Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress

Shen, Zhijun; Qin, Yingying; Luo, Mei-Rong; Li, Zan; Ma, Dongna; Wang, Wenhua; Zheng, Hai-Lei

doi:10.1016/j.jprot.2021.104349

Cited by 16 publications

(14 citation statements)

References 79 publications

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“…Leaves were collected at 0, 3, 6, 12, and 24 h for each group of treatments. They were frozen immediately in liquid nitrogen for RNA extraction according to Shen et al (2021) . For each sample, three biological replicates and three technical replicates were conducted.…”

Section: Materials and Methodsmentioning

confidence: 99%

“…It is a complex process involving many molecular, biochemical, and physiological changes ( John et al, 2016 ). It has been reported that cold acclimated Sonneratia apetala seedlings have lower relative electrolyte leakage and malondialdehyde (MDA) content than non-acclimated seedlings ( Shen et al, 2021 ). Furthermore, it has been shown that cold acclimated Hordeum vulgare (barley) plants have higher cold tolerance and photosynthesis rates than non-acclimated control plants ( Jurczyk et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

Zhang

Gong

Sun³

et al. 2022

PeerJ

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C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops.

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Section: Materials and Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

Zhang

Gong

Sun³

et al. 2022

PeerJ

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“…Mangroves grow in harsh conditions involving anaerobic soils, extreme tides, high salinity, strong winds, sea-level rise, and extreme climate events ( Guo et al., 2017 ). Cold stress is one of the most crucial factors limiting the development, growth, and geographical distribution of mangrove plants among all of these abiotic stresses ( Shen et al., 2021 ). Cold stress (low temperature) can be categorized into chilling stress (0−15°C) or freezing stress (< 0°C) according to its intensity ( Jiang et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

You

Yang

et al. 2022

Front. Plant Sci.

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BackgroundKandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.MethodsThe KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.ResultsA total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.ConclusionsSeventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.

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“…One MDH protein (O48905) was suppressed in BE and expressed in OG, while one MDH protein (Q08062) was expressed in TE only. In previous studies, the MDH proteins were suppressed in Brassica [ 79 ] and upregulated in S. apetala under chilling stress [ 80 ]. Citrate synthase, mitochondrial (P49298), and isocitrate dehydrogenase [NAD] (Q8LFC0) proteins were suppressed in BE.…”

Section: Discussionmentioning

confidence: 99%

Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress

Saand

et al. 2022

IJMS

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Oil palm (Elaeis guineensis Jacq.) is an economically important tropical oil crop widely cultivated in tropical zones worldwide. Being a tropical crop, low-temperature stress adversely affects the oil palm. However, integrative leaf transcriptomic and proteomic analyses have not yet been conducted on an oil palm crop under cold stress. In this study, integrative omics transcriptomic and iTRAQ-based proteomic approaches were employed for three oil palm varieties, i.e., B × E (Bamenda × Ekona), O × G (E. oleifera × Elaeis guineensis), and T × E (Tanzania × Ekona), in response to low-temperature stress. In response to low-temperature stress at (8 °C) for 5 days, a total of 5175 up- and 2941 downregulated DEGs in BE-0_VS_BE-5, and a total of 3468 up- and 2443 downregulated DEGs for OG-0_VS_OG-5, and 3667 up- and 2151 downregulated DEGs for TE-0_VS_TE-5 were identified. iTRAQ-based proteomic analysis showed 349 up- and 657 downregulated DEPs for BE-0_VS_BE-5, 372 up- and 264 downregulated DEPs for OG-0_VS_OG-5, and 500 up- and 321 downregulated DEPs for TE-0_VS_TE-5 compared to control samples treated at 28 °C and 8 °C, respectively. The KEGG pathway correlation of oil palm has shown that the metabolic synthesis and biosynthesis of secondary metabolites pathways were significantly enriched in the transcriptome and proteome of the oil palm varieties. The correlation expression pattern revealed that TE-0_VS_TE-5 is highly expressed and BE-0_VS_BE-5 is suppressed in both the transcriptome and proteome in response to low temperature. Furthermore, numerous transcription factors (TFs) were found that may regulate cold acclimation in three oil palm varieties at low temperatures. Moreover, this study identified proteins involved in stresses (abiotic, biotic, oxidative, and heat shock), photosynthesis, and respiration in iTRAQ-based proteomic analysis of three oil palm varieties. The increased abundance of stress-responsive proteins and decreased abundance of photosynthesis-related proteins suggest that the TE variety may become cold-resistant in response to low-temperature stress. This study may provide a basis for understanding the molecular mechanism for the adaptation of oil palm varieties in response to low-temperature stress in China.

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Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress

Cited by 16 publications

References 79 publications

Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress

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