Plant Cell Environ , IF:7.228 , 2021 Oct doi: 10.1111/pce.14196
Cytosolic proline is required for basal freezing tolerance in Arabidopsis.
Department of Plant Biotechnology, University of Stuttgart, Institute of Biomaterials & Biomolecular Systems, Stuttgart, Germany.; Department of Biology, University of Konstanz, Constance, Germany.
The amino acid proline accumulates in many plant species under abiotic stress conditions, and various protective functions have been proposed. During cold stress, however, proline content in Arabidopsis thaliana does not correlate with freezing tolerance. Freezing sensitivity of a starchless plastidic phosphoglucomutase mutant (pgm) indicated that localization of proline in the cytosol might stabilize the plasma membrane during freeze-thaw events. Here, we show that re-allocation of proline from cytosol to vacuole was similar in the pyrroline-5-carboxylate synthase 2-1 (p5cs2-1) mutant and the pgm mutant and caused similar reduction of basal freezing tolerance. In contrast, the starch excess 1-1 mutant (sex1-1) had even lower freezing tolerance than pgm but did not affect sub-cellular localization of proline. Freezing sensitivity of sex1-1 mutants affected primarily the photosynthetic electron transport and was enhanced in a sex1-1::p5cs2-1 double mutant. These findings indicate that several independent factors determine basal freezing tolerance. In a pgm::p5cs2-1 double mutant, freezing sensitivity and proline allocation to the vacuole were the same as in the parental lines, indicating that the lack of cytosolic proline was the common cause of reduced basal freezing tolerance in both mutants. We conclude that cytosolic proline is an important factor in freezing tolerance of non-acclimated plants.
PMID: 34605046
Int J Mol Sci , IF:5.923 , 2021 Oct , V22 (20) doi: 10.3390/ijms222011017
Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses.
Key Laboratory of Weed Biology and Management, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
Aegilops tauschii (Coss.) is an aggressive and serious annual grass weed in China. Its DD genome is a rich source of genetic material and performs better under different abiotic stress conditions (salinity, drought, temperature, etc.). Reverse-transcribed quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for reference gene selection and validation. This work aimed to evaluate the stability of reference gene expression in Ae. tauschii under different abiotic stresses (salinity, drought, hot, and cold) and developmental stages (seedling and development). The results show that the ubiquitin-conjugating enzyme E2 36-like (UBC36) and protein microrchidia 2-like (HSP) are the most stable genes under control and salinity conditions, respectively. Under drought stress conditions, UBC36 is more stable as compared with others. Glyceraldehyde-3-phosphate dehydrogenase (GADPH) is the most stable reference gene during heat stress conditions and thioredoxin-like protein (YLS) under cold stress condition. Phosphate2A serine/threonine-protein phosphatase 2A (PP2A) and eukaryotic translation initiation factor 3 (ETIF3) are the most stable genes at seedling and developmental stages. Intracellular transport protein (CAC) is recommended as the most stable gene under different abiotic stresses and at developmental stages. Furthermore, the relative expression levels of NHX1 and DREB under different levels of salinity and drought stress conditions varied with the most (HSP and UBC36) and least (YLS and ACT) stable genes. This study provides reliable reference genes for understanding the tolerance mechanisms in Ae. tauschii under different abiotic stress conditions.
PMID: 34681677
Int J Mol Sci , IF:5.923 , 2021 Oct , V22 (19) doi: 10.3390/ijms221910850
Saussurea involucrata (Snow Lotus) ICE1 and ICE2 Orthologues Involved in Regulating Cold Stress Tolerance in Transgenic Arabidopsis.
Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan.; The Society of Wilderness, Taipei 10073, Taiwan.; Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Zhongli, Taoyuan 32003, Taiwan.; Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan.
As with other environmental stresses, cold stress limits plant growth, geographical distribution, and agricultural productivity. CBF/DREB (CRT-binding factors/DRE-binding proteins) regulate tolerance to cold/freezing stress across plant species. ICE (inducer of CBF expression) is regarded as the upstream inducer of CBF expression and plays a crucial role as a main regulator of cold acclimation. Snow lotus (Saussurea involucrata) is a well-known traditional Chinese herb. This herb is known to have greater tolerance to cold/freezing stress compared to other plants. According to transcriptome datasets, two putative ICE homologous genes, SiICE1 and SiICE2, were identified in snow lotus. The predicted SiICE1 cDNA contains an ORF of 1506 bp, encoding a protein of 501 amino acids, whereas SiICE2 cDNA has an ORF of 1482 bp, coding for a protein of 493 amino acids. Sequence alignment and structure analysis show SiICE1 and SiICE2 possess a S-rich motif at the N-terminal region, while the conserved ZIP-bHLH domain and ACT domain are at the C-terminus. Both SiICE1 and SiICE2 transcripts were cold-inducible. Subcellular localization and yeast one-hybrid assays revealed that SiICE1 and SiICE2 are transcriptional regulators. Overexpression of SiICE1 (35S::SiICE1) and SiICE2 (35S::SiICE2) in transgenic Arabidopsis increased the cold tolerance. In addition, the expression patterns of downstream stress-related genes, CBF1, CBF2, CBF3, COR15A, COR47, and KIN1, were up-regulated when compared to the wild type. These results thus provide evidence that SiICE1 and SiICE2 function in cold acclimation and this cold/freezing tolerance may be regulated through a CBF-controlling pathway.
PMID: 34639192
Front Plant Sci , IF:5.753 , 2021 , V12 : P737004 doi: 10.3389/fpls.2021.737004
PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species.
State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China.; Biology Group, Jiamusi No.1 High School, Jiamusi, China.; Economic Forest Laboratory, Mudanjiang Branch of Heilongjiang Academy of Forestry, Mudanjiang, China.
In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.
PMID: 34691113
Front Plant Sci , IF:5.753 , 2021 , V12 : P721681 doi: 10.3389/fpls.2021.721681
Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.).
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.; College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou, China.
Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.
PMID: 34691103
Front Plant Sci , IF:5.753 , 2021 , V12 : P690040 doi: 10.3389/fpls.2021.690040
Genome-Wide Identification and Function of Aquaporin Genes During Dormancy and Sprouting Periods of Kernel-Using Apricot (Prunus armeniaca L.).
State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China.; State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China.; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States.
Aquaporins (AQPs) are essential channel proteins that play a major role in plant growth and development, regulate plant water homeostasis, and transport uncharged solutes across biological membranes. In this study, 33 AQP genes were systematically identified from the kernel-using apricot (Prunus armeniaca L.) genome and divided into five subfamilies based on phylogenetic analyses. A total of 14 collinear blocks containing AQP genes between P. armeniaca and Arabidopsis thaliana were identified by synteny analysis, and 30 collinear blocks were identified between P. armeniaca and P. persica. Gene structure and conserved functional motif analyses indicated that the PaAQPs exhibit a conserved exon-intron pattern and that conserved motifs are present within members of each subfamily. Physiological mechanism prediction based on the aromatic/arginine selectivity filter, Froger's positions, and three-dimensional (3D) protein model construction revealed marked differences in substrate specificity between the members of the five subfamilies of PaAQPs. Promoter analysis of the PaAQP genes for conserved regulatory elements suggested a greater abundance of cis-elements involved in light, hormone, and stress responses, which may reflect the differences in expression patterns of PaAQPs and their various functions associated with plant development and abiotic stress responses. Gene expression patterns of PaAQPs showed that PaPIP1-3, PaPIP2-1, and PaTIP1-1 were highly expressed in flower buds during the dormancy and sprouting stages of P. armeniaca. A PaAQP coexpression network showed that PaAQPs were coexpressed with 14 cold resistance genes and with 16 cold stress-associated genes. The expression pattern of 70% of the PaAQPs coexpressed with cold stress resistance genes was consistent with the four periods [Physiological dormancy (PD), ecological dormancy (ED), sprouting period (SP), and germination stage (GS)] of flower buds of P. armeniaca. Detection of the transient expression of GFP-tagged PaPIP1-1, PaPIP2-3, PaSIP1-3, PaXIP1-2, PaNIP6-1, and PaTIP1-1 revealed that the fusion proteins localized to the plasma membrane. Predictions of an A. thaliana ortholog-based protein-protein interaction network indicated that PaAQP proteins had complex relationships with the cold tolerance pathway, PaNIP6-1 could interact with WRKY6, PaTIP1-1 could interact with TSPO, and PaPIP2-1 could interact with ATHATPLC1G. Interestingly, overexpression of PaPIP1-3 and PaTIP1-1 increased the cold tolerance of and protein accumulation in yeast. Compared with wild-type plants, PaPIP1-3- and PaTIP1-1-overexpressing (OE) Arabidopsis plants exhibited greater tolerance to cold stress, as evidenced by better growth and greater antioxidative enzyme activities. Overall, our study provides insights into the interaction networks, expression patterns, and functional analysis of PaAQP genes in P. armeniaca L. and contributes to the further functional characterization of PaAQPs.
PMID: 34671366
Biology (Basel) , IF:5.079 , 2021 Oct , V10 (10) doi: 10.3390/biology10100996
Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis.
Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian 271018, China.
Freezing stress in winter is the biggest obstacle to the survival of C. sinensis in mid-latitude and high-latitude areas, which has a great impact on the yield, quality, and even life of C. sinensis every year. In this study, transcriptome and metabolome were used to clarify the freezing resistance mechanism of 60-year-old natural overwintering C. sinensis under freezing stress. Next, 3880 DEGs and 353 DAMs were obtained. The enrichment analysis showed that pathways of MAPK and ABA played a key role in the signal transduction of freezing stress, and Pyr/PYL-PP2C-SnRK2 in the ABA pathway promoted stomatal closure. Then, the water holding capacity and the freezing resistance of C. sinensis were improved. The pathway analysis showed that DEGs and DAMs were significantly enriched and up-regulated in the three-related pathways of phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. In addition, the carbohydrate and fatty acid synthesis pathways also had a significant enrichment, and the synthesis of these substances facilitated the freezing resistance. These results are of great significance to elucidate the freezing resistance mechanism and the freezing resistance breeding of C. sinensis.
PMID: 34681095
Nanomaterials (Basel) , IF:5.076 , 2021 Oct , V11 (10) doi: 10.3390/nano11102670
Mechanisms of Chitosan Nanoparticles in the Regulation of Cold Stress Resistance in Banana Plants.
Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.; Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 13324-8824, Saudi Arabia.; Department of Biology, College of Science, Taif University, Taif 21944, Saudi Arabia.; Department of Soils and Water, Faculty of Agriculture, Al-Azhar University (Assiut Branch), Assiut 71524, Egypt.; Agricultural Research Center, Field Crops Research Institute, Giza 12112, Egypt.; Department of Soils and Water, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt.
Exposure of banana plants, one of the most important tropical and subtropical plants, to low temperatures causes a severe drop in productivity, as they are sensitive to cold and do not have a strong defense system against chilling. Therefore, this study aimed to improve the growth and resistance to cold stress of banana plants using foliar treatments of chitosan nanoparticles (CH-NPs). CH-NPs produced by nanotechnology have been used to enhance tolerance and plant growth under different abiotic stresses, e.g., salinity and drought; however, there is little information available about their effects on banana plants under cold stress. In this study, banana plants were sprayed with four concentrations of CH-NPs-i.e., 0, 100, 200, and 400 mg L(-1) of deionized water-and a group that had not been cold stressed or undergone CH-NP treatment was used as control. Banana plants (Musa acuminata var. Baxi) were grown in a growth chamber and exposed to cold stress (5 degrees C for 72 h). Foliar application of CH-NPs caused significant increases (p < 0.05) in most of the growth parameters and in the nutrient content of the banana plants. Spraying banana plants with CH-NPs (400 mg L(-1)) increased the fresh and dry weights by 14 and 41%, respectively, compared to the control. A positive correlation was found between the foliar application of CH-NPs, on the one hand, and photosynthesis pigments and antioxidant enzyme activities on the other. Spraying banana plants with CH-NPs decreased malondialdehyde (MDA) and reactive oxygen species (ROS), i.e., hydrogen peroxide (H2O2), hydroxyl radicals ((*)OH), and superoxide anions (O2(*-)). CH-NPs (400 mg L(-1)) decreased MDA, H2O2, (*)OH, and O2(*-) by 33, 33, 40, and 48%, respectively, compared to the unsprayed plants. We hypothesize that CH-NPs increase the efficiency of banana plants in the face of cold stress by reducing the accumulation of reactive oxygen species and, in consequence, the degree of oxidative stress. The accumulation of osmoprotectants (soluble carbohydrates, proline, and amino acids) contributed to enhancing the cold stress tolerance in the banana plants. Foliar application of CH-NPs can be used as a sustainable and economically feasible approach to achieving cold stress tolerance.
PMID: 34685113
Plant Cell Physiol , IF:4.927 , 2021 Oct , V62 (6) : P948-958 doi: 10.1093/pcp/pcab060
RsmD, a Chloroplast rRNA m2G Methyltransferase, Plays a Role in Cold Stress Tolerance by Possibly Affecting Chloroplast Translation in Arabidopsis.
Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea.; Faculty of Forestry Agriculture, Tay Nguyen University, Buon Ma Thuot, Daklak 63000, Vietnam.; The Western Highlands Agriculture and Forestry Science Institute, Buon Ma Thuot, Daklak 63000, Vietnam.
Ribosomal RNA (rRNA) methylation is a pivotal process in the assembly and activity of ribosomes, which in turn play vital roles in the growth, development and stress responses of plants. Although few methyltransferases responsible for rRNA methylation have been identified in plant chloroplasts, the nature and function of these enzymes in chloroplasts remain largely unknown. In this study, we characterized ArabidopsisRsmD (At3g28460), an ortholog of the methyltransferase responsible for N2-methylguanosine (m2G) modification of 16S rRNA in Escherichia coli. Confocal microscopic analysis of an RsmD- green fluorescent protein fusion protein revealed that RsmD is localized to chloroplasts. Primer extension analysis indicated that RsmD is responsible for m2G methylation at position 915 in the 16S rRNA of Arabidopsis chloroplasts. Under cold stress, rsmd mutant plants exhibited retarded growth, i.e. had shorter roots, lower fresh weight and pale-green leaves, compared with wild-type (WT) plants. However, these phenotypes were not detected in response to drought or salt stress. Notably, the rsmd mutant was hypersensitive to erythromycin or lincomycin and accumulated fewer chloroplast proteins compared with the WT, suggesting that RsmD influences translation in chloroplasts. Complementation lines expressing RsmD in the rsmd mutant background recovered WT phenotypes. Importantly, RsmD harbored RNA methyltransferase activity. Collectively, the findings of this study indicate that RsmD is a chloroplast 16S rRNA methyltransferase responsible for m2G915 modification that plays a role in the adaptation of Arabidopsisto cold stress.
PMID: 34015128
Microb Ecol , IF:4.552 , 2021 Oct doi: 10.1007/s00248-021-01849-x
Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges.
Department of Microbiology, Akal College of Basic Sciences, Eternal University, Sirmaur, Himachal Pradesh, India.; Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India.; Division of Crop Research, Research Complex for Eastern Region, Patna, Bihar, India.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.; Forest Research Institute, Dehradun, 2480 06, India.; Rain Forest Research Institute, Jorhat, 785 010, India.; Department of Biotechnology, Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, 243123, Uttar Pradesh, India.; Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwa Vidyalaya, Raipur, Chhattisgarh, India.; Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India.; Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.; Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India. ajar@eternaluniversity.edu.in.
The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.
PMID: 34647148
Sci Rep , IF:4.379 , 2021 Oct , V11 (1) : P21094 doi: 10.1038/s41598-021-00506-0
Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology.
Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea.; Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan, Chungnam, 32439, Korea.; Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, Korea.; Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, Korea. kyongcheul.park@kangwon.ac.kr.; Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea. soonjaekwon@kaeri.re.kr.
Faba bean (Vicia faba L.), a globally important grain legume providing a stable source of dietary protein, was one of the earliest plant cytogenetic models. However, the lack of draft genome annotations and unclear structural information on mRNA transcripts have impeded its genetic improvement. To address this, we sequenced faba bean leaf transcriptome using the PacBio single-molecule long-read isoform sequencing platform. We identified 28,569 nonredundant unigenes, ranging from 108 to 9669 bp, with a total length of 94.5 Mb. Many unigenes (3597, 12.5%) had 2-20 isoforms, indicating a highly complex transcriptome. Approximately 96.5% of the unigenes matched sequences in public databases. The predicted proteins and transcription factors included NB-ARC, Myb_domain, C3H, bHLH, and heat shock proteins, implying that this genome has an abundance of stress resistance genes. To validate our results, we selected WCOR413-15785, DHN2-12403, DHN2-14197, DHN2-14797, COR15-14478, and HVA22-15 unigenes from the ICE-CBF-COR pathway to analyze their expression patterns in cold-treated samples via qRT-PCR. The expression of dehydrin-related genes was induced by cold stress. The assembled data provide the first insights into the deep sequencing of full-length RNA from faba bean at the single-molecule level. This study provides an important foundation to improve gene modeling and protein prediction.
PMID: 34702863
Plant Physiol Biochem , IF:4.27 , 2021 Oct , V168 : P70-82 doi: 10.1016/j.plaphy.2021.09.030
Identification and characterization of AnICE1 and AnCBFs involved in cold tolerance from Ammopiptanthus nanus.
Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China.; Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032, China.; CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, 110161, China. Electronic address: zfguo@syau.edu.cn.
The ICE-CBF-COR pathway plays a vital role in improving the cold tolerance of plants. As an evergreen small shrub, Ammopiptanthus nanus has a high tolerance to cold stress because of its special growth conditions. Regrettably, no cold-responsive genes in the ICE-CBF-COR pathway have been reported in A. nanus. In the current study, we isolated AnICE1, AnCBF1, and AnCBF2 in A. nanus and analyzed their sequence structure. Evolutionary analysis indicated that these genes are most closely related to those from Ammopiptanthus mongolicus, Glycine max, Spatholobus suberectus, and Cajanus cajan, all belonging to the Fabaceae. Expression analysis showed that the expression levels of these genes were induced under cold stress and treatment with several plant hormones. As a critical upstream regulator in the ICE-CBF-COR pathway, the function of AnICE1 was further identified. The subcellular localization indicated that AnICE1 is predominantly localized in the plasma membrane and less in the nucleus. Overexpression of AnICE1 in Arabidopsis thaliana improved seed germination and growth of transgenic seedlings during cold stress. Moreover, some physiological indices such as relative electrical conductivity, contents of proline and malondialdehyde, catalase activity, and Nitro Blue tetrazolium and 3.3'-diaminobenzidine staining were investigated by transient expression in A. nanus seedlings and stable overexpression in A. thaliana. These results indicated that AnICE1 enhanced cold tolerance in A. nanus and transgenic A. thaliana. This study is significant for understanding the cold-resistant mechanism of ICE and CBF genes in A. nanus.
PMID: 34624610
BMC Plant Biol , IF:4.215 , 2021 Oct , V21 (1) : P472 doi: 10.1186/s12870-021-03246-5
Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress.
Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning, China.; Agricultural College, Inner Mongolia Minzu University, Tongliao, 028000, China.; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.; College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China.; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China. jiajunleisy@163.com.; Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning, China. laasy@189.cn.
BACKGROUND: Rose is one of most popular ornamental plants worldwide and is of high economic value and great cultural importance. However, cold damage restricts its planting application in cold areas. To elucidate the metabolic response of rose under low temperature stress, we conducted transcriptome and de novo analysis of Rosa xanthina f. spontanea. RESULTS: A total of 124,106 unigenes from 9 libraries were generated by de novo assembly, with N50 length was 1470 bp, under 4 degrees C and - 20 degrees C stress (23 degrees C was used as a control). Functional annotation and prediction analyses identified 55,084 unigenes, and 67.72% of these unigenes had significant similarity (BLAST, E
PMID: 34654360
BMC Plant Biol , IF:4.215 , 2021 Oct , V21 (1) : P460 doi: 10.1186/s12870-021-03181-5
Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.; National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, 100083, People's Republic of China.; Forestry Science Research Institute of Wufeng County, Wufeng, 443400, Hubei Province, China.; College of Forestry, Engineering Technology Research Center of Pinus tabuliformis of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, China. jiazk@bjfu.edu.cn.; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. maluyi@bjfu.edu.cn.; National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, 100083, People's Republic of China. maluyi@bjfu.edu.cn.
BACKGROUND: Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 degrees C, 4 degrees C and 0 degrees C, was compared by RNA sequencing. RESULTS: Over 426 million clean reads were produced from three libraries (22 degrees C, 4 degrees C and 0 degrees C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation. CONCLUSION: M. denudata exhibits responses to non-freezing cold temperature (4 degrees C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 degrees C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.
PMID: 34625030
Tree Physiol , IF:4.196 , 2021 Oct doi: 10.1093/treephys/tpab130
Characterization of the early gene expression profile in Populus ussuriensis under cold stress using PacBio SMRT sequencing integrated with RNA-seq reads.
State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.; School of Pharmacy, Harbin University of Commerce, Harbin 150028, China.
Populus ussuriensis is an important and fast-growing afforestation plant species in north-eastern China. The whole-genome sequencing of P. ussuriensis has not been completed. Also, the transcriptional network of P. ussuriensis response to cold stress remains unknown. To unravel the early response of P. ussuriensis to chilling (3 degrees C) stress and freezing (-3 degrees C) stresses at the transcriptional level, we performed Single-Molecule Real-Time (SMRT) and Illumina RNA sequencing for P. ussuriensis. SMRT long-read isoform sequencing led to the identification of 29,243,277 subreads, and 575,481 circular consensus sequencing (CCS) reads. Approximately 50,910 high-quality (HQ) isoforms were generated, and 2,272 simple sequence repeats (SSRs), 8,086 long non-coding RNAs (lncRNAs) were identified. The Ca2+ content and abscisic acid (ABA) content in P. ussuriensis were significantly increased under cold stresses, while the value in freezing stress treatment group was significantly higher than chilling stress treatment group. A total of 49 genes that are involved in the signal transduction pathways related to perception and transmission of cold stress signals, such as Ca2+ signaling pathway, ABA signaling pathway, and MAPK signaling cascade, were found to be differentially expressed. In addition, 158 transcription factors (TFs) from 21 different families, such as MYB, WRKY, and AP2/ERF, were differentially expressed during chilling and freezing treatments. Moreover, the measurement of physiological indicators and bioinformatics observations demonstrated the altered expression pattern of genes involved in reactive oxygen species (ROS) balance, and sugar metabolism pathway during chilling and freezing stresses. This is the first time to report the early responses of P. ussuriensis to cold stress, which lays the foundation for future studies on the regulatory mechanisms in cold stress response. Besides, the full-length reference transcriptome of P. ussuriensis deciphered could be used in future studies on P. ussuriensis.
PMID: 34625806
Genes (Basel) , IF:4.096 , 2021 Oct , V12 (10) doi: 10.3390/genes12101610
Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress.
Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
Solenopsis japonica, as a fire ant species, shows some predatory behavior towards earthworms and woodlice, and preys on the larvae of other ant species by tunneling into a neighboring colony's brood chamber. This study focused on the molecular response process and gene expression profiles of S. japonica to low (9 degrees C)-temperature stress in comparison with normal temperature (25 degrees C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. The results were 81 GO subgroups and 18 EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) keywords. Differentially expressed genes (DEGs) with log2fold change (FC) > 1 and log2FC < -1 with p-value
PMID: 34681004
Genes (Basel) , IF:4.096 , 2021 Oct , V12 (10) doi: 10.3390/genes12101589
A Cold-Shock Protein from the South Pole-Dwelling Soil Bacterium Arthrobacter sp. Confers Cold Tolerance to Rice.
Biosafety Division, National Institute of Agricultural Sciences, Jeonju 54874, Korea.; Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin 17060, Korea.; Genomics Genetics Institute, GreenGene BioTech, Inc., 16-4 Dongbaek jungang-ro 16beon-gil, Giheung-gu, Yongin 17015, Korea.
Low temperature is a critical environmental factor restricting the physiology of organisms across kingdoms. In prokaryotes, cold shock induces the expression of various genes and proteins involved in cellular processes. Here, a cold-shock protein (ArCspA) from the South Pole-dwelling soil bacterium Arthrobacter sp. A2-5 was introduced into rice, a monocot model plant species. Four-week-old 35S:ArCspA transgenic rice plants grown in a cold chamber at 4 degrees C survived for 6 days. Cold stress significantly decreased the chlorophyll content in WT plants after 4 days compared with that in 35S:ArCspA transgenic plants. RNA-seq analysis was performed on WT and 35S:ArCspA transgenic rice with/without cold stress. GO terms such as "response to stress (GO:0006950)", "response to cold (GO:0009409)", and "response to heat (GO:0009408)" were significantly enriched among the upregulated genes in the 35S:ArCspA transgenic rice under normal conditions, even without cold-stress treatment. The expression of five cold stress-related genes, Rab16B (Os11g0454200), Rab21 (Os11g0454300), LEA22 (Os01g0702500), ABI5 (Os01 g0859300), and MAPK5 (Os03g0285800), was significantly upregulated in the transgenic rice compared with the WT rice. These results indicate that the ArCspA gene might be involved in the induction of cold-responsive genes and provide cold tolerance.
PMID: 34680989
Plant Biol (Stuttg) , IF:3.081 , 2021 Oct doi: 10.1111/plb.13350
Rice OsClo5, a caleosin protein, negatively regulates cold tolerance through the jasmonate signalling pathway.
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.; Guangdong Key Lab of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China.
Caleosin is a lipid droplet-binding protein involved in maintenance of the lipid droplet structure and in signal transduction. However, the role of caleosin proteins in stress resistance is limited. Here, we report data for a rice caleosin protein gene, OsPXG1, involved in cold stress tolerance via influence and regulation of the JA signalling pathway. Overexpression lines and RNAi lines of OsClo5 were subjected to cold stress and recovery to measure electrolyte leakage and survival rate. Changes were also detected in the genome-wide transcriptome of OsClo5 overexpressed plants. OsClo5 is located mainly in lipid droplets and expressed in all tissues tested. Its expression was upregulated by various stress conditions when subjected to cold treatment. Overexpression of OsClo5 decreased cold tolerance, and RNAi lines of OsClo5 had higher survival than WT seedlings. OsClo5 inhibited one jasmonate biosynthetic gene and several jasmonate ZIM domain (JAZ) genes, which were upregulated in response to cold stress. OsClo5 is a constitutively expressed caleosin protein that regulates plant cold resistance through inhibition of jasmonate signalling and JA synthesis.
PMID: 34694678
Ecotoxicology , IF:2.823 , 2021 Nov , V30 (9) : P1826-1840 doi: 10.1007/s10646-021-02483-6
Comparative physiological and proteomic analyses of mangrove plant Kandelia obovata under cold stress.
State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.; Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China.; State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. yswang@scsio.ac.cn.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China. yswang@scsio.ac.cn.; Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences, Guangzhou, 510301, China. yswang@scsio.ac.cn.; Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China. yswang@scsio.ac.cn.; Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
Cold events had broadly affected the survival and geographic distribution of mangrove plants. Kandelia obovata, has an excellent cold tolerance as a true halophyte and widespread mangrove species. In this study, physiological characters and comparative proteomics of leaves of K. obovata were performed under cold treatment. The physiological analysis showed that K. obovata could alleviate its cold-stress injuries through increasing the levels of antioxidants, the activities of related enzymes, as well as osmotic regulation substances (proline). It was detected 184 differentially expressed protein spots, and of 129 (70.11%) spots were identified. These proteins have been involved in several pathways such as the stress and defense, photosynthesis and photorespiration, signal transduction, transcription factors, protein biosynthesis and degradation, molecular chaperones, ATP synthesis, the tricarboxylic acid (TCA) cycle and primary metabolisms. The protein post-translational modification may be a common phenomenon and plays a key role in cold-response process in K. obovata. According to our precious work, a schematic diagram was drawn for the resistance or adaptation strategy of mangrove plants under cold stress. This study provided valuable information to understand the mechanism of cold tolerance of K. obovata.
PMID: 34618290