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Molecular Mechanisms of Abiotic Stress Responses in Trees
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Molecular Mechanisms of Abiotic Stress Responses in Trees

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 25801

Special Issue Editors

Prof. Dr. Chuanping Yang

E-Mail Website
Guest Editor
School of Forest, Northeast Forestry University, Harbin 150400, China
Interests: breeding of improved forest varieties; intensive breeding technology; molecular biology of forest trees
Prof. Dr. Chenghao Li

E-Mail Website
Guest Editor
School of Forest, Northeast Forestry University, Harbin 150040, China
Interests: tree genetics and breeding; poplar
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Although there is a wealth of data available, it is important to note that studies on abiotic stress response in trees are relatively fragmented compared to Arabidopsis and crop species. For example, it is difficult to map sequential signaling pathways from receptors to effectors, and the identity of specific sensors that trigger abiotic stress responses remains unclear. By the increasing availability of the genomes of tree species, to uncover the mechanisms of issue-specific signaling and stress resistance is no longer a threshold. Understanding of the molecular machanisms of abiotic stress responses in trees will provide the strategies to predict and potentially promote tree adaptation to avieties of stress conditions. Our aim is to provide scientists involved in the abiotic stress of trees with the possibility of communication of the field.

In this Special Issue of IJMS, entitled “Molecular mechanisms of abiotic stress responses in trees” will deal with a variety of abiotic stress in trees in terms of: the physiological, cellular and molecular responses to abiotic stress, and their regulation, in both the short and long term; the molecular mechanisms of stressful stimulation, including within and between individuals; application of adaptive mechanisms, coping strategies, and breeding of new tree varieties. Welcomes submissions on wild and cultivated woody species in the special issue.

Prof. Dr. Chuanping Yang
Prof. Dr. Chenghao Li
Guest Editors

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Keywords

  • drought stress
  • nitrogen and phosphate deficiency
  • heavy metal stress
  • low- and high-temperature stress
  • bioinformatics
  • transcriptional and epigenetic regulation
  • poplar

Published Papers (15 papers)

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21 pages, 17130 KiB  
Article
Molecular and Physiological Responses of Citrus sinensis Leaves to Long-Term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics
by Ning-Wei Lai, Zhi-Chao Zheng, Dan Hua, Jiang Zhang, Huan-Huan Chen, Xin Ye, Zeng-Rong Huang, Jiuxin Guo, Lin-Tong Yang and Li-Song Chen
Int. J. Mol. Sci. 2022, 23(10), 5844; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23105844 - 23 May 2022
Cited by 4 | Viewed by 2191
Abstract
Low pH-induced alterations in gene expression profiles and organic acids (OA) and free amino acid (FAA) abundances were investigated in sweet orange [Citrus sinensis (L.) Osbeck cv. Xuegan] leaves. We identified 503 downregulated and 349 upregulated genes in low pH-treated leaves. Further [...] Read more.
Low pH-induced alterations in gene expression profiles and organic acids (OA) and free amino acid (FAA) abundances were investigated in sweet orange [Citrus sinensis (L.) Osbeck cv. Xuegan] leaves. We identified 503 downregulated and 349 upregulated genes in low pH-treated leaves. Further analysis indicated that low pH impaired light reaction and carbon fixation in photosynthetic organisms, thereby lowering photosynthesis in leaves. Low pH reduced carbon and carbohydrate metabolisms, OA biosynthesis and ATP production in leaves. Low pH downregulated the biosynthesis of nitrogen compounds, proteins, and FAAs in leaves, which might be conducive to maintaining energy homeostasis during ATP deprivation. Low pH-treated leaves displayed some adaptive responses to phosphate starvation, including phosphate recycling, lipid remodeling, and phosphate transport, thus enhancing leaf acid-tolerance. Low pH upregulated the expression of some reactive oxygen species (ROS) and aldehyde detoxifying enzyme (peroxidase and superoxidase) genes and the concentrations of some antioxidants (L-tryptophan, L-proline, nicotinic acid, pantothenic acid, and pyroglutamic acid), but it impaired the pentose phosphate pathway and VE and secondary metabolite biosynthesis and downregulated the expression of some ROS and aldehyde detoxifying enzyme (ascorbate peroxidase, aldo-keto reductase, and 2-alkenal reductase) genes and the concentrations of some antioxidants (pyridoxine and γ-aminobutyric acid), thus disturbing the balance between production and detoxification of ROS and aldehydes and causing oxidative damage to leaves. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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16 pages, 12233 KiB  
Article
Effects of Donor Ages and Propagation Methods on Seedling Growth of Platycladus orientalis (L.) Franco in Winter
by Yao Dong, Wenfa Xiao, Wei Guo, Yifu Liu, Wen Nie, Ruizhi Huang, Cancan Tan, Zirui Jia, Jianfeng Liu, Zeping Jiang and Ermei Chang
Int. J. Mol. Sci. 2023, 24(8), 7170; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24087170 - 12 Apr 2023
Cited by 2 | Viewed by 1324
Abstract
To evaluate the effects of donor ages on growth and stress resistance of 6-year-old seedlings propagated from 5-, 2000-, and 3000-year-old Platycladus orientalis donors with grafting, cutting, and seed sowing, growth indicators and physiological and transcriptomic analyses were performed in 6-year-old seedlings in [...] Read more.
To evaluate the effects of donor ages on growth and stress resistance of 6-year-old seedlings propagated from 5-, 2000-, and 3000-year-old Platycladus orientalis donors with grafting, cutting, and seed sowing, growth indicators and physiological and transcriptomic analyses were performed in 6-year-old seedlings in winter. Results showed that basal stem diameters and plant heights of seedlings of the three propagation methods decreased with the age of the donors, and the sown seedlings were the thickest and tallest. The contents of soluble sugar, chlorophyll, and free fatty acid in apical leaves of the three propagation methods were negatively correlated with donor ages in winter, while the opposite was true for flavonoid and total phenolic. The contents of flavonoid, total phenolic, and free fatty acid in cutting seedlings were highest in the seedlings propagated in the three methods in winter. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis of differentially expressed genes showed phenylpropanoid biosynthesis and fatty acid metabolism pathways, and their expression levels were up-regulated in apical leaves from 6-year-old seedlings propagated from 3000-year-old P. orientalis donors. In addition, hub genes analysis presented that C4H, OMT1, CCR2, PAL, PRX52, ACP1, AtPDAT2, and FAD3 were up-regulated in cutting seedlings, and the gene expression levels decreased in seedlings propagated from 2000- and 3000-year-old donors. These findings demonstrate the resistance stability of cuttings of P. orientalis and provide insights into the regulatory mechanisms of seedlings of P. orientalis propagated from donors at different ages in different propagation methods against low-temperature stress. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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19 pages, 8872 KiB  
Article
Genomic Survey of Heat Shock Proteins in Liriodendron chinense Provides Insight into Evolution, Characterization, and Functional Diversities
by Yongchao Ke, Mingyue Xu, Delight Hwarari, Jinhui Chen and Liming Yang
Int. J. Mol. Sci. 2022, 23(23), 15051; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232315051 - 30 Nov 2022
Cited by 1 | Viewed by 1191
Abstract
Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles [...] Read more.
Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles in cells. However, the HSP gene family has not yet been analyzed in the Liriodendron chinense genome. In current study, 60 HSP genes were identified in the L. chinense genome, including 7 LchiHSP90s, 23 LchiHSP70s, and 30 LchiHSP20s. We investigated the phylogenetic relationships, gene structure and arrangement, gene duplication events, cis-acting elements, 3D-protein structures, protein–protein interaction networks, and temperature stress responses in the identified L. chinense HSP genes. The results of the comparative phylogenetic analysis of HSP families in 32 plant species showed that LchiHSPs are closely related to the Cinnamomum kanehirae HSP gene family. Duplication events analysis showed seven segmental and six tandem duplication events that occurred in the LchiHSP gene family, which we speculated to have played an important role in the LchiHSP gene expansion and evolution. Furthermore, the Ka/Ks analysis indicated that these genes underwent a purifying selection. Analysis in the promoter region evidenced that the promoter region LchiHSPs carry many stress-responsive and hormone-related cis-elements. Investigations in the gene expression patterns of the LchiHSPs using transcriptome data and the qRT-PCR technique indicated that most LchiHSPs were responsive to cold and heat stress. In total, our results provide new insights into understanding the LchiHSP gene family function and their regulatory mechanisms in response to abiotic stresses. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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21 pages, 9525 KiB  
Article
Comparative Transcriptomic and Metabolic Analyses Reveal the Coordinated Mechanisms in Pinus koraiensis under Different Light Stress Conditions
by Yuxi Li, Xinxin Zhang, Kewei Cai, Qinhui Zhang, Luping Jiang, Hanxi Li, Yuzhe Lv, Guanzheng Qu and Xiyang Zhao
Int. J. Mol. Sci. 2022, 23(17), 9556; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179556 - 23 Aug 2022
Cited by 6 | Viewed by 1586
Abstract
Light is one of the most important environmental cues that affects plant development and regulates its behavior. Light stress directly inhibits physiological responses and plant tissue development and even induces mortality in plants. Korean pine (Pinus koraiensis) is an evergreen conifer [...] Read more.
Light is one of the most important environmental cues that affects plant development and regulates its behavior. Light stress directly inhibits physiological responses and plant tissue development and even induces mortality in plants. Korean pine (Pinus koraiensis) is an evergreen conifer species widely planted in northeast China that has important economic and ecological value. However, the effects of light stress on the growth and development of Korean pine are still unclear. In this study, the effects of different shading conditions on physiological indices, molecular mechanisms and metabolites of Korean pine were explored. The results showed that auxin, gibberellin and abscisic acid were significantly increased under all shading conditions compared with the control. The contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoid also increased as the shading degree increased. Moreover, a total of 8556, 3751 and 6990 differentially expressed genes (DEGs) were found between the control and HS (heavy shade), control and LS (light shade), LS vs. HS, respectively. Notably, most DEGs were assigned to pathways of phytohormone signaling, photosynthesis, carotenoid and flavonoid biosynthesis under light stress. The transcription factors MYB-related, AP2-ERF and bHLH specifically increased expression during light stress. A total of 911 metabolites were identified, and 243 differentially accumulated metabolites (DAMs) were detected, among which flavonoid biosynthesis (naringenin chalcone, dihydrokaempferol and kaempferol) metabolites were significantly different under light stress. These results will provide a theoretical basis for the response of P. koraiensis to different light stresses. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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21 pages, 3003 KiB  
Article
Acclimation Strategy of Masson Pine (Pinus massoniana) by Limiting Flavonoid and Terpenoid Production under Low Light and Drought
by Zheng Shi, Xiuxiu Deng, Lixiong Zeng, Shengqing Shi, Lei Lei and Wenfa Xiao
Int. J. Mol. Sci. 2022, 23(15), 8441; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158441 - 29 Jul 2022
Cited by 4 | Viewed by 1654
Abstract
Low light and drought often limit the growth and performance of Masson pines (Pinus massoniana) in the subtropical forest ecosystem of China. We speculated that stress-induced defensive secondary metabolites, such as flavonoids and terpenoids, might influence the growth of Masson pines, [...] Read more.
Low light and drought often limit the growth and performance of Masson pines (Pinus massoniana) in the subtropical forest ecosystem of China. We speculated that stress-induced defensive secondary metabolites, such as flavonoids and terpenoids, might influence the growth of Masson pines, considering the existence of tradeoffs between growth and defense. However, the mechanisms of Masson pines responsive to low light and drought at the levels of these two metabolites remain unclear. In the present work, the compositions of flavonoids and terpenoids, as well as their biosynthetic pathways, were revealed through metabolome and transcriptome analyses, respectively, coupled with a study on carbon allocation using a 13CO2-pulse-labeling experiment in two-year-old seedlings under low light (LL), drought (DR), and their combined stress (DL) compared to a control (CK). A total of 35 flavonoids and derivatives (LL vs. CK: 18; DR vs. CK: 20; and DL vs. CK: 18), as well as 29 terpenoids and derivatives (LL vs. CK: 23; DR vs. CK: 13; and DL vs. CK: 7), were differentially identified in the leaves. Surprisingly, most of them were decreased under all three stress regimes. At the transcriptomic level, most or all of the detected DEGs (differentially expressed genes) involved in the biosynthetic pathways of flavonoids and terpenoids were downregulated in phloem and xylem under stress treatments. This indicated that stress treatments limited the production of flavonoids and terpenoids. The reduction in the 13C allocation to stems might suggest that it is necessary for maintaining the growth of Masson pine seedlings at the whole-plant level by attenuating energetic resources to the biosynthetic pathways of flavonoids and terpenoids when facing the occurrence of adverse environments. Our results provide new insight into understanding the acclimation strategy of Masson pines or other conifers in adverse environments. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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13 pages, 3081 KiB  
Article
PsnWRKY70 Negatively Regulates NaHCO3 Tolerance in Populus
by Wei Wang, Xiang-Dong Bai, Kun Chen, Xiao-Yue Zhang, Chen-Rui Gu, Jing Jiang, Chuan-Ping Yang and Gui-Feng Liu
Int. J. Mol. Sci. 2022, 23(21), 13086; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232113086 - 28 Oct 2022
Cited by 2 | Viewed by 1150
Abstract
Poplar is an important afforestation and ornamental tree species in Northeast China. The distribution area of saline-alkali land is approximately 765 hm2 in Northeast China. The breeding of saline-alkali-resistant transgenic trees could be an effective method of afforestation in saline-alkali land. WRKY [...] Read more.
Poplar is an important afforestation and ornamental tree species in Northeast China. The distribution area of saline-alkali land is approximately 765 hm2 in Northeast China. The breeding of saline-alkali-resistant transgenic trees could be an effective method of afforestation in saline-alkali land. WRKY transcription factors play a crucial role in abiotic stress. In this study, we analyzed the genetic stability of the two-year-old PsnWRKY70 transgenic poplars. The results showed that PsnWRKY70 of transgenic poplars had been expressed stably and normally at the mRNA level. The gene interference expression (RE) lines had no significant effect on the growth of PsnWRKY70 under NaHCO3 stress, and the alkali damage index of RE lines was significantly lower than that of WT and overexpression (OE) lines at day 15 under NaHCO3 stress. POD activity was significantly higher in RE lines than in WT. The MDA content of the RE line was lower than that of the WT line. Transcriptome analysis showed that RE lines up-regulated genes enriched in cell wall organization or biogenesis pathway-related genes such as EXPA8, EXPA4, EXPA3, EXPA1, EXPB3, EXP10, PME53, PME34, PME36, XTH9, XTH6, XTH23, CESA1, CESA3, CES9; FLA11, FLA16 and FLA7 genes. These genes play an important role in NaHCO3 stress. Our study showed that the interference expression of the PsnWRKY70 gene can enhance the tolerance of NaHCO3 in poplar. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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14 pages, 3878 KiB  
Article
Overexpression of PagERF072 from Poplar Improves Salt Tolerance
by Xuemei Zhang, Zihan Cheng, Wenjing Yao, Yuan Gao, Gaofeng Fan, Qing Guo, Boru Zhou and Tingbo Jiang
Int. J. Mol. Sci. 2022, 23(18), 10707; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810707 - 14 Sep 2022
Cited by 5 | Viewed by 1746
Abstract
Extreme environments, especially drought and high salt conditions, seriously affect plant growth and development. Ethylene-responsive factor (ERF) transcription factors play an important role in salt stress response. In this study, a significantly upregulated ERF gene was identified in 84K (Populus alba × [...] Read more.
Extreme environments, especially drought and high salt conditions, seriously affect plant growth and development. Ethylene-responsive factor (ERF) transcription factors play an important role in salt stress response. In this study, a significantly upregulated ERF gene was identified in 84K (Populus alba × P. glandulosa), which was named PagERF072. PagERF072 was confirmed to be a nuclear-localized protein. The results of yeast two-hybrid (Y2H) assay showed that PagERF072 protein exhibited no self-activating activity, and yeast one-hybrid (Y1H) demonstrated that PagERF072 could specifically bind to GCC-box element. Under salt stress, the transgenic poplar lines overexpressing PagERF072 showed improved salt tolerance. The activities of peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) in transgenic poplars were significantly increased relative to those of wild-type (WT) plants, whereas malondialdehyde (MDA) content showed an opposite trend. In addition, reactive oxygen species (ROS) was significantly reduced, and the expression levels of POD- and SOD-related genes were significantly increased in transgenic poplars under salt stress compared with WT. All results indicate that overexpression of the PagERF072 gene can improve the salt tolerance of transgenic poplars. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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15 pages, 5291 KiB  
Article
Transcriptome Analysis Reveals That Ascorbic Acid Treatment Enhances the Cold Tolerance of Tea Plants through Cell Wall Remodeling
by Qianyuan Fu, Hongli Cao, Lu Wang, Lei Lei, Taimei Di, Yufan Ye, Changqing Ding, Nana Li, Xinyuan Hao, Jianming Zeng, Yajun Yang, Xinchao Wang, Meng Ye and Jianyan Huang
Int. J. Mol. Sci. 2023, 24(12), 10059; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241210059 - 13 Jun 2023
Cited by 2 | Viewed by 1282
Abstract
Cold stress is a major environmental factor that adversely affects the growth and productivity of tea plants. Upon cold stress, tea plants accumulate multiple metabolites, including ascorbic acid. However, the role of ascorbic acid in the cold stress response of tea plants is [...] Read more.
Cold stress is a major environmental factor that adversely affects the growth and productivity of tea plants. Upon cold stress, tea plants accumulate multiple metabolites, including ascorbic acid. However, the role of ascorbic acid in the cold stress response of tea plants is not well understood. Here, we report that exogenous ascorbic acid treatment improves the cold tolerance of tea plants. We show that ascorbic acid treatment reduces lipid peroxidation and increases the Fv/Fm of tea plants under cold stress. Transcriptome analysis indicates that ascorbic acid treatment down-regulates the expression of ascorbic acid biosynthesis genes and ROS-scavenging-related genes, while modulating the expression of cell wall remodeling-related genes. Our findings suggest that ascorbic acid treatment negatively regulates the ROS-scavenging system to maintain ROS homeostasis in the cold stress response of tea plants and that ascorbic acid’s protective role in minimizing the harmful effects of cold stress on tea plants may occur through cell wall remodeling. Ascorbic acid can be used as a potential agent to increase the cold tolerance of tea plants with no pesticide residual concerns in tea. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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23 pages, 10739 KiB  
Article
Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Neolamarckia cadamba
by Zuowei Xu, Yutong Liu, Huiting Fang, Yanqiong Wen, Ying Wang, Jianxia Zhang, Changcao Peng and Jianmei Long
Int. J. Mol. Sci. 2023, 24(8), 7537; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24087537 - 19 Apr 2023
Cited by 1 | Viewed by 1507
Abstract
The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a ‘miracle tree’ for its [...] Read more.
The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a ‘miracle tree’ for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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17 pages, 4252 KiB  
Article
Comprehensive Analysis of the NF-YB Gene Family and Expression under Abiotic Stress and Hormone Treatment in Larix kaempferi
by Lu Li, Xi Ren, Liying Shao, Xun Huang, Chunyan Zhang, Xuhui Wang, Jingli Yang and Chenghao Li
Int. J. Mol. Sci. 2023, 24(10), 8910; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24108910 - 17 May 2023
Cited by 1 | Viewed by 1174
Abstract
NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have [...] Read more.
NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have not yet been explored in Larix kaempferi, a tree species with high economic and ecological values in northeast China and other regions, limiting the breeding of anti-stress L. kaempferi. In order to explore the roles of NF-YB transcription factors in L. kaempferi, we identified 20 LkNF-YB family genes from L. kaempferi full-length transcriptome data and carried out preliminary characterization of them through series of analyses on their phylogenetic relationships, conserved motif structure, subcellular localization prediction, GO annotation, promoter cis-acting elements as well as expression profiles under treatment of phytohormones (ABA, SA, MeJA) and abiotic stresses (salt and drought). The LkNF-YB genes were classified into three clades through phylogenetic analysis and belong to non-LEC1 type NF-YB transcription factors. They have 10 conserved motifs; all genes contain a common motif, and their promoters have various phytohormones and abiotic stress related cis-acting elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the sensitivity of the LkNF-YB genes to drought and salt stresses was higher in leaves than roots. The sensitivity of LKNF-YB genes to ABA, MeJA, SA stresses was much lower than that to abiotic stress. Among the LkNF-YBs, LkNF-YB3 showed the strongest responses to drought and ABA treatments. Further protein interaction prediction analysis for LkNF-YB3 revealed that LkNF-YB3 interacts with various factors associated with stress responses and epigenetic regulation as well as NF-YA/NF-YC factors. Taken together, these results unveiled novel L. kaempferi NF-YB family genes and their characteristics, providing the basic knowledge for further in-depth studies on their roles in abiotic stress responses of L. kaempferi. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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19 pages, 7992 KiB  
Article
Genome-Wide Analysis of SIMILAR TO RCD ONE (SRO) Family Revealed Their Roles in Abiotic Stress in Poplar
by Yuting Wang, Ruiqi Wang, Yue Yu, Yongmei Gu, Shuang Wang, Shixian Liao, Xiaoya Xu, Tingbo Jiang and Wenjing Yao
Int. J. Mol. Sci. 2023, 24(4), 4146; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24044146 - 19 Feb 2023
Cited by 6 | Viewed by 1963
Abstract
SIMILAR TO RCD ONE (SRO) gene family is a small plant-specific gene family responsible for growth, development, and stress responses. In particular, it plays a vital role in responding to abiotic stresses such as salt, drought, and heavy metals. Poplar SROs are rarely [...] Read more.
SIMILAR TO RCD ONE (SRO) gene family is a small plant-specific gene family responsible for growth, development, and stress responses. In particular, it plays a vital role in responding to abiotic stresses such as salt, drought, and heavy metals. Poplar SROs are rarely reported to date. In this study, a total of nine SRO genes were identified from Populus simonii × Populus nigra, which are more similar to dicotyledon SRO members. According to phylogenetic analysis, the nine PtSROs can be divided into two groups, and the members in the same cluster have a similar structure. There were some cis-regulatory elements related to abiotic stress response and hormone-induced factors identified in the promoter regions of PtSROs members. Subcellular localization and transcriptional activation activity of PtSRO members revealed a consistent expression profile of the genes with similar structural profiles. In addition, both RT-qPCR and RNA-Seq results indicated that PtSRO members responded to PEG-6000, NaCl, and ABA stress in the roots and leaves of Populus simonii × Populus nigra. The PtSRO genes displayed different expression patterns and peaked at different time points in the two tissues, which was more significant in the leaves. Among them, PtSRO1c and PtSRO2c were more prominent in response to abiotic stress. Furthermore, protein interaction prediction showed that the nine PtSROs might interact with a broad range of transcription factors (TFs) involved in stress responses. In conclusion, the study provides a solid basis for functional analysis of the SRO gene family in abiotic stress responses in poplar. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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21 pages, 5121 KiB  
Article
Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing
by Wenlong Li, Zhiwei Liu, He Feng, Jingli Yang and Chenghao Li
Int. J. Mol. Sci. 2022, 23(7), 3840; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073840 - 30 Mar 2022
Cited by 7 | Viewed by 2282
Abstract
In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. [...] Read more.
In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca2+, proline, and total soluble sugars, were further confirmed in P. ussuriensis roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in P. ussuriensis and meaningful information for genetic engineering research in the future. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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26 pages, 13322 KiB  
Article
Overexpression of TgERF1, a Transcription Factor from Tectona grandis, Increases Tolerance to Drought and Salt Stress in Tobacco
by Perla Novais de Oliveira, Fernando Matias, Cristina Martínez-Andújar, Purificación Andrea Martinez-Melgarejo, Ángela Sánchez Prudencio, Esteban Galeano, Francisco Pérez-Alfocea and Helaine Carrer
Int. J. Mol. Sci. 2023, 24(4), 4149; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24044149 - 19 Feb 2023
Cited by 4 | Viewed by 1566
Abstract
Teak (Tectona grandis) is one of the most important wood sources, and it is cultivated in tropical regions with a significant market around the world. Abiotic stresses are an increasingly common and worrying environmental phenomenon because it causes production losses in [...] Read more.
Teak (Tectona grandis) is one of the most important wood sources, and it is cultivated in tropical regions with a significant market around the world. Abiotic stresses are an increasingly common and worrying environmental phenomenon because it causes production losses in both agriculture and forestry. Plants adapt to these stress conditions by activation or repression of specific genes, and they synthesize numerous stress proteins to maintain their cellular function. For example, APETALA2/ethylene response factor (AP2/ERF) was found to be involved in stress signal transduction. A search in the teak transcriptome database identified an AP2/ERF gene named TgERF1 with a key AP2/ERF domain. We then verified that the TgERF1 expression is rapidly induced by Polyethylene Glycol (PEG), NaCl, and exogenous phytohormone treatments, suggesting a potential role in drought and salt stress tolerance in teak. The full-length coding sequence of TgERF1 gene was isolated from teak young stems, characterized, cloned, and constitutively overexpressed in tobacco plants. In transgenic tobacco plants, the overexpressed TgERF1 protein was localized exclusively in the cell nucleus, as expected for a transcription factor. Furthermore, functional characterization of TgERF1 provided evidence that TgERF1 is a promising candidate gene to be used as selective marker on plant breeding intending to improve plant stress tolerance. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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11 pages, 1178 KiB  
Review
Peroxisome-Mediated Reactive Oxygen Species Signals Modulate Programmed Cell Death in Plants
by Lichao Huang, Yijing Liu, Xiaqin Wang, Cheng Jiang, Yanqiu Zhao, Mengzhu Lu and Jin Zhang
Int. J. Mol. Sci. 2022, 23(17), 10087; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231710087 - 03 Sep 2022
Cited by 6 | Viewed by 2119
Abstract
Peroxisomes are a class of simple organelles that play an important role in plant reactive oxygen species (ROS) metabolism. Experimental evidence reveals the involvement of ROS in programmed cell death (PCD) in plants. Plant PCD is crucial for the regulation of plant growth, [...] Read more.
Peroxisomes are a class of simple organelles that play an important role in plant reactive oxygen species (ROS) metabolism. Experimental evidence reveals the involvement of ROS in programmed cell death (PCD) in plants. Plant PCD is crucial for the regulation of plant growth, development and environmental stress resistance. However, it is unclear whether the ROS originated from peroxisomes participated in cellular PCD. Enzymes involved in the peroxisomal ROS metabolic pathways are key mediators to figure out the relationship between peroxisome-derived ROS and PCD. Here, we summarize the peroxisomal ROS generation and scavenging pathways and explain how peroxisome-derived ROS participate in PCD based on recent progress in the functional study of enzymes related to peroxisomal ROS generation or scavenging. We aimed to elucidate the role of the peroxisomal ROS regulatory system in cellular PCD to show its potential in terms of accurate PCD regulation, which contribute to environmental stress resistance. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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24 pages, 4745 KiB  
Article
Transcriptomics Reveals the Effect of Short-Term Freezing on the Signal Transduction and Metabolism of Grapevine
by Xing Han, Yi-Han Li, Mo-Han Yao, Fei Yao, Zhi-Lei Wang, Hua Wang and Hua Li
Int. J. Mol. Sci. 2023, 24(4), 3884; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043884 - 15 Feb 2023
Cited by 3 | Viewed by 1552
Abstract
Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of [...] Read more.
Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of dormant cv. Cabernet Sauvignon exposed to several low-temperature conditions to identify differentially expressed genes and determine their function based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)enrichment analyses. Our results indicated that exposure to subzero low temperatures resulted in damage to plant cell membranes and extravasation of intracellular electrolytes, and that this damage increased with decreasing temperature or increasing duration. The number of differential genes increased as the duration of stress increased, but most of the common differentially expressed genes reached their highest expression at 6 h of stress, indicating that 6 h may be a turning point for vines to tolerate extreme low temperatures. Several pathways play key roles in the response of Cabernet Sauvignon to low-temperature injury, namely: (1) the role of calcium/calmodulin-mediated signaling; (2) carbohydrate metabolism, including the hydrolysis of cell wall pectin and cellulose, decomposition of sucrose, synthesis of raffinose, and inhibition of glycolytic processes; (3) the synthesis of unsaturated fatty acids and metabolism of linolenic acid; and (4) the synthesis of secondary metabolites, especially flavonoids. In addition, pathogenesis-related protein may also play a role in plant cold resistance, but the mechanism is not yet clear. This study reveals possible pathways for the freezing response and leads to new insights into the molecular basis of the tolerance to low temperature in grapevine. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Abiotic Stress Responses in Trees)
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