/s11105-019-01168-z

Cited by 16 publications

(5 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This research gives a more comprehensive overview of how Dunaliella cells response to salt stress than the previous published papers do (Li et al, 2019;Lv et al, 2021;Panahi and Hejazi, 2021) due to high quality genomic data of this algae and appropriated stress time course setting. From the point of evolution, all plant cells, including higher plants, lower plants, and green algae, have similar cellular structure and respond to environmental stress similarly (Chapin, 1991), so this is also an overview of how photosynthetic cells response to salt stress.…”

Section: Discussionmentioning

confidence: 97%

The RNA landscape of Dunaliella salina in response to short-term salt stress

Zhang,

Deng,

Wang

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

Using the halotolerant green microalgae Dunaliella salina as a model organism has special merits, such as a wide range of salt tolerance, unicellular organism, and simple life cycle and growth conditions. These unique characteristics make it suitable for salt stress study. In order to provide an overview of the response of Dunaliella salina to salt stress and hopefully to reveal evolutionarily conserved mechanisms of photosynthetic organisms in response to salt stress, the transcriptomes and the genome of the algae were sequenced by the second and the third-generation sequencing technologies, then the transcriptomes under salt stress were compared to the transcriptomes under non-salt stress with the newly sequenced genome as the reference genome. The major cellular biological processes that being regulated in response to salt stress, include transcription, protein synthesis, protein degradation, protein folding, protein modification, protein transport, cellular component organization, cell redox homeostasis, DNA repair, glycerol synthesis, energy metabolism, lipid metabolism, and ion homeostasis. This study gives a comprehensive overview of how Dunaliella salina responses to salt stress at transcriptomic level, especially characterized by the nearly ubiquitous up-regulation of the genes involving in protein folding, DNA repair, and cell redox homeostasis, which may confer the algae important mechanisms to survive under salt stress. The three fundamental biological processes, which face huge challenges under salt stress, are ignored by most scientists and are worth further deep study to provide useful information for breeding economic important plants competent in tolerating salt stress, other than only depending on the commonly acknowledged osmotic balance and ion homeostasis.

show abstract

Section: Discussionmentioning

confidence: 97%

The RNA landscape of Dunaliella salina in response to short-term salt stress

Zhang,

Deng,

Wang

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…It is apparent that several pathways and processes with connection to different mechanisms are contributed to salt stress responses of D. salina . Previously transcriptome analysis, which solely has been focused on DEGs identification showed that “post-translational modifications”, “signal transduction mechanisms”; “translation, ribosomal structure, and biogenesis”; and “RNA processing and modification” similarly enriched in both types of analyses 6 , 25 . Although, systems biology approach applied here rediscovered these processes as responsive mechanisms; however, our analysis showed that some processes such as “sulfur-based metabolisms” and “Proteasome” distinctively enriched in non-preserved modules.…”

Section: Discussionmentioning

confidence: 99%

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

Panahi

Hejazi

2021

Sci Rep

View full text Add to dashboard Cite

Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (kME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.

show abstract

“…With the rapid development of transcriptome sequencing (RNA-Seq) [13], an investigation of the molecular mechanisms of algal cells to salt stress becomes convenient. Li et al [14] found that the expression of photosynthesis and the glycerol metabolism of key genes were upregulated under salt stress by analyzing transcriptome data of Dunaliella salina. Chlamydomonas reinhardtii maintained lipid homeostasis by regulating phosphatidic acid and enhancing glycolytic metabolism to decrease carbohydrate accumulation in response to salt stress [15].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis of Ulva prolifera in Response to Salt Stress

Zhuo

Wang

et al. 2022

Water

View full text Add to dashboard Cite

Since 2007, Ulva prolifera, a green macroalgal species that blooms periodically in the Yellow Sea of China, has caused the world’s biggest green tide, which induced harmful ecological impacts and economic losses. When the alga is subject to prolonged exposure to air, it suffers abiotic stresses. To explore the physiological and molecular mechanisms of salt stress, the transcriptome data of U. prolifera at different salinities (30, 50, and 90 psu) were obtained by high-throughput sequencing using the Illumina HiSeq platform, and photosynthetic physiological parameters were also measured. The results showed that a total of 89,626 unigenes were obtained after de novo assembly, of which 60,441 unigenes were annotated in the databases (NR, NT, KO, SWISS-PROT, PFAM, GO, and KOG). GO functional enrichment analysis revealed that the enrichment of differentially expressed genes (DEGs) was mainly in cellular, cell, and binding processes. KEGG metabolic pathway enrichment analysis showed that the most frequently enriched pathways of DEGs included glycolysis, pyruvate metabolism, peroxisome, and fatty acid biosynthesis. In addition, resistance-associated proteins, such as heat-shock proteins, microtubule-associated proteins, ubiquitin-associated proteins, abscisic-acid-signaling-pathway-associated proteins, and antioxidant-related proteins are upregulated under salt stress. Genes associated with photosynthesis and carbon fixation pathways are also upregulated, accompanied by an increase in photosynthetic oxygen release rates. These findings provide a basis for understanding the molecular mechanisms of the response of U. prolifera to salinity change, thus providing a theoretical basis for the analysis of the green tide outbreak mechanism.

show abstract

Transcriptome Profiling of the Salt-Stress Response in the Halophytic Green Alga Dunaliella salina

Cited by 16 publications

References 35 publications

The RNA landscape of Dunaliella salina in response to short-term salt stress

The RNA landscape of Dunaliella salina in response to short-term salt stress

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

Transcriptomic Analysis of Ulva prolifera in Response to Salt Stress

Contact Info

Product

Resources

About