New Phytol , IF:8.512 , 2020 Jan , V225 (1) : P385-399 doi: 10.1111/nph.16130
MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper-containing proteins in monocots.
Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.; China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, Guangzhou, 510642, China.; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
Plant microRNAs (miRNAs) regulate vital cellular processes, including responses to extreme temperatures with which reactive oxygen species (ROS) are often closely associated. In the present study, it was found that aberrant temperatures caused extensive changes in abundance to numerous miRNAs in banana fruit, especially the copper (Cu)-associated miRNAs. Among them, miR528 was significantly downregulated under cold stress and it was found to target genes encoding polyphenol oxidase (PPO), different from those identified in rice and maize. Expression of PPO genes was upregulated by > 100-fold in cold conditions, leading to ROS surge and subsequent peel browning of banana fruit. Extensive comparative genomic analyses revealed that the monocot-specific miR528 can potentially target a large collection of genes encoding Cu-containing proteins. Most of them are actively involved in cellular ROS metabolism, including not only ROS generating oxidases, but also ROS scavenging enzymes. It also was demonstrated that miR528 has evolved a distinct preference of target genes in different monocots, with its target site varying in position among/within gene families, implying a highly dynamic process of target gene diversification. Its broad capacity to target genes encoding Cu-containing protein implicates miR528 as a key regulator for modulating the cellular ROS homeostasis in monocots.
PMID: 31429090
Cell Rep , IF:8.109 , 2020 Jan , V30 (1) : P229-242.e5 doi: 10.1016/j.celrep.2019.12.012
STCH4/REIL2 Confers Cold Stress Tolerance in Arabidopsis by Promoting rRNA Processing and CBF Protein Translation.
Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Institute of Plant Physiology and Ecology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.; Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.; The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, 311300 Lin'an, Hangzhou, People's Republic of China.; Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, South Korea.; Department of Life Science, Sogang University, Seoul 04107, South Korea.; Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA. Electronic address: huazhong.shi@ttu.edu.; Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Institute of Plant Physiology and Ecology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA. Electronic address: jkzhu@sibs.ac.cn.
Plants respond to cold stress by inducing the expression of transcription factors that regulate downstream genes to confer tolerance to freezing. We screened an Arabidopsis transfer DNA (T-DNA) insertion library and identified a cold-hypersensitive mutant, which we named stch4 (sensitive to chilling 4). STCH4/REIL2 encodes a ribosomal biogenesis factor that is upregulated upon cold stress. Overexpression of STCH4 confers chilling and freezing tolerance in Arabidopsis. The stch4 mutation reduces CBF protein levels and thus delayed the induction of C-repeat-binding factor (CBF) regulon genes. Ribosomal RNA processing is reduced in stch4 mutants, especially under cold stress. STCH4 associates with multiple ribosomal proteins, and these interactions are modulated by cold stress. These results suggest that the ribosome is a regulatory node for cold stress responses and that STCH4 promotes an altered ribosomal composition and functions in low temperatures to facilitate the translation of proteins important for plant growth and survival under cold stress.
PMID: 31914389
Plant Physiol , IF:6.902 , 2020 Jan , V182 (1) : P255-271 doi: 10.1104/pp.19.00832
DEAD-Box RNA Helicase 42 Plays a Critical Role in Pre-mRNA Splicing under Cold Stress.
Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China chungan@cc.ncu.edu.tw.; Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China.
Low temperature is an important environmental stress that adversely affects rice (Oryza sativa) growth and productivity. Splicing of pre-mRNA is a crucial posttranscriptional regulatory step in gene expression in plants and is sensitive to temperature. DEAD-box RNA helicases belong to an RNA helicase family involved in the rearrangement of ribonucleoprotein complexes and the modification of RNA structure and are therefore involved in all aspects of RNA metabolism. In this study, we demonstrate that the rate of pre-mRNA splicing is reduced in rice at low temperatures and that the DEAD-box RNA Helicase42 (OsRH42) is necessary to support effective splicing of pre-mRNA during mRNA maturation at low temperatures. OsRH42 expression is tightly coupled to temperature fluctuation, and OsRH42 is localized in the splicing speckles and interacts directly with U2 small nuclear RNA. Retarded pre-mRNA splicing and plant growth defects were exhibited by OsRH42-knockdown transgenic lines at low temperatures, thus indicating that OsRH42 performs an essential role in ensuring accurate pre-mRNA splicing and normal plant growth under low ambient temperature. Unexpectedly, our results show that OsRH42 overexpression significantly disrupts the pre-mRNA splicing pathway, causing retarded plant growth and reducing plant cold tolerance. Combined, these results indicate that accurate control of OsRH42 homeostasis is essential for rice plants to respond to changes in ambient temperature. In addition, our study presents the molecular mechanism of DEAD-box RNA helicase function in pre-mRNA splicing, which is required for adaptation to cold stress in rice.
PMID: 31753844
J Exp Bot , IF:5.908 , 2020 Jan , V71 (1) : P422-434 doi: 10.1093/jxb/erz444
Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing.
Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.; Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses. Alternative splicing is responsible for reprogramming of the transcriptome and the sensitivity of cassava plants to cold.
PMID: 31713628
J Exp Bot , IF:5.908 , 2020 Jan , V71 (1) : P435-449 doi: 10.1093/jxb/erz450
Expression of galactinol synthase from Ammopiptanthus nanus in tomato improves tolerance to cold stress.
Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, PR China.; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenhe District, PR China.; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenhe District, PR China.; College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenhe District, PR China.; Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenhe District, PR China.
Soluble carbohydrates not only directly affect plant growth and development but also act as signal molecules in processes that enhance tolerance to cold stress. Raffinose family oligosaccharides (RFOs) are an example and play an important role in abiotic stress tolerance. This study aimed to determine whether galactinol, a key limiting factor in RFO biosynthesis, functions as a signal molecule in triggering cold tolerance. Exposure to low temperatures induces the expression of galactinol synthase (AnGolS1) in Ammopiptanthus nanus, a desert plant that survives temperatures between -30 degrees C to 47 degrees C. AnGolS1 has a greater catalytic activity than tomato galactinol synthase (SlGolS2). Moreover, SlGolS2 is expressed only at low levels. Expression of AnGolS1 in tomato enhanced cold tolerance and led to changes in the sugar composition of the seeds and seedlings. AnGolS1 transgenic tomato lines exhibited an enhanced capacity for ethylene (ET) signaling. The application of galactinol abolished the repression of the ET signaling pathway by 1-methylcyclopropene during seed germination. In addition, the expression of ERF transcription factors was increased. Galactinol may therefore act as a signal molecule affecting the ET pathway.
PMID: 31616940
J Exp Bot , IF:5.908 , 2020 Jan , V71 (1) : P36-48 doi: 10.1093/jxb/erz419
Upstream of gene expression: what is the role of microtubules in cold signalling?
College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China.; Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.; Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Cold stress is a major abiotic stress, restricting plant growth and development. Therefore, gene expression in response to cold stress and during cold acclimation has been studied intensively, including the ICE-CBF-COR pathway, as well as the modulation of this cascade by secondary messengers, for instance mitogen-activated protein kinase (MAPK) cascades. In contrast, the early events of cold perception and cold adaption have received far less attention. This is partially due to the fact that cold is a physical signal, which requires the conceptual framework to be adjusted. In this review, we address the role of microtubules in cold sensing, and propose a model whereby microtubules, while not being part of signalling itself, act as modulators of cold sensitivity. The purpose of this model is to derive implications for future experiments that will help to provide a more complete understanding of cold adaptation.
PMID: 31560041
J Exp Bot , IF:5.908 , 2020 Jan , V71 (3) : P1092-1106 doi: 10.1093/jxb/erz466
Brassinosteroids act as a positive regulator of NBR1-dependent selective autophagy in response to chilling stress in tomato.
Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China.; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China.; Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Agricultural Ministry of China, Hangzhou, China.
Autophagy is a highly conserved and regulated catabolic process involved in the degradation of protein aggregates, which plays critical roles in eukaryotes. In plants, multiple molecular processes can induce or suppress autophagy but the mechanism of its regulation by phytohormones is poorly understood. Brassinosteroids (BRs) are steroid phytohormones that play crucial roles in plant response to stresses. Here, we investigate the role of BRs in NBR1-dependent selective autophagy in response to chilling stress in tomato. BRs and their signaling element BZR1 can induce autophagy and accumulation of the selective autophagy receptor NBR1 in tomato under chilling stress. Cold increased the stability of BZR1, which was promoted by BRs. Cold- and BR-induced increased BZR1 stability activated the transcription of several autophagy-related genes (ATGs) and NBR1 genes by directly binding to their promoters, which resulted in selective autophagy. Furthermore, silencing of these ATGs or NBR1 genes resulted in a decreased accumulation of several functional proteins and an increased accumulation of ubiquitinated proteins, subsequently compromising BR-induced cold tolerance. These results strongly suggest that BRs regulate NBR1-dependent selective autophagy in a BZR1-dependent manner in response to chilling stress in tomato.
PMID: 31639824
Food Res Int , IF:4.972 , 2020 Jan , V127 : P108727 doi: 10.1016/j.foodres.2019.108727
Changes in low molecular weight carbohydrates in kale during development and acclimation to cold temperatures determined by chromatographic techniques coupled to mass spectrometry.
Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.; Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse 9-11, Oldenburg 26111, Germany.; Instituto de Quimica Organica General (CSIC), Juan de la Cierva, 3, Madrid 28028, Spain.; Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany. Electronic address: n.kuhnert@jacobs-university.de.
Kale (Brassica oleracea) is a cool-season vegetable widely employed in the elaboration of diverse products such as tea and smoothies in USA or in the Northern German cuisine in wintertime. Besides, kale is gaining attention due to the diverse health benefits reported in the literature for its consumption, e.g. antigenotoxic and anticarcinogenic effect, protection of cardiovascular system and gastrointestinal tract. Low molecular weight carbohydrates (LMWC) are compounds directly related with kale flavour and nutritional quality. Despite different studies focusing on the chemical composition of kale, few information on LMWC is available. Thus, in this work a multianalytical approach was conducted in order to perform a comprehensive study of kale LMWC; their evolution during plant development and acclimation to cool temperatures was also evaluated. Gas chromatography coupled to mass spectrometry allowed the identification of 13 LMWC, being myo-inositol, galactinol, maltose and melibiose described for the first time in kale. Eight major LMWC were quantified in three different commercial kale cultivars using hydrophilic interaction liquid chromatography coupled to mass spectrometry to monitor possible differences in their content during plant development and as consequence of plant acclimation to cold temperatures. Overall, for all types of kales under study, the content of maltose and sucrose decreased during the plant development while the concentration of fructose, melibiose, maltose, raffinose and galactinol was increased in all kale types exposed to low temperatures. These results underline the importance of controlling the temperature during kale cultivation in order to obtain products with a high nutritional value.
PMID: 31882079
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (3) doi: 10.3390/ijms21030846
Transcriptomic Analyses of Camellia oleifera 'Huaxin' Leaf Reveal Candidate Genes Related to Long-Term Cold Stress.
Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha 410004, China.; Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha 410004, China.
'Huaxin' is a new high-yielding timber cultivar of Camellia oleifera of high economic value, and has been widely cultivated in the red soil hilly region of Hunan Province of the People s Republic of China in recent years. However, its quality and production are severely affected by low temperatures during flowering. To find genes related to cold tolerance and further explore new candidategenes for chilling-tolerance, Illumina NGS (Next Generation Sequencing) technology was used to perform transcriptomic analyses of C. oleifera 'Huaxin' leaves under long-term cold stress. Nine cDNA libraries were sequenced, and 58.31 Gb high-quality clean reads were obtained with an average of 5.92 Gb reads for each sample. A total of 191,150 transcripts were obtained after assembly. Among them, 100,703 unigenes were generated, and 44,610 unigenes were annotated. In total, 1564 differentially expressed genes (DEGs) were identified both in the A_B and A_C gene sets. In the current study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, andrevealed a group of cold-responsive genes related to hormone regulation, photosynthesis, membrane systems, and osmoregulation; these genes encoded many key proteins in plant biological processes, such as serine/threonine-protein kinase (STPK), transcription factors (TFs), fatty acid desaturase (FAD), lipid-transfer proteins (LTPs), soluble sugars synthetases, and flavonoid biosynthetic enzymes. Some physiological indicators of C. oleifera 'Huaxin' were determined under three temperature conditions, and the results were consistent with the molecular sequencing. In addition, the expression levels of 12 DEGs were verified using quantitative real-time polymerase chain reaction (qRT-PCR). In summary, the results of DEGs analysis together with qRT-PCR tests contribute to the understanding of cold tolerance and further exploring new candidate genes for chilling-tolerance in molecular breeding programs of C. oleifera 'Huaxin'.
PMID: 32013013
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (2) doi: 10.3390/ijms21020621
Jasmonic Acid Signaling Pathway in Response to Abiotic Stresses in Plants.
Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
Plants as immovable organisms sense the stressors in their environment and respond to them by means of dedicated stress response pathways. In response to stress, jasmonates (jasmonic acid, its precursors and derivatives), a class of polyunsaturated fatty acid-derived phytohormones, play crucial roles in several biotic and abiotic stresses. As the major immunity hormone, jasmonates participate in numerous signal transduction pathways, including those of gene networks, regulatory proteins, signaling intermediates, and proteins, enzymes, and molecules that act to protect cells from the toxic effects of abiotic stresses. As cellular hubs for integrating informational cues from the environment, jasmonates play significant roles in alleviating salt stress, drought stress, heavy metal toxicity, micronutrient toxicity, freezing stress, ozone stress, CO2 stress, and light stress. Besides these, jasmonates are involved in several developmental and physiological processes throughout the plant life. In this review, we discuss the biosynthesis and signal transduction pathways of the JAs and the roles of these molecules in the plant responses to abiotic stresses.
PMID: 31963549
Int J Mol Sci , IF:4.556 , 2020 Jan , V21 (3) doi: 10.3390/ijms21030762
The SWI/SNF ATP-Dependent Chromatin Remodeling Complex in Arabidopsis Responds to Environmental Changes in Temperature-Dependent Manner.
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.; Maria Sklodowska-Curie Cancer Center Institute of Oncology, 02-781 Warsaw, Poland.; Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland .; Max-Planck Institut fur Pflanzenzuchtungsforschung, 50829 Koln, Germany.; Institute of Plant Biology, Biological Research Center of Hungarian Academy, 6726 Szeged, Hungary.
SWI/SNF ATP-dependent chromatin remodeling complexes (CRCs) play important roles in the regulation of transcription, cell cycle, DNA replication, repair, and hormone signaling in eukaryotes. The core of SWI/SNF CRCs composed of a SWI2/SNF2 type ATPase, a SNF5 and two of SWI3 subunits is sufficient for execution of nucleosome remodeling in vitro. The Arabidopsis genome encodes four SWI2/SNF2 ATPases, four SWI3, a single SNF5 and two SWP73 subunits. Genes of the core SWI/SNF components have critical but not fully overlapping roles during plant growth, embryogenesis, and sporophyte development. Here we show that the Arabidopsis swi3c mutant exhibits a phenotypic reversion when grown at lower temperature resulting in partial restoration of its embryo, root development and fertility defects. Our data indicates that the swi3c mutation alters the expression of several genes engaged in low temperature responses. The location of SWI3C-containing SWI/SNF CRCs on the ICE1, MYB15 and CBF1 target genes depends on the temperature conditions, and the swi3c mutation thus also influences the transcription of several cold-responsive (COR) genes. These findings, together with genetic analysis of swi3c/ice1 double mutant and enhanced freezing tolerance of swi3c plants illustrate that SWI/SNF CRCs contribute to fine-tuning of plant growth responses to different temperature regimes.
PMID: 31979421
Plant Cell Physiol , IF:4.062 , 2020 Jan , V61 (1) : P88-104 doi: 10.1093/pcp/pcz180
Poaceae Type II Galactinol Synthase 2 from Antarctic Flowering Plant Deschampsia antarctica and Rice Improves Cold and Drought Tolerance by Accumulation of Raffinose Family Oligosaccharides in Transgenic Rice Plants.
Division of Life Science, Department of Systems Biology, Yonsei University, Seoul 03722, Korea.; Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.; Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.; Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Korea.; Polar Science, University of Science & Technology, Daejeon 34113, Korea.
Deschampsia antarctica is a Poaceae grass that has adapted to and colonized Antarctica. When D. antarctica plants were subjected to cold and dehydration stress both in the Antarctic field and in laboratory experiments, galactinol, a precursor of raffinose family oligosaccharides (RFOs) and raffinose were highly accumulated, which was accompanied by upregulation of galactinol synthase (GolS). The Poaceae monocots have a small family of GolS genes, which are divided into two distinct groups called types I and II. Type II GolSs are highly expanded in cold-adapted monocot plants. Transgenic rice plants, in which type II D. antarctica GolS2 (DaGolS2) and rice GolS2 (OsGolS2) were constitutively expressed, were markedly tolerant to cold and drought stress as compared to the wild-type rice plants. The RFO contents and GolS enzyme activities were higher in the DaGolS2- and OsGolS2-overexpressing progeny than in the wild-type plants under both normal and stress conditions. DaGolS2 and OsGolS2 overexpressors contained reduced levels of reactive oxygen species (ROS) relative to the wild-type plants after cold and drought treatments. Overall, these results suggest that Poaceae type II GolS2s play a conserved role in D. antarctica and rice in response to drought and cold stress by inducing the accumulation of RFO and decreasing ROS levels.
PMID: 31513272
Plant Cell Physiol , IF:4.062 , 2020 Jan , V61 (1) : P3-20 doi: 10.1093/pcp/pcz196
The Roots of Plant Frost Hardiness and Tolerance.
Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.; Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium.
Frost stress severely affects agriculture and agroforestry worldwide. Although many studies about frost hardening and resistance have been published, most of them focused on the aboveground organs and only a minority specifically targets the roots. However, roots and aboveground tissues have different physiologies and stress response mechanisms. Climate models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will greatly decrease plant primary production due to damage at the root level. Molecular and metabolic responses inducing root cold hardiness are complex. They involve a variety of processes related to modifications in cell wall composition, maintenance of the cellular homeostasis and the synthesis of primary and secondary metabolites. After a summary of the current climatic models, this review details the specificity of freezing stress at the root level and explores the strategies roots developed to cope with freezing stress. We then describe the level to which roots can be frost hardy, depending on their age, size category and species. After that, we compare the environmental signals inducing cold acclimation and frost hardening in the roots and aboveground organs. Subsequently, we discuss how roots sense cold at a cellular level and briefly describe the following signal transduction pathway, which leads to molecular and metabolic responses associated with frost hardening. Finally, the current options available to increase root frost tolerance are explored and promising lines of future research are discussed.
PMID: 31626277
Ann Bot , IF:4.005 , 2020 Jan , V124 (7) : P1211-1226 doi: 10.1093/aob/mcz149
Symbiosis at its limits: ecophysiological consequences of lichenization in the genus Prasiola in Antarctica.
Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena sn, 48940 Leioa, Spain.; Department of Botany, Ecology and Physiology, University of La Laguna (ULL), 38200 La Laguna, Canarias, Spain.; Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears (UIB) - Instituto de Investigaciones Agroambientales y de Economia del Agua (INAGEA), Carretera de Valldemossa Km 7.5, 07122, Palma, Illes Balears, Spain.; Global Change Institute, School of GeoSciences, University of Edinburgh, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK.; Museo Nacional de Ciencias Naturales (MNCN-CSIC), Serrano 115 dpdo, 28006 Madrid, Spain.; Botany Section, Fac. Farmacia, Universidad Complutense, 28040 Madrid, Spain.; Laboratory of Macromolecular Chemistry (Labquimac), Department of Physical Chemistry, University of the Basque Country (UPV/EHU), Barrio Sarriena sn, 48940 Leioa, Spain.; Real Jardin Botanico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain.
BACKGROUND AND AIMS: Lichens represent a symbiotic relationship between at least one fungal and one photosynthetic partner. The association between the lichen-forming fungus Mastodia tessellata (Verrucariaceae) and different species of Prasiola (Trebouxiophyceae) has an amphipolar distribution and represents a unique case study for the understanding of lichen symbiosis because of the macroalgal nature of the photobiont, the flexibility of the symbiotic interaction and the co-existence of free-living and lichenized forms in the same microenvironment. In this context, we aimed to (1) characterize the photosynthetic performance of co-occurring populations of free-living and lichenized Prasiola and (2) assess the effect of the symbiosis on water relations in Prasiola, including its tolerance of desiccation and its survival and performance under sub-zero temperatures. METHODS: Photochemical responses to irradiance, desiccation and freezing temperature and pressure-volume curves of co-existing free-living and lichenized Prasiola thalli were measured in situ in Livingston Island (Maritime Antarctica). Analyses of photosynthetic pigment, glass transition and ice nucleation temperatures, surface hydrophobicity extent and molecular analyses were conducted in the laboratory. KEY RESULTS: Free-living and lichenized forms of Prasiola were identified as two different species: P. crispa and Prasiola sp., respectively. While lichenization appears to have no effect on the photochemical performance of the alga or its tolerance of desiccation (in the short term), the symbiotic lifestyle involves (1) changes in water relations, (2) a considerable decrease in the net carbon balance and (3) enhanced freezing tolerance. CONCLUSIONS: Our results support improved tolerance of sub-zero temperature as the main benefit of lichenization for the photobiont, but highlight that lichenization represents a delicate equilibrium between a mutualistic and a less reciprocal relationship. In a warmer climate scenario, the spread of the free-living Prasiola to the detriment of the lichen form would be likely, with unknown consequences for Maritime Antarctic ecosystems.
PMID: 31549137
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P1362 doi: 10.1038/s41598-020-58328-5
Selection and Validation of Reference Genes for Gene Expression Studies in Codonopsis pilosula Based on Transcriptome Sequence Data.
Institute of soil and water conservation, CAS & MWR, Yangling, 712100, P. R. China.; College of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, P. R. China.; University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.; College of Life Sciences, Northwest A&F University, Yangling, 712100, P. R. China.; Institute of Food Science and Biological Engineering, Guilin Tourism University, Guilin, 541006, P. R. China.; Buchang Pharmaceuticals Co., Ltd, Xi'an, 712000, P. R. China.; School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, P. R. China.; Institute of soil and water conservation, CAS & MWR, Yangling, 712100, P. R. China. liangzs@ms.iswc.ac.cn.; College of Life Sciences, Northwest A&F University, Yangling, 712100, P. R. China. liangzs@ms.iswc.ac.cn.; College of Life Sciences, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, P. R. China. liangzs@ms.iswc.ac.cn.
Relative gene expression analyses by RT-qPCR (reverse transcription-quantitative PCR) are highly dependent on the reference genes in normalizing the expression data of target genes. Therefore, inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, and the selection and validation of suitable internal reference genes becomes essential. In this study, we retrieved the commonly used reference genes in transcriptome datasets of Codonopsis pilosula by RNA-Seq (unpublished data), and selected 15 candidate reference genes according to the coefficient of variation (CV) and fold change (FC) value of gene expression. The expression levels of candidate reference genes, which is at different growth stages, undergoing cold stress and drought stress, was determined by RT-qPCR. The expression stability of these genes was evaluated using software packages and algorithms including DeltaCt, geNorm, NormFinder and Bestkeeper. Then appropriate reference genes were screened and validated by target gene-UDGPase (UDP glucose pyrophosphorylase). The optimal RGs combinations of C. pilosula, including PP2A59gamma, CPY20-1, UBCE32, RPL5B and UBC18 for developmental stage, RPL5B, RPL13 and PP2A59gamma for cold treatment, RPL13 and PP2A59gamma for drought treatment, were found and proposed as reference genes for future work. This paper laid foundations for both the selection of reference genes and exploration in metabolic mechanism of C. pilosula.
PMID: 31992780
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P689 doi: 10.1038/s41598-019-56797-x
Acclimation, priming and memory in the response of Arabidopsis thaliana seedlings to cold stress.
Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universitat Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany.; Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universitat Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany. tschmue@zedat.fu-berlin.de.
Because stress experiences are often recurrent plants have developed strategies to remember a first so-called priming stress to eventually respond more effectively to a second triggering stress. Here, we have studied the impact of discontinuous or sustained cold stress (4 degrees C) on in vitro grown Arabidopsis thaliana seedlings of different age and their ability to get primed and respond differently to a later triggering stress. Cold treatment of 7-d-old seedlings induced the expression of cold response genes but did not cause a significantly enhanced freezing resistance. The competence to increase the freezing resistance in response to cold was associated with the formation of true leaves. Discontinuous exposure to cold only during the night led to a stepwise modest increase in freezing tolerance provided that the intermittent phase at ambient temperature was less than 32 h. Seedlings exposed to sustained cold treatment developed a higher freezing tolerance which was further increased in response to a triggering stress during three days after the priming treatment had ended indicating cold memory. Interestingly, in all scenarios the primed state was lost as soon as the freezing tolerance had reached the level of naive plants indicating that an effective memory was associated with an altered physiological state. Known mutants of the cold stress response (cbfs, erf105) and heat stress memory (fgt1) did not show an altered behaviour indicating that their roles do not extend to memory of cold stress in Arabidopsis seedlings.
PMID: 31959824
Sci Rep , IF:3.998 , 2020 Jan , V10 (1) : P521 doi: 10.1038/s41598-020-57451-7
Identification, functional prediction, and key lncRNA verification of cold stress-related lncRNAs in rats liver.
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. byndlsz@163.com.; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. 250507411@qq.com.
Cold stimulation reduces the quality of animal products and increases animal mortality, causing huge losses to the livestock industry in cold regions. Long non-coding RNAs (lncRNAs) take part in many biological processes through transcriptional regulation, intracellular material transport, and chromosome remodeling. Although cold stress-related lncRNAs have been reported in plants, no research is available on the characteristic and functional analysis of lncRNAs after cold stress in rats. Here, we built a cold stress animal model firstly. Six SPF male Wistar rats were randomly divided to the acute cold stress group (4 degrees C, 12 h) and the normal group (24 degrees C, 12 h). lncRNA libraries were constructed by high-throughput sequencing (HTS) using rat livers. 2,120 new lncRNAs and 273 differentially expressed (DE) lncRNAs were identified in low temperature environments. The target genes of DElncRNA were predicted by cis and trans, and then functional and pathway analysis were performed to them. GO and KEGG analysis revealed that lncRNA targets were mainly participated in the regulation of nucleic acid binding, cold stimulation reaction, metabolic process, immune system processes, PI3K-Akt signaling pathway and pathways in cancer. Next, a interaction network between lncRNA and its targets was constructed. To further reveal the mechanism of cold stress, DElncRNA and DEmRNA were extracted to reconstruct a co-expression sub-network. We found the key lncRNA MSTRG.80946.2 in sub-network. Functional analysis of key lncRNA targets showed that targets were significantly enriched in fatty acid metabolism, the PI3K-Akt signaling pathway and pathways in cancer under cold stress. qRT-PCR confirmed the sequencing results. Finally, hub lncRNA MSTRG.80946.2 was characterized, and verified its relationship with related mRNAs by antisense oligonucleotide (ASO) interference and qRT-PCR. Results confirmed the accuracy of our analysis. To sum up, our work was the first to perform detailed characterization and functional analysis of cold stress-related lncRNAs in rats liver. lncRNAs played crucial roles in energy metabolism, growth and development, immunity and reproductive performance in cold stressed rats. The MSTRG.80946.2 was verified by network and experiments to be a key functional lncRNA under cold stress, regulating ACP1, TSPY1 and Tsn.
PMID: 31949263
Plant Physiol Biochem , IF:3.72 , 2020 Jan , V146 : P238-248 doi: 10.1016/j.plaphy.2019.11.021
Genome-wide expression of low temperature response genes in Rosa hybrida L.
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Agriculture, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.; Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; USDA-ARS, Urbana, IL, 61801, USA.; Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Agriculture, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.; Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. Electronic address: korban@illinois.edu.
Plants respond to low temperature stress during cold acclimation, a complex process involving changes in physiological and biochemical modifications. The rose serves as a good model to investigate low temperature responses in perennial ornamentals. In this study, a heterologous apple microarray is used to investigate genome-wide expression profiles in Rosa hybrida subjected to low temperature dark treatment. Transcriptome profiles are determined in floral buds at 0h, 2h, and 12h of low temperature treatment (4 degrees C). It is observed that a total of 134 transcripts are up-regulated and 169 transcripts are down-regulated in response to low temperature. Interestingly, a total of eight up-regulated genes, including those coding for two cytochrome P450 proteins, two ankyrin repeat family proteins, two metal ion binding proteins, and two zinc finger protein-related transcription factors, along with a single down-regulated gene, coding for a dynamin-like protein, are detected. Transcript profiles of 12 genes known to be involved in cold stress response are also validated using qRT-PCR. Furthermore, expression patterns of the AP2/ERF gene family of transcription factors are investigated in both floral buds and leaves. Overall, AP2/ERFs genes are more rapidly induced in leaves than in floral buds. Moreover, differential expression of several AP2/ERF genes are detected earlier in vegetative rather than in reproductive tissues. These findings highlight important roles of various low temperature response genes in mediating cold acclimation, thereby allowing roses to adapt to low temperatures, but without adversely affecting flower bud development and subsequent flowering, while vegetative tissues undergo early adaptation to low temperatures.
PMID: 31765955
Plant Physiol Biochem , IF:3.72 , 2020 Jan , V146 : P112-123 doi: 10.1016/j.plaphy.2019.11.012
MusaMPK5, a mitogen activated protein kinase is involved in regulation of cold tolerance in banana.
Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.; Department of Biotechnology, University of Mumbai, Mumbai, 400098, India.; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.; Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India. Electronic address: trgana@barc.gov.in.
Mitogen activated protein kinases (MAPKs) are known to play important functions in stress responses of plants. We have functionally characterized a MAPK, MusaMPK5 from banana and demonstrated its function in cold tolerance response of banana plants. Expression of MusaMPK5 showed positive response to cold, methyl-jasmonate and salicylic acid treatment. Transgenic banana plants harbouring PMusaMPK5::GUS after exposure to cold stress (8 degrees C) showed strong induction of GUS in cells surrounding central vascular cylinder of corm and cortical cells of pseudostem. Transgenic banana lines overexpressing MusaMPK5 were regenerated and four different transgenic lines were confirmed for T-DNA insertions by Southern blot and PCR analysis. In an in-vitro growth assay transgenic lines gained better shoot length and fresh weight during recovery from cold stress indicating improved cold tolerance ability of transgenic lines than control plants. Leaf discs of transgenic lines bleached less and retain lower MDA content than leaf discs of control plants after cold stress (4 degrees C and 8 degrees C). Cold stress tolerance analysis using two month old plants suggested that improved cold tolerance ability of transgenic lines might be associated with increased level of proline and reduced MDA content. MusaMPK5 gets localized in cytoplasm as observed in onion epidermal cells transiently overexpressing either MusaMPK5-GFP or MusaMPK5-GUS fusion protein. MusaMPK5 is a functional kinase as it autophosphorylate itself and phosphorylate myelin basic protein (MBP) in an in vitro reaction. Purified MusaMPK5 can phosphorylate NAC042 and SNAC67 transcription factors of banana which are important regulators of stress tolerance in banana plants.
PMID: 31739146
Plant Physiol Biochem , IF:3.72 , 2020 Jan , V146 : P98-111 doi: 10.1016/j.plaphy.2019.11.002
VvNAC17, a novel stress-responsive grapevine (Vitis vinifera L.) NAC transcription factor, increases sensitivity to abscisic acid and enhances salinity, freezing, and drought tolerance in transgenic Arabidopsis.
College of Enology, Northwest A & F University, Yangling, Shaanxi, 712100, China. Electronic address: juyanlun2016@nwsuaf.edu.cn.; College of Enology, Northwest A & F University, Yangling, Shaanxi, 712100, China. Electronic address: yuexiaofeng@nwsuaf.edu.cn.; Department of Brewing Engineering, Moutai University, Renhuai, Guizhou, 564507, China. Electronic address: minzhuo@nwsuaf.edu.cn.; College of Enology, Northwest A & F University, Yangling, Shaanxi, 712100, China. Electronic address: wangxianhang@nwsuaf.edu.cn.; College of Enology, Northwest A & F University, Yangling, Shaanxi, 712100, China. Electronic address: fangyulin@nwsuaf.edu.cn.; Ningxia Grape and Wine Research Institute, Ningxia University, Yinchuan, Ningxia, 750000, China. Electronic address: zhangjunxiang@126.com.
Drought stress is the primary factor limiting the growth and fruit quality of grapevines worldwide. However, the biological function of the NAC [No apical meristem (NAM), Arabidopsis transcription activation factor (ATAF), Cup-shaped cotyledon (CUC)] transcription factor (TF) in grapevine is not clear. In this study, we reported that VvNAC17, a novel NAC transcription factor, was expressed in various tissues following drought, high temperature (45 degrees C), freezing (4 degrees C), salicylic acid (SA), and abscisic acid (ABA) treatments in grapevine. The VvNAC17 protein was localized in the nucleus of Arabidopsis thaliana protoplasts and demonstrated transcriptional activation activities at its C-terminus in yeast. The VvNAC17 gene was overexpressed in Arabidopsis thaliana. Under mannitol and salt stress, the germination rates of the VvNAC17-overexpression lines were higher than those of the wild-type plants, as were the root lengths. The VvNAC17-overexpression lines showed greater tolerance to freezing stress along with a higher survival rate. Following ABA treatment, the seed germination rate and the root length of the VvNAC17-overexpression lines were inhibited, and the stomatal opening and stomatal density were reduced. When subjected to drought and dehydration stress, the VvNAC17-overexpression lines showed improved survival and reduced water loss rates in comparison to the wild-type plants. Under drought conditions, the VvNAC17-overexpression lines had lower malondialdehyde and H2O2 contents, but higher peroxidase, superoxide dismutase, and catalase activities as well as higher proline content. Moreover, the expression of marker genes, including ABI5, AREB1, COR15A, COR47, P5CS, RD22, and RD29A, was up-regulated in the VvNAC17-overexpression lines when subjected to ABA and drought treatments. The results suggest that in transgenic Arabidopsis over-expression of VvNAC17 enhances resistance to drought while up-regulating the expression of ABA- and stress-related genes.
PMID: 31734522
Plant Physiol Biochem , IF:3.72 , 2020 Jan , V146 : P31-41 doi: 10.1016/j.plaphy.2019.10.041
Chrysanthemum (Chrysanthemum morifolium) CmICE2 conferred freezing tolerance in Arabidopsis.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: 2014204029@njau.edu.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: luzhu@jaas.ac.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: aiping_song@njau.edu.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: hb@njau.edu.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: chensm@njau.edu.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: jiangjiafu@njau.edu.cn.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: chenfd@njau.edu.cn.
Genes of the ICE (Inducer of CBF Expression) family play a key role in cold and freezing stresses response via the CBF regulatory pathway. In this work, we identified the ICE family gene, CmICE2, from Chrysanthemum morifolium 'Jinba'. CmICE2 encodes a 451-amino acid protein with a conserved nuclear localization domain, a bHLH domain and ACT domain. CmICE2 is expressed in abundance in leaves and flowers, and the expression of CmICE2 is induced by freezing and drought stresses. CmICE2 localized to the nucleus, and has transcriptional activity in yeast cells. After a 24-hour 4 degrees C acclimation, Arabidopsis plants overexpressing CmICE2 were more tolerant to freezing stress (-9 degrees C for 6h) than the Col-0. When exposed to -9 degrees C for 6h, the expression levels of genes such as AtCBF1, AtCBF2, AtCBF4, AtCOR 6.6A, AtCOR 414 and AtKIN1 were up-regulated significantly in CmICE2 overexpression plant lines compared to wild type. The proline contents, activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were also increased in plants overexpressing CmICE2. In summary, CmICE2 confers to plant response to freezing stress.
PMID: 31726380
BMC Genomics , IF:3.594 , 2020 Jan , V21 (1) : P65 doi: 10.1186/s12864-020-6491-6
Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant.
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China. liushengrui@ahau.edu.cn.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China. weichl@ahau.edu.cn.
BACKGROUND: Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis). RESULTS: In this study, the AS transcriptional landscape was characterized in the tea plant genome using high-throughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents. CONCLUSION: Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.
PMID: 31959105
BMC Genomics , IF:3.594 , 2020 Jan , V21 (1) : P52 doi: 10.1186/s12864-019-6441-3
SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum.
Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.; Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China. wzc_ttt@sina.com.
BACKGROUND: Pennisetum giganteum, an abundant, fast-growing perennial C4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a source of forage for cattle and sheep, and as a tool to remedy soil erosion. However, having a chilling-sensitive nature, P. giganteum seedlings need to be protected while overwintering in most temperate climate regions. RESULTS: To elucidate the cold stress responses of P. giganteum, we carried out comprehensive full-length transcriptomes from leaf and root tissues under room temperature (RT) and chilling temperature (CT) using PacBio Iso-Seq long reads. We identified 196,124 and 140,766 full-length consensus transcripts in the RT and CT samples, respectively. We then systematically performed functional annotation, transcription factor identification, long non-coding RNAs (lncRNAs) prediction, and simple sequence repeat (SSR) analysis of those full-length transcriptomes. Isoform analysis revealed that alternative splicing events may be induced by cold stress in P. giganteum, and transcript variants may be involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in P. giganteum. Furthermore, the fatty acid composition determination and gene expression level analysis supported that C18 unsaturated fatty acid biosynthesis and metabolism pathways may play roles during cold stress in P. giganteum. CONCLUSIONS: We provide the first comprehensive full-length transcriptomic resource for the abundant and fast-growing perennial grass Pennisetum giganteum. Our results provide a useful transcriptomic resource for exploring the biological pathways involved in the cold stress responses of P. giganteum.
PMID: 31948405
BMC Genomics , IF:3.594 , 2020 Jan , V21 (1) : P10 doi: 10.1186/s12864-019-6401-y
Transcriptomic analyses of Pinus koraiensis under different cold stresses.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People's Republic of China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People's Republic of China. chensunefu@163.com.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People's Republic of China. zhaoxyphd@163.com.
BACKGROUND: Pinus koraiensis is an evergreen tree species with strong cold resistance. However, the transcriptomic patterns in response to cold stress are poorly understood for P. koraiensis. In this study, global transcriptome profiles were generated for P. koraiensis under cold stress (- 20 degrees C) over time by high-throughput sequencing. RESULTS: More than 763 million clean reads were produced, which assembled into a nonredundant data set of 123,445 unigenes. Among them, 38,905 unigenes had homology with known genes, 18,239 were assigned to 54 gene ontology (GO) categories and 18,909 were assigned to 25 clusters of orthologous groups (COG) categories. Comparison of transcriptomes of P. koraiensis seedlings grown at room temperature (20 degrees C) and low temperature (- 20 degrees C) revealed 9842 differential expressed genes (DEGs) in the 6 h sample, 9250 in the 24 h sample, and 9697 in the 48 h sample. The number of DEGs in the pairwise comparisons of 6 h, 24 h and 48 h was relatively small. The accuracy of the RNA-seq was validated by analyzing the expression patterns of 12 DEGs by quantitative real-time PCR (qRT-PCR). In this study, 34 DEGs (22 upregulated and 12 downregulated) were involved in the perception and transmission of cold signals, 96 DEGs (41 upregulated and 55 downregulated) encoding 8 transcription factors that regulated cold-related genes expression, and 27 DEGs (17 upregulated and 10 downregulated) were involved in antioxidant mechanisms in response to cold stress. Among them, the expression levels of c63631_g1 (annexin D1), c65620_g1 (alpha-amylase isozyme 3C), c61970_g1 (calcium-binding protein KIC), c51736_g1 (ABA), c58408_g1 (DREB3), c66599_g1 (DREB3), c67548_g2 (SOD), c55044_g1 (CAT), c71938_g2 (CAT) and c11358_g1 (GPX) first increased significantly and then decreased significantly with the extension of stress time. CONCLUSIONS: A large number of DEGs were identified in P. koraiensis under cold stress, especially the DEGs involved in the perception and transmission of cold signals, the DEGs encoding TFs related to cold regulation and the DEGs removing ROS in antioxidation mechanisms. The transcriptome and digital expression profiling of P. koraiensis could facilitate the understanding of the molecular control mechanism related to cold responses and provide the basis for the molecular breeding of conifers.
PMID: 31900194
J Proteomics , IF:3.509 , 2020 Jan , V211 : P103528 doi: 10.1016/j.jprot.2019.103528
Plasma membrane proteome analyses of Arabidopsis thaliana suspension-cultured cells during cold or ABA treatment: Relationship with freezing tolerance and growth phase.
College of Plant Science, Jilin University, Changchun 130062, China; United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan.; United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.; United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Department of Plant-bioscience, Iwate University, Morioka 020-8550, Japan.; United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Department of Plant-bioscience, Iwate University, Morioka 020-8550, Japan. Electronic address: uemura@iwate-u.ac.jp.
Cold acclimation (CA) and abscisic acid (ABA) treatments affected freezing tolerance of Arabidopsis thaliana suspension-cultured cells: cells at the lag and log phases increased their freezing tolerance but cells at the stationery phase rather decreased after the treatments. To further characterize the differential responses of the cells to these treatments depending on growth phase, plasma membrane (PM) proteome were analyzed using label-free protein quantification technology. Abundance of 841 proteins changed during the progression of growth phase, CA and/or ABA treatment. Among them, 392 proteins changed in their abundance in cells during growth phase progression and were categorized into various functional groups, suggesting changes in physiological characteristics of the PM depending on the growth phase. Comparison of CA- and ABA-responsive proteins indicated that ABA is one of the important signals for PM proteome changes in response to CA, but multiple signals are required for the response of PM proteins to CA. Involvement of ABA in the CA process diminished with the progression of growth phase. Taken together, the results suggest that dynamic alterations of the PM proteome with the progression of growth phase influence the PM proteome responses to CA and ABA, which may effect the difference in freezing tolerance capability. SIGNIFICANCE: After cold acclimation (CA) or abscisic acid treatment (ABA), Arabidopsis thaliana suspension-cultured cells (T87 line) exhibited freezing tolerance capability dependent on the cell growth phase. However, whether the plasma membrane (PM) proteome profile differs among growth phases and the differences are associated with growth-phase-dependent freezing tolerance have not been elucidated. In the present study, PM proteomics was conducted in association with CA and ABA treatment of Arabidopsis suspension-cultured cells at three growth phases. Characteristics of the PM proteome changed considerably with progression of the growth phase and ABA was indicated to be an important signal for PM protein changes during CA. The results also revealed that multiple signals are required to complete the response of PM proteins to CA. Therefore, dynamic alterations of the PM proteome with the advance of the growth phase influence the responses of PM proteome to CA and ABA, which may result in the differences in freezing tolerance of the cultured cells.
PMID: 31541795
BMC Plant Biol , IF:3.497 , 2020 Jan , V20 (1) : P15 doi: 10.1186/s12870-019-2233-9
Metabolomic analyses reveal substances that contribute to the increased freezing tolerance of alfalfa (Medicago sativa L.) after continuous water deficit.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.; College of Grassland Science, Qingdao Agricultural University, Qingdao, People's Republic of China.; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China. lxl@caas.cn.
BACKGROUND: Alfalfa is a high-quality forage cultivated widely in northern China. Recently, the failure of alfalfa plants to survive the winter has caused substantial economic losses. Water management has attracted considerable attention as a method for the potential improvement of winter survival. The aim of this study was to determine whether and how changes in the water regime affect the freezing tolerance of alfalfa. RESULTS: The alfalfa variety WL353LH was cultivated under water regimes of 80 and 25% of water-holding capacity, and all the plants were subjected to low temperatures at 4/0 degrees C (light/dark) and then - 2/- 6 degrees C (light/dark). The semi-lethal temperatures were lower for water-stressed than well-watered alfalfa. The pool sizes of total soluble sugars, total amino acids, and proline changed substantially under water-deficit and low-temperature conditions. Metabolomics analyses revealed 72 subclasses of differential metabolites, among which lipid and lipid-like molecules (e.g., fatty acids, unsaturated fatty acids, and glycerophospholipids) and amino acids, peptides, and analogues (e.g., proline betaine) were upregulated under water-deficit conditions. Some carbohydrates (e.g., D-maltose and raffinose) and flavonoids were also upregulated at low temperatures. Finally, Kyoto Encyclopedia of Genes and Genomes analyses revealed 18 significantly enriched pathways involved in the biosynthesis and metabolism of carbohydrates, unsaturated fatty acids, amino acids, and glycerophospholipids. CONCLUSIONS: Water deficit significantly enhanced the alfalfa' freezing tolerance, and this was correlated with increased soluble sugar, amino acid, and lipid and lipid-like molecule contents. These substances are involved in osmotic regulation, cryoprotection, and the synthesis, fluidity, and stability of the cellular membrane. Our study provides a reference for improving alfalfa' winter survival through water management.
PMID: 31914920
Planta , IF:3.39 , 2020 Jan , V251 (2) : P38 doi: 10.1007/s00425-019-03331-y
Elucidating the regulatory roles of microRNAs in maize (Zea mays L.) leaf growth response to chilling stress.
Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey. faydinoglu@gtu.edu.tr.
MAIN CONCLUSION: miRNAs control leaf size of maize crop during chilling stress tolerance by regulating developmentally important transcriptional factors and sustaining redox homeostasis of cells. Chilling temperature (0-15 degrees C) is a major constraint for the cultivation of maize (Zea mays) which inhibits the early growth of maize leading to reduction in leaf size. Growth and development take place in meristem, elongation, and mature zones that are linearly located along the leaf base to tip. To prevent shortening of leaf caused by chilling, this study aims to elucidate the regulatory roles of microRNA (miRNA) genes in the controlling process switching between growth and developmental stages. In this respect, hybrid maize ADA313 seedlings were treated to the chilling temperature which caused 26% and 29% reduction in the final leaf length and a decline in cell production of the fourth leaf. The flow cytometry data integrated with the expression analysis of cell cycle genes indicated that the reason for the decline was a failure proceeding from G2/M rather than G1/S. Through an miRNome analysis of 321 known maize miRNAs, 24, 6, and 20 miRNAs were assigned to putative meristem, elongation, and mature zones, respectively according to their chilling response. To gain deeper insight into decreased cell production, in silico, target prediction analysis was performed for meristem specific miRNAs. Among the miRNAs, miR160, miR319, miR395, miR396, miR408, miR528, and miR1432 were selected for confirming the potential of negative regulation with their predicted targets by qRT-PCR. These findings indicated evidence for improvement of growth and yield under chilling stress of the maize.
PMID: 31907623
Environ Sci Pollut Res Int , IF:3.056 , 2020 Jan , V27 (1) : P380-390 doi: 10.1007/s11356-019-06760-0
Identification and expression analysis of conserved microRNAs during short and prolonged chromium stress in rice (Oryza sativa).
Amity Institute of Biotechnology, Amity University, Sector-125, Noida, U.P, 201313, India. sdubey1@amity.edu.; Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P, 201307, India.; Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.; Transcriptome Laboratory, Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P, 201307, India. vibha.rani@jiit.ac.in.
MicroRNAs (miRNAs) are one of the most critical epigenetic regulators of gene expression which modulate a spectrum of development and defence response processes in plants. Chromium (Cr) contamination in rice imposes a serious concern to human health as rice is used as staple food throughout the world. Although several studies have established the differential response of miRNAs in rice during heavy metal (arsenic, cadmium) and heat or cold stress, no report is available about the response of miRNAs during Cr stress. In the present study, we identified 512 and 568 known miRNAs from Cr treated and untreated samples, respectively. Expression analysis revealed that 13 conserved miRNAs (miR156, miR159, miR160, miR166, miR169, miR171, miR396, miR397, miR408, miR444, miR1883, miR2877, miR5072) depicted preferential up- or down-regulation (> 4-fold change; P value < 0.05). Target gene prediction of differentially expressed miRNAs and their functional annotation suggested the important role of miRNAs in defence and detoxification of Cr though ATP-binding cassette transporters (ABC transporters), transcription factors, heat shock proteins, auxin response, and metal ion transport. Real-time PCR analysis validated the differential expression of selected miRNAs and their putative target genes. In conclusion, our study identifies and predicts miRNA-mediated regulation of signalling pathway in rice during Cr stress.
PMID: 31792790
J Plant Physiol , IF:3.013 , 2020 Jan , V244 : P153081 doi: 10.1016/j.jplph.2019.153081
Reduced C-to-U RNA editing rates might play a regulatory role in stress response of Arabidopsis.
College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.; College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China. Electronic address: weilai_bnu@163.com.
C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The C-to-U editing rates are constantly very high. During genome evolution, those edited cytidines are likely to be replaced with thymidines at the DNA level. C-to-U editing events are suggested to be designed for reversing the unfavorable T-to-C DNA mutations. Despite the existing theory showing the importance of editing mechanisms, few studies have investigated the genome-wide adaptive signals of the C-to-U editome or the potential function of C-to-U editing events in the stress response. By analyzing the transcriptome and translatome data of normal and heat-shocked Arabidopsis thaliana and the RNA-seq from cold-stressed plants, combined with genome-wide comparison of mitochondrial/chloroplast genes and nuclear genes from multiple aspects, we present the conservational and translational features of each gene and depict the dynamic mitochondrial/chloroplast C-to-U RNA editome. We found that the tAI (tRNA adaptation index) and basic translation levels are lower for mitochondrial/chloroplast genes than for nuclear genes. Interestingly, although we found adaptive signals for the global C-to-U RNA editome in mitochondrial/chloroplast genes, the C-to-U (T) alteration would usually cause a reduction in the codon tAI value. Moreover, the C-to-U editing rates are significantly reduced under heat or cold stress when compared to the normal condition. This reduction is irrelevant to the temperature-sensitive RNA structures. Several cases have illustrated that under heat stress, the reduced C-to-U editing rates alleviate ribosome stalling and consequently facilitate the local translation. Our study reveals that in Arabidopsis thaliana the mitochondrial/chloroplast C-to-U RNA editing rates are reduced under heat or cold stress. This reduction is associated with the alleviation of decreased tAI/translation rate of edited codons. The regulation of C-to-U editing rates could be the tradeoff between quantity and quality. We profile the dynamic change of C-to-U RNA editome under heat stress and propose a potential role of editing sites in the heat response. Our work should be appealing to the plant physiologists as well as the RNA editing community.
PMID: 31783167
J Plant Physiol , IF:3.013 , 2020 Jan , V244 : P153049 doi: 10.1016/j.jplph.2019.153049
Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley.
Department of Plant Physiology, University of Agriculture, Podluzna 3, 30-239, Krakow, Poland. Electronic address: bednarczyk.an@gmail.com.; Department of Plant Physiology, University of Agriculture, Podluzna 3, 30-239, Krakow, Poland. Electronic address: rrrapacz@cyf-kr.edu.pl.
Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.
PMID: 31760347
Plants (Basel) , IF:2.762 , 2020 Jan , V9 (1) doi: 10.3390/plants9010083
Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley.
Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360 Keszthely, Hungary.; Agricultural Institute, Centre for Agricultural Research, 2462 Martonvasar, Hungary.; Department of Genetics and Plant Breeding, Crop Research Institute, 161 06 Prague 6, Czech Republic.
It is established that, besides the cold, incident light also has a crucial role in the cold acclimation process. To elucidate the interaction between these two external hardening factors, barley plantlets were grown under different light conditions with low, normal, and high light intensities at 5 and 15 degrees C. The expression of the HvCBF14 gene and two well-characterized members of the C-repeat binding factor (CBF)-regulon HvCOR14b and HvDHN5 were studied. In general, the expression level of the studied genes was several fold higher at 5 degrees C than that at 15 degrees C independently of the applied light intensity or the spectra. The complementary far-red (FR) illumination induced the expression of HvCBF14 and also its target gene HvCOR14b at both temperatures. However, this supplementation did not affect significantly the expression of HvDHN5. To test the physiological effects of these changes in environmental conditions, freezing tests were also performed. In all the cases, we found that the reduced R:FR ratio increased the frost tolerance of barley at every incident light intensity. These results show that the combined effects of cold, light intensity, and the modification of the R:FR light ratio can greatly influence the gene expression pattern of the plants, which can result in increased plant frost tolerance.
PMID: 31936533
Plant Biol (Stuttg) , IF:2.167 , 2020 Jan , V22 Suppl 1 : P133-142 doi: 10.1111/plb.12955
Deep-sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response.
Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.; Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA.
Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.
PMID: 30597710