Transcriptome analysis of harvested bell peppers (Capsicum annuum L.) in response to cold stress.
Kong Xi-Man,Zhou Qian,Luo Feng,Wei Bao-Dong,Wang Ya-Juan,Sun Hua-Jun,Zhao Ying-Bo,Ji Shu-Juan
Plant physiology and biochemistry : PPB
Bell peppers are valued for their plentiful vitamin C and nutritional content. Pepper fruits are susceptible to cold storage, which leads to chilling injury (CI); however, the crucial metabolic product and molecular basis response to cold stress have not been elucidated definitely yet. To comprehensively understand the gene regulation network and CI mechanisms in response to cold stress on a molecular level, we performed high-throughput RNA-Seq analysis to investigate genome-wide expression profiles in bell peppers at different storage temperatures (4 °C and 10 °C). A total of 61.55 Gb of clean data were produced; 3863 differentially expressed genes (DEGs) including 1669 up-regulated and 2194 down-regulated were annotated and classified between the CI group and control. Together, a total of 41 cold-induced transcription factor families comprising 250 transcription factors (TFs) were identified. Notably, numerous DEGs involved in biomembrane stability, dehydration and osmoregulation, and plant hormone signal transduction processes were discovered. The transcriptional level of 20 DEGs was verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Our results present transcriptome profiles of bell peppers in response to cold stress; the data obtained may be useful for the identification of key candidate genes and elucidation of the mechanisms underlying membrane damage during chilling injury.
10.1016/j.plaphy.2019.03.033
RNA helicases and abiotic stress.
Owttrim George W
Nucleic acids research
RNA helicases function as molecular motors that rearrange RNA secondary structure, potentially performing roles in any cellular process involving RNA metabolism. Although RNA helicase association with a range of cellular functions is well documented, their importance in response to abiotic stress is only beginning to emerge. This review summarizes the available data on the expression, biochemistry and physiological function(s) of RNA helicases regulated by abiotic stress. Examples originate primarily from non-mammalian organisms while instances from mammalian sources are restricted to post-translational regulation of helicase biochemical activity. Common emerging themes include the requirement of a cold-induced helicase in non-homeothermic organisms, association and regulation of helicase activity by stress-induced phosphorylation cascades, altered nuclear-cytoplasmic shuttling in eukaryotes, association with the transcriptional apparatus and the diversity of biochemical activities catalyzed by a subgroup of stress-induced helicases. The data are placed in the context of a mechanism for RNA helicase involvement in cellular response to abiotic stress. It is proposed that stress-regulated helicases can catalyze a nonlinear, reversible sequence of RNA secondary structure rearrangements which function in RNA maturation or RNA proofreading, providing a mechanism by which helicase activity alters the activation state of target RNAs through regulation of the reaction equilibrium.
10.1093/nar/gkl408
Photoperiod and temperature differentially regulate the expression of two dehydrin genes during overwintering of birch (Betula pubescens Ehrh.).
Welling Annikki,Rinne Päivi,Viherä-Aarnio Anneli,Kontunen-Soppela Sari,Heino Pekka,Palva E Tapio
Journal of experimental botany
The overwintering of trees in northern areas depends on processes regulated by photoperiod and temperature. To identify the physiological and genetic factors involved in this environmental control, three latitudinal ecotypes of pubescent birch (Betula pubescens Ehrh.) growing in a common garden experiment were used. Each ecotype responded to the shortening of the photoperiod according to its specific critical daylength, resulting in the induction of freezing tolerance and dehydration of buds first in the northern ecotype, followed by the central and southern ecotypes, respectively. By contrast, there was no clear difference in the timing of dormancy release, bud rehydration, and deacclimation in the spring, suggesting that these traits were controlled mainly by temperature. To elucidate the role of dehydrins (DHN) in the overwintering process, two DHN genomic clones were isolated from pubescent birch and expression of the corresponding genes, both in field and under controlled conditions, was characterized. BpuDhn1 was found to encode an Y(n)K(n)-type of basic DHN, while BpuDhn2 encoded an acidic, SK(n)-type of DHN. In field-grown trees the level of BpuDhn1 increased in buds during the autumn, while the level of BpuDhn2 was highest during the coldest winter months. Under controlled conditions BpuDhn1 increased in response to the combined effect of short daylength and low, non-freezing temperatures whereas the expression of BpuDhn2 was mainly controlled by low temperature while photoperiod had less effect on its expression. These results suggest that DHNs participate in the sensitive environmental regulation of the overwintering process in birch.
10.1093/jxb/erh045
Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress.
Sharma Rinku,Singh Garima,Bhattacharya Sudeepto,Singh Ashutosh
PloS one
Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as-'photosynthesis', 'respiratory burst', 'response to hormone', 'signal transduction', 'metabolic process', 'response to water deprivation', which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules.
10.1371/journal.pone.0203266
Overexpression of Fagopyrum tataricum FtbHLH2 enhances tolerance to cold stress in transgenic Arabidopsis.
Yao Panfeng,Sun Zhaoxia,Li Chenglei,Zhao Xuerong,Li Maofei,Deng Renyu,Huang Yunji,Zhao Haixia,Chen Hui,Wu Qi
Plant physiology and biochemistry : PPB
bHLH transcription factors play important roles in the abiotic stress response in plants, but their characteristics and functions in Tartary buckwheat (Fagopyrum tataricum), a traditional coarse cereal with a strong stress tolerance, haven't been sufficiently studied. Here, we found that the expression of a bHLH gene, FtbHLH2, was induced significantly by cold treatments in Tartary buckwheat seedlings. Subcellular localization indicated that FtbHLH2 localized in nucleus. Its overexpression in Arabidopsis increased tolerance to cold. The Arabidopsis plants overexpressing FtbHLH2 displayed higher root length and photosynthetic efficiency, and had lower malondialdehyde (MDA) and reactive oxygen species (ROS) after cold treatment compared to wild type (WT) plants. Meanwhile, the expression levels of some stress-related genes in transgenic plants were remarkably higher than that in wild type under normal and/or stress conditions. Furthermore, transgenic Arabidopsis lines with the FtbHLH2 promoter had higher GUS activity after cold stress. On the whole, the results suggest that FtbHLH2 may play a positive regulatory in cold stress of Tartary buckwheat.
10.1016/j.plaphy.2018.01.028
Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants.
Wang Da-Zhi,Jin Ya-Nan,Ding Xi-Han,Wang Wen-Jia,Zhai Shan-Shan,Bai Li-Ping,Guo Zhi-Fu
Biochemistry. Biokhimiia
Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. In this review, we focus on the function of each member, interrelation among members, and the influence of manipulators and repressors in the ICE-CBF-COR pathway. In addition, regulation and signal transduction concerning plant hormones, circadian clock, and light are discussed. The studies presented provide a detailed picture of the ICE-CBF-COR pathway.
10.1134/S0006297917100030
RNA Regulation in Plant Cold Stress Response.
Nakaminami Kentaro,Seki Motoaki
Advances in experimental medicine and biology
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
10.1007/978-981-13-1244-1_2
Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis.
Li Yeyun,Wang Xuewen,Ban Qiuyan,Zhu Xiangxiang,Jiang Changjun,Wei Chaoling,Bennetzen Jeffrey L
BMC genomics
BACKGROUND:Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly grown in warm areas. Camellia sinensis var. sinensis (CSS) has greater cold tolerance than Camellia sinensis var. assamica (CSA). To gain deep insight into the molecular mechanisms underlying cold adaptation, we investigated the physiological responses and transcriptome profiles by RNA-Seq in two tea varieties, cold resistant SCZ (classified as CSS) and cold susceptible YH9 (classified as CSA), during cold acclimation. RESULTS:Under freezing stress, lower relative electrical conductivity and higher chlorophyll fluorescence (Fv/Fm) values were detected in SCZ than in YH9 when subjected to freezing acclimation. During cold treatment, 6072 and 7749 DEGs were observed for SCZ and YH9, respectively. A total of 978 DEGs were common for both SCZ and YH9 during the entire cold acclimation process. DEGs were enriched in pathways of photosynthesis, hormone signal transduction, and transcriptional regulation of plant-pathogen interactions. Further analyses indicated that decreased expression of Lhca2 and higher expression of SnRK2.8 are correlated with cold tolerance in SCZ. CONCLUSIONS:Compared with CSA, CSS was significantly more resistant to freezing after cold acclimation, and this increased resistance was associated with an earlier expression of cold-induced genes. Because the greater transcriptional differentiation during cold acclimation in SCZ may contribute to its greater cold tolerance, our studies identify specific genes involved in photoinhibition, ABA signal conduction, and plant immunity that should be studied for understanding the processes involved in cold tolerance. Marker-assisted breeding focused on the allelic variation at these loci provides an avenue for the possible generation of CSA cultivars that have CSS-level cold tolerance.
10.1186/s12864-019-5988-3
Differences in cold hardiness, carbohydrates, dehydrins and related gene expressions under an experimental deacclimation and reacclimation in Prunus persica.
Shin Hyunsuk,Oh Youngjae,Kim Daeil
Physiologia plantarum
To boost our understanding of a recent outbreak of freezing injury, we sought to confirm distinctive features between the shoot tissues of the peach (Prunus persica) cultivars Daewol and Kiraranokiwami by mimicking unseasonable changes of temperatures that occur in the early spring through repeated deacclimation and reacclimation treatments. Patterns of cold hardiness declined dramatically during the deacclimation and rose during the reacclimation in both cultivars. Our results indicated that 'Daewol' possessed higher capacity in response to repeated deacclimation and reacclimation treatments than 'Kiraranokiwami'. 'Daewol' showed more sensitive changes in the carbohydrates in response to warm and low temperatures compared with 'Kiraranokiwami'. 'Daewol' indicated almost similar repeated down- and up-patterns in soluble sugar content in response to repeated deacclimation and reacclimation, whereas it indicated repeated up- and down-patterns in starch content. However, 'Kiraranokiwami' showed a progressive increase in the soluble sugar content and a progressive decrease in starch content. Notably, patterns of accumulation of a 60-kDa dehydrin protein encoded by the PpDhn1 gene were confirmed through western blotting and paralleled fluctuations of cold hardiness in both cultivars. Expression of this dehydrin was weak in both cultivars during deacclimation but its band intensity increased during reacclimation. Changes in related genes (β-amylase, PpDhn1, PpDhn2 and PpDhn3) were positively correlated with changes in cold hardiness throughout the experiment. Our results indicate that recent repeated warm periods may cause premature deacclimation in the early spring, and that more cold-tolerant cultivar may be more resilient to freezing injury caused by unstable temperature conditions.
10.1111/ppl.12293
PsCor413pm2, a Plasma Membrane-Localized, Cold-Regulated Protein from , Confers Low Temperature Tolerance in .
Zhou Aimin,Liu Enhui,Li He,Li Yang,Feng Shuang,Gong Shufang,Wang Jingang
International journal of molecular sciences
Low temperature stress adversely affects plant growth and development. Isolation and characterization of cold response genes from cold-tolerant plants help to understand the mechanism underlying low temperature tolerance. In this study, , a cold-regulated (COR) gene isolated from , was transferred to plants to investigate its function. Real-time quantitative PCR analysis revealed that expression was induced by cold. Subcellular localization revealed that the PsCor413pm2-green fluorescent protein (GFP) fusion protein localized to the plasma membrane in tobacco and plants. Furthermore, overexpression of in plants enhanced tolerance to low temperature stress. Transgenic roots had more influx of Ca after a cold shock than wild-type plants, as shown using non-invasive micro-test technology (NMT). Moreover, the transcription abundance of five and two C-repeat (CRT) binding factor (CBF) genes in transgenic plants was higher than that in the wild-type plants under cold stress. Taken together, our results suggest that overexpression of enhances low temperature tolerance in plants by affecting Ca flux and the expression of stress-related and genes.
10.3390/ijms19092579
A novel cold-regulated gene from Phlox subulata, PsCor413im1, enhances low temperature tolerance in Arabidopsis.
Zhou Aimin,Sun Hongwei,Feng Shuang,Zhou Mi,Gong Shufang,Wang Jingang,Zhang Shuzhen
Biochemical and biophysical research communications
Low temperature stress adversely affects plant growth, development, and crop productivity. Analysis of the function of genes in the response of plants to low temperature stress is essential for understanding the mechanism of chilling and freezing tolerance. In this study, PsCor413im1, a novel cold-regulated gene isolated from Phlox subulata, was transferred to Arabidopsis to investigate its function under low temperature stress. Real-time quantitative PCR analysis revealed that PsCor413im1 expression was induced by cold and abscisic acid. Subcellular localization revealed that PsCor413im1-GFP fusion protein was localized to the periphery of the chloroplast, consistent with the localization of chloroplast inner membrane protein AtCor413im1, indicating that PsCor413im1 is a chloroplast membrane protein. Furthermore, the N-terminal of PsCor413im1 was determined to be necessary for its localization. Compared to the wild-type plants, transgenic plants showed higher germination and survival rates under cold and freezing stress. Moreover, the expression of AtCor15 in transgenic plants was higher than that in the wild-type plants under cold stress. Taken together, our results suggest that the overexpression of PsCor413im1 enhances low temperature tolerance in Arabidopsis.
10.1016/j.bbrc.2017.12.042
A novel cold-regulated protein isolated from Saussurea involucrata confers cold and drought tolerance in transgenic tobacco (Nicotiana tabacum).
Plant science : an international journal of experimental plant biology
Adverse environmental conditions, such as cold and drought, can inhibit plant growth, development, and productivity. The isolation and characterization of stress response genes from stress-tolerant plants can provide a better understanding of the underlying adaptive mechanisms. In this study, a novel cold-regulated gene, SikCOR413PM1, was isolated from Saussurea involucrata Kar. et Kir., which is a plant that survives at the high altitudes and in the low temperatures of alpine slopes in northwestern China. SikCOR413PM1 was induced in response to cold and drought in S. involucrata, and phylogenetic analysis revealed that the gene groups with a COR gene encoding a COR413PM protein family member. Subcellular localization of a SikCOR413PM1-green fluorescent fusion protein showed that SikCOR413PM1 was localized to the plasma membrane. A transgenic tobacco (Nicotiana tabacum) system was employed to investigate the possible role of SikCOR413PM1 in cold and drought tolerance. Analyses of growth, germination and survival rates, relative water content, malondialdehyde content, relative electrolyte leakage, and maximal photochemical efficiency of photosystem II showed that transgenic tobacco plants expressing SikCOR413PM1 were more tolerant to cold and drought stresses than WT plants. SikCOR413PM1 overexpression was also accompanied by constitutive activation of NtDREB1 and NtDREB3, two cold-responsive transcription factor genes, and NtERD10A and NtERD10B, two cold-induced genes. The expression levels of downstream transcription factor genes NtDREB3, NtERD10C, NtERD10D, and NtLEA5 were also induced in SikCOR413PM1-expressing transgenic plants under drought conditions. Our results suggest that the overexpression of SikCOR413PM1 induces changes in tobacco plants, and facilitates enhanced tolerance to cold and drought stresses.
10.1016/j.plantsci.2019.110246
BRASSINOSTEROID-INSENSITIVE2 Negatively Regulates the Stability of Transcription Factor ICE1 in Response to Cold Stress in Arabidopsis.
The Plant cell
Cold acclimation is a crucial strategy for plant survival at freezing temperatures. - () genes are rapidly and transiently induced by low temperature and play important roles in cold acclimation. However, the mechanism underlying the attenuation of expression during the later stages of the cold stress response is obscure. Here, we show that the protein kinase BRASSINOSTEROID-INSENSITIVE2 (BIN2) interacts with and phosphorylates INDUCER OF CBF EXPRESSION1 (ICE1) in Arabidopsis () under prolonged cold stress, facilitating the interaction between ICE1 and the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 and thereby promoting ICE1 degradation. The kinase activity of BIN2 is inhibited during the early stages of the cold stress response and is subsequently restored, suggesting that BIN2 mainly downregulates ICE1 abundance when expression is attenuated. A loss-of-function mutation of partially suppresses the cold-induced expression of and compromises the enhanced freezing tolerance of - These findings reveal an important role for BIN2 in fine-tuning expression, and thus in balancing plant growth and the cold stress response.
10.1105/tpc.19.00058
High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans).
BMC plant biology
BACKGROUND:Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas. RESULT:Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana. CONCLUSIONS:In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.
10.1186/s12870-018-1483-2
Comparative metabolomics analysis of the response to cold stress of resistant and susceptible Tibetan hulless barley (Hordeum distichon).
Yang Chunbao,Yang Haizhen,Xu Qijun,Wang Yulin,Sang Zha,Yuan Hongjun
Phytochemistry
Plants cultivated on the Qinghai-Tibetan Plateau grow in an extremely cold environment and thus are exposed to cold stress. To assess the metabolic processes during cold exposure of Tibetan hulless barley (Hordeum distichon L.), metabolic analyses were conducted on one tolerant (XiLa) and one sensitive (ZangQing) cultivar exposed to six temperatures (24 °C, 12 °C, 5 °C, 0 °C, -5 °C, -8 °C) for 24 h. In total, 770 metabolites were identified, including amino acids and derivatives, carbohydrates, flavonoids, lipids, nucleotides and derivatives, and phenolamides. In principal component analysis, the samples were clearly grouped according to the cultivar, suggesting that the two cultivars have differential responses to cold stress. In cold-grown plants, eight metabolites, including monoacylglycerol (MAG, 18:2), MAG (18:3), deoxyadenosine, 6-methylmercaptopurine, and coniferin, were significantly altered in XiLa, but not in ZangQing when compared to the levels in control plants, and thus, these compounds can be considered as potential biomarkers of exposure to cold stress in hulless barley. Furthermore, differentially altered metabolites between seedlings exposed to -8 °C and those maintained at 24 °C were significantly enriched in glutathione metabolism. The findings of this study will be useful for the development of cultivars with cold stress tolerance.
10.1016/j.phytochem.2020.112346
MicroRNA156 amplifies transcription factor-associated cold stress tolerance in plant cells.
Zhou Mingqin,Tang Wei
Molecular genetics and genomics : MGG
MicroRNAs may increase cold stress tolerance by regulating stress-related signal transduction pathways and by modulating the expression of transcription factors. However, the molecular mechanism by which microRNAs enhance cold stress tolerance is not fully understood. Here, we report that overexpression of rice microRNA156 (OsmiR156) results in increased cell viability and growth rate under cold stress in Arabidopsis, pine, and rice. OsmiR156 increases cold stress tolerance by targeting OsSPL3. OsSPL3 positively regulates the expression of OsWRKY71, a negative regulator of the transcription factors OsMYB2 and OsMYB3R-2. OsMYB2 counteracts cold stress by activating the expression of the stress-response genes OsLEA3, OsRab16A, and OsDREB2A. OsMYB3R-2 counteracts cold stress by activating the expression of OsKNOLLE2, OsCTP1, OsCycB1.1, OsCycB2.1, and OsCDC20.1. In OsmiR156 transgenic rice cell lines, the transcript levels of OsLEA3, OsRab16A, OsDREB2A, OsKNOLLE2, OsCTP1, OsCycB1.1, OsCycB2.1, and OsCDC20.1 were increased by OsWRKY71 knockdown and inversely regulated by OsWRKY71 overexpression, indicating that OsmiR156 enhances cold stress tolerance by regulating the expression of transcription factor genes in plant cells. These results will increase our understanding of microRNA-related cold stress tolerance in different plant species, including monocotyledonous, dicotyledonous, and gymnosperm plant species, and will be valuable in plant molecular biotechnology.
10.1007/s00438-018-1516-4
Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer.
Chen Jing,Zhou Yuanhang,Zhang Qi,Liu Qian,Li Li,Sun Chunyu,Wang Kangyu,Wang Yanfang,Zhao Mingzhu,Li Hongjie,Han Yilai,Chen Ping,Li Ruiqi,Lei Jun,Zhang Meiping,Wang Yi
PloS one
The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.
10.1371/journal.pone.0226055
Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato.
Genome biology
BACKGROUND:Cold stress can greatly affect plant growth and development. Plants have developed special systems to respond to and tolerate cold stress. While plant scientists have discovered numerous genes involved in responses to cold stress, few studies have been dedicated to investigation of genome-wide chromatin dynamics induced by cold or other abiotic stresses. RESULTS:Genomic regions containing active cis-regulatory DNA elements can be identified as DNase I hypersensitive sites (DHSs). We develop high-resolution DHS maps in potato (Solanum tuberosum) using chromatin isolated from tubers stored under room (22 °C) and cold (4 °C) conditions. We find that cold stress induces a large number of DHSs enriched in genic regions which are frequently associated with differential gene expression in response to temperature variation. Surprisingly, active genes show enhanced chromatin accessibility upon cold stress. A large number of active genes in cold-stored tubers are associated with the bivalent H3K4me3-H3K27me3 mark in gene body regions. Interestingly, upregulated genes associated with the bivalent mark are involved in stress response, whereas downregulated genes with the bivalent mark are involved in developmental processes. In addition, we observe that the bivalent mark-associated genes are more accessible than others upon cold stress. CONCLUSIONS:Collectively, our results suggest that cold stress induces enhanced chromatin accessibility and bivalent histone modifications of active genes. We hypothesize that in cold-stored tubers, the bivalent H3K4me3-H3K27me3 mark represents a distinct chromatin environment with greater accessibility, which may facilitate the access of regulatory proteins required for gene upregulation or downregulation in response to cold stress.
10.1186/s13059-019-1731-2
Quantitative Proteomic Analysis of the Response to Cold Stress in Jojoba, a Tropical Woody Crop.
Gao Fei,Ma Pengju,Wu Yingxin,Zhou Yijun,Zhang Genfa
International journal of molecular sciences
Jojoba () is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba's growth, development and yield and limit introduction of jojoba in the vast temperate arid areas. To get insight into the molecular mechanisms of the cold stress response of jojoba, a combined physiological and quantitative proteomic analysis was conducted. Under cold stress, the photosynthesis was repressed, the level of malondialdehyde (MDA), relative electrolyte leakage (REL), soluble sugars, superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) were increased in jojoba leaves. Of the 2821 proteins whose abundance were determined, a total of 109 differentially accumulated proteins (DAPs) were found and quantitative real time PCR (qRT-PCR) analysis of the coding genes for 7 randomly selected DAPs were performed for validation. The identified DAPs were involved in various physiological processes. Functional classification analysis revealed that photosynthesis, adjustment of cytoskeleton and cell wall, lipid metabolism and transport, reactive oxygen species (ROS) scavenging and carbohydrate metabolism were closely associated with the cold stress response. Some cold-induced proteins, such as cold-regulated 47 (COR47), staurosporin and temperature sensitive 3-like a (STT3a), phytyl ester synthase 1 (PES1) and copper/zinc superoxide dismutase 1, might play important roles in cold acclimation in jojoba seedlings. Our work provided important data to understand the plant response to the cold stress in tropical woody crops.
10.3390/ijms20020243
Membrane sterols and genes of sterol biosynthesis are involved in the response of Triticum aestivum seedlings to cold stress.
Valitova Julia,Renkova Albina,Mukhitova Fakhima,Dmitrieva Svetlana,Beckett Richard P,Minibayeva Farida V
Plant physiology and biochemistry : PPB
Cold stress can significantly alter the composition and functioning of the major membrane lipids in plants. However, the roles of the sterol component of plant membranes in stress tolerance remain unclear. In the work presented here we investigated the role of sterols in the response of wheat to cold stress. Initial experiments demonstrated that the roots and leaves of wheat seedlings are differentially sensitive to low positive temperatures. In the roots, cold stress induced disturbance of membrane integrity and accumulation of ROS followed by the induction of autophagy. The absence of such changes in leaves suggests that in wheat, the roots are more sensitive to cold than the leaves. The roots display a time-dependent parabolic pattern of cold stress response, characterized by raised levels of sterols and markers of oxidative stress during short-term treatment, and a decline of these parameters after prolonged treatment. MβCD-induced sterol depletion aggravated the negative effects of cold on the roots. In the leaves the changes also displayed parabolic patterns, with significant changes occurring in 24-ethyl sterols and major PLs. Constitutively high levels of sterols, glycolipids and PLs, and up-regulation of TaSMTs in the leaves may provide membrane stability and cold tolerance. Taken together, results suggest that sterols play important roles in the response of wheat seedlings to cold stress.
10.1016/j.plaphy.2019.07.026
An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana.
Klepikova Anna V,Kulakovskiy Ivan V,Kasianov Artem S,Logacheva Maria D,Penin Aleksey A
BMC plant biology
BACKGROUND:Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS:The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS:Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .
10.1186/s12870-019-1636-y