Cargando…
Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55
It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908243/ https://www.ncbi.nlm.nih.gov/pubmed/35283918 http://dx.doi.org/10.3389/fpls.2022.828321 |
_version_ | 1784665835406622720 |
---|---|
author | Zhang, Luo-Yan Xing, Zhao-Tian Chen, Li-Qian Zhang, Xue-Jie Fan, Shou-Jin |
author_facet | Zhang, Luo-Yan Xing, Zhao-Tian Chen, Li-Qian Zhang, Xue-Jie Fan, Shou-Jin |
author_sort | Zhang, Luo-Yan |
collection | PubMed |
description | It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2–4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response. |
format | Online Article Text |
id | pubmed-8908243 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-89082432022-03-11 Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 Zhang, Luo-Yan Xing, Zhao-Tian Chen, Li-Qian Zhang, Xue-Jie Fan, Shou-Jin Front Plant Sci Plant Science It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2–4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response. Frontiers Media S.A. 2022-02-24 /pmc/articles/PMC8908243/ /pubmed/35283918 http://dx.doi.org/10.3389/fpls.2022.828321 Text en Copyright © 2022 Zhang, Xing, Chen, Zhang and Fan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Zhang, Luo-Yan Xing, Zhao-Tian Chen, Li-Qian Zhang, Xue-Jie Fan, Shou-Jin Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title | Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title_full | Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title_fullStr | Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title_full_unstemmed | Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title_short | Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55 |
title_sort | comprehensive time-course transcriptome and co-expression network analyses identify salt stress responding mechanisms in chlamydomonas reinhardtii strain gy-d55 |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908243/ https://www.ncbi.nlm.nih.gov/pubmed/35283918 http://dx.doi.org/10.3389/fpls.2022.828321 |
work_keys_str_mv | AT zhangluoyan comprehensivetimecoursetranscriptomeandcoexpressionnetworkanalysesidentifysaltstressrespondingmechanismsinchlamydomonasreinhardtiistraingyd55 AT xingzhaotian comprehensivetimecoursetranscriptomeandcoexpressionnetworkanalysesidentifysaltstressrespondingmechanismsinchlamydomonasreinhardtiistraingyd55 AT chenliqian comprehensivetimecoursetranscriptomeandcoexpressionnetworkanalysesidentifysaltstressrespondingmechanismsinchlamydomonasreinhardtiistraingyd55 AT zhangxuejie comprehensivetimecoursetranscriptomeandcoexpressionnetworkanalysesidentifysaltstressrespondingmechanismsinchlamydomonasreinhardtiistraingyd55 AT fanshoujin comprehensivetimecoursetranscriptomeandcoexpressionnetworkanalysesidentifysaltstressrespondingmechanismsinchlamydomonasreinhardtiistraingyd55 |