J Pineal Res , IF:13.007 , 2024 Jan , V76 (1) : Pe12937 doi: 10.1111/jpi.12937
Melatonin as a key regulator in seed germination under abiotic stress.
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.; CAS Research Center for Ecology and Environment of Central Asia, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.; Phytohormones & Plant Development Laboratory, Department of Plant Biology (Plant Physiology), University of Murcia, Murcia, Spain.
Seed germination (SG) is the first stage in a plant's life and has an immense importance in sustaining crop production. Abiotic stresses reduce SG by increasing the deterioration of seed quality, and reducing germination potential, and seed vigor. Thus, to achieve a sustainable level of crop yield, it is important to improve SG under abiotic stress conditions. Melatonin (MEL) is an important biomolecule that interplays in developmental processes and regulates many adaptive responses in plants, especially under abiotic stresses. Thus, this review specifically summarizes and discusses the mechanistic basis of MEL-mediated SG under abiotic stresses. MEL regulates SG by regulating some stress-specific responses and some common responses. For instance, MEL induced stress specific responses include the regulation of ionic homeostasis, and hydrolysis of storage proteins under salinity stress, regulation of C-repeat binding factors signaling under cold stress, starch metabolism under high temperature and heavy metal stress, and activation of aquaporins and accumulation of osmolytes under drought stress. On other hand, MEL mediated regulation of gibberellins biosynthesis and abscisic acid catabolism, redox homeostasis, and Ca(2+) signaling are amongst the common responses. Nonetheless factors such as endogenous MEL contents, plant species, and growth conditions also influence above-mentioned responses. In conclusion, MEL regulates SG under abiotic stress conditions by interacting with different physiological mechanisms.
PMID: 38241678
Plant Cell , IF:11.277 , 2024 Jan doi: 10.1093/plcell/koae025
Histone deacetylase OsHDA716 chilling out with OsbZIP46: antagonistically regulating cold stress tolerance in rice.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; John Innes Centre, Norwich Research Park, NR4 7UH, UK.
PMID: 38267564
Glob Chang Biol , IF:10.863 , 2024 Jan , V30 (1) : Pe17016 doi: 10.1111/gcb.17016
Climate warming could free cold-adapted trees from C-conservative allocation strategy of storage over growth.
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.; Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.; University of Chinese Academy of Sciences, Beijing, China.; College of Science, Tibet University, Lhasa, China.
Carbon allocation has been fundamental for long-lived trees to survive cold stress at their upper elevation range limit. Although carbon allocation between non-structural carbohydrate (NSC) storage and structural growth is well-documented, it still remains unclear how ongoing climate warming influences these processes, particularly whether these two processes will shift in parallel or respond divergently to warming. Using a combination of an in situ downward-transplant warming experiment and an ex situ chamber warming treatment, we investigated how subalpine fir trees at their upper elevation limit coordinated carbon allocation priority among different sinks (e.g., NSC storage and structural growth) at whole-tree level in response to elevated temperature. We found that transplanted individuals from the upper elevation limit to lower elevations generally induced an increase in specific leaf area, but there was no detected evidence of warming effect on leaf-level saturated photosynthetic rates. Additionally, our results challenged the expectation that climate warming will accelerate structural carbon accumulation while maintaining NSC constant. Instead, individuals favored allocating available carbon to NSC storage over structural growth after 1 year of warming, despite the amplification in total biomass encouraged by both in situ and ex situ experimental warming. Unexpectedly, continued warming drove a regime shift in carbon allocation priority, which was manifested in the increase of NSC storage in synchrony to structural growth enhancement. These findings imply that climate warming would release trees at their cold edge from C-conservative allocation strategy of storage over structural growth. Thus, understanding the strategical regulation of the carbon allocation priority and the distinctive function of carbon sink components is of great implication for predicting tree fate in the future climate warming.
PMID: 37921358
J Hazard Mater , IF:10.588 , 2024 Feb , V463 : P132802 doi: 10.1016/j.jhazmat.2023.132802
Performance and mechanism of SMX removal by an electrolysis-integrated ecological floating bed at low temperatures: A new perspective of plant activity, iron plaque, and microbial functions.
Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.; School of Life Sciences, Anhui Medical University, Hefei 230032, China.; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China. Electronic address: lushy2000@163.com.; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China. Electronic address: lxh7786@ouc.edu.cn.; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
Improvements in plant activity and functional microbial communities are important to ensure the stability and efficiency of pollutant removal measures in cold regions. Although electrochemistry is known to accelerate pollutant degradation, cold stress acclimation of plants and the stability and activity of plant-microbial synergism remain poorly understood. The sulfamethoxazole (SMX) removal, iron plaque morphology, plant activity, microbial community, and function responses were investigated in an electrolysis-integrated ecological floating bed (EFB) at 6 +/- 2 ℃. Electrochemistry significantly improved SMX removal and plant activity. Dense and uniform iron plaque was found on root surfaces in L-E-Fe which improved the plant adaptability at low temperatures and provided more adsorption sites for bacteria. The microbial community structure was optimized and the key functional bacteria for SMX degradation (e.g., Actinobacteriota, Pseudomonas) were enriched. Electrochemistry improves the relative abundance of enzymes related to energy metabolism, thereby increasing energy responses to SMX and low temperatures. Notably, electrochemistry improved the expression of target genes (sadB and sadC, especially sadC) involved in SMX degradation. Electrochemistry enhances hydrogen bonding and electrostatic interactions between SMX and sadC, thereby enhancing SMX degradation and transformation. This study provides a deeper understanding of the electrochemical stability of antibiotic degradation at low temperatures.
PMID: 37922584
New Phytol , IF:10.151 , 2024 Jan , V241 (1) : P283-297 doi: 10.1111/nph.19339
REVEILLE2 thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock.
School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK.; RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany.; Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.; Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. We demonstrate that REVEILLE2 undergoes alternative splicing after chilling that increases accumulation of a transcript isoform encoding a MYB-like transcription factor. We explore the biological function of REVEILLE2 in Arabidopsis thaliana using a combination of molecular genetics, transcriptomics, and physiology. Disruption of REVEILLE2 alternative splicing alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently upregulated. The response of REVEILLE2 to chilling extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes.
PMID: 37897048
New Phytol , IF:10.151 , 2024 Jan doi: 10.1111/nph.19514
COG3 confers the chilling tolerance to mediate OsFtsH2-D1 module in rice.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
The chilling stress induced by the global climate change harms rice production, especially at seedling and booting stage, which feed half the population of the world. Although there are key quantitative trait locus genes identified in the individual stage, few genes have been reported and functioned at both stages. Utilizing chromosome segment substitution lines (CSSLs) and a combination of map-based cloning and phenotypes of the mutants and overexpression lines, we identified the major gene Chilling-tolerance in Geng/japonica rice 3 (COG3) of q chilling-tolerance at the booting and seedling stage 11 (qCTBS11) conferred chilling tolerance at both seedling and booting stages. COG3 was significantly upregulated in Nipponbare under chilling treatment compared with its expression in 93-11. The loss-of-function mutants cog3 showed a reduced chilling tolerance. On the contrary, overexpression enhanced chilling tolerance. Genome evolution and genetic analysis suggested that COG3 may have undergone strong selection in temperate japonica during domestication. COG3, a putative calmodulin-binding protein, physically interacted with OsFtsH2 at chloroplast. In cog3-1, OsFtsH2-mediated D1 degradation was impaired under chilling treatment compared with wild-type. Our results suggest that COG3 is necessary for maintaining OsFtsH2 protease activity to regulate chilling tolerance at the booting and seedling stage.
PMID: 38173177
Plant Biotechnol J , IF:9.803 , 2024 Feb , V22 (2) : P413-426 doi: 10.1111/pbi.14195
Banana MaNAC1 activates secondary cell wall cellulose biosynthesis to enhance chilling resistance in fruit.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, South China Agricultural University, Guangzhou, China.; Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China.
Chilling injury has a negative impact on the quantity and quality of crops, especially subtropical and tropical plants. The plant cell wall is not only the main source of biomass production, but also the first barrier to various stresses. Therefore, improving the understanding of the alterations in cell wall architecture is of great significance for both biomass production and stress adaptation. Herein, we demonstrated that the cell wall principal component cellulose accumulated during chilling stress, which was caused by the activation of MaCESA proteins. The sequence-multiple comparisons show that a cold-inducible NAC transcriptional factor MaNAC1, a homologue of Secondary Wall NAC transcription factors, has high sequence similarity with Arabidopsis SND3. An increase in cell wall thickness and cellulosic glucan content was observed in MaNAC1-overexpressing Arabidopsis lines, indicating that MaNAC1 participates in cellulose biosynthesis. Over-expression of MaNAC1 in Arabidopsis mutant snd3 restored the defective secondary growth of thinner cell walls and increased cellulosic glucan content. Furthermore, the activation of MaCESA7 and MaCESA6B cellulose biosynthesis genes can be directly induced by MaNAC1 through binding to SNBE motifs within their promoters, leading to enhanced cellulose content during low-temperature stress. Ultimately, tomato fruit showed greater cold resistance in MaNAC1 overexpression lines with thickened cell walls and increased cellulosic glucan content. Our findings revealed that MaNAC1 performs a vital role as a positive modulator in modulating cell wall cellulose metabolism within banana fruit under chilling stress.
PMID: 37816143
Plant Physiol , IF:8.34 , 2024 Jan , V194 (2) : P1075-1090 doi: 10.1093/plphys/kiad578
Transcription factor SlWRKY50 enhances cold tolerance in tomato by activating the jasmonic acid signaling.
National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
Tomato (Solanum lycopersicum) is a cold-sensitive crop but frequently experiences low-temperature stimuli. However, tomato responses to cold stress are still poorly understood. Our previous studies have shown that using wild tomato (Solanum habrochaites) as rootstock can significantly enhance the cold resistance of grafted seedlings, in which a high concentration of jasmonic acids (JAs) in scions exerts an important role, but the mechanism of JA accumulation remains unclear. Herein, we discovered that tomato SlWRKY50, a Group II WRKY transcription factor that is cold inducible, responds to cold stimuli and plays a key role in JA biosynthesis. SlWRKY50 directly bound to the promoter of tomato allene oxide synthase gene (SlAOS), and overexpressing SlWRKY50 improved tomato chilling resistance, which led to higher levels of Fv/Fm, antioxidative enzymes, SlAOS expression, and JA accumulation. SlWRKY50-silenced plants, however, exhibited an opposite trend. Moreover, diethyldithiocarbamate acid (a JA biosynthesis inhibitor) foliar treatment drastically reduced the cold tolerance of SlWRKY50-overexpression plants to wild-type levels. Importantly, SlMYC2, the key regulator of the JA signaling pathway, can control SlWRKY50 expression. Overall, our research indicates that SlWRKY50 promotes cold tolerance by controlling JA biosynthesis and that JA signaling mediates SlWRKY50 expression via transcriptional activation by SlMYC2. Thus, this contributes to the genetic knowledge necessary for developing cold-resistant tomato varieties.
PMID: 37935624
Food Chem , IF:7.514 , 2024 Apr , V438 : P138005 doi: 10.1016/j.foodchem.2023.138005
Metabolic profiling of Oryza sativa seedlings under chilling stress using nanoliter electrospray ionization mass spectrometry.
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China; School of Life Sciences, Nanchang Normal University, Nanchang, 330031, PR China; School of Life Sciences, Nanchang University, Nanchang 330031, PR China.; College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China.; School of Life Sciences, Nanchang Normal University, Nanchang, 330031, PR China.; School of Life Sciences, Nanchang University, Nanchang 330031, PR China.; School of Life Sciences, Nanchang University, Nanchang 330031, PR China. Electronic address: lluo2@126.com.
Low temperatures significantly impact on rice (Oryza sativa) yield and quality. Traditional metabolomic techniques, often involving time-consuming chromatography-mass spectrometry procedures, are currently in use. This study investigated metabolomic responses of rice seedlings under low-temperature stress using nanoliter electrospray ionization mass spectrometry (nanoESI-MS) in combination with multivariate analysis. Results revealed distinct metabolic profiles in 'Qiutianxiaoting' (japonica) and '93-11' (indica) rice seedlings. Among the 36 identified compounds in rice, seven key metabolites, comprising l-glutamic acid, asparagine, tryptophan, citric acid, alpha-linolenic acid, malic acid, and inositol, were identified as responsive to cold stress. Notably, malic acid content reached 1332.40 mug/g dry weight in Qiutianxiaoting and 1444.13 mug/g in 93-11. Both the qualitative and quantitative results of nanoESI-MS were further confirmed through gas chromatography-mass spectrometry validation. The findings highlight the potential of nanoESI-MS for rapidly characterizing crucial metabolites across diverse plant species under exposure to stress.
PMID: 37983997
Plant Cell Environ , IF:7.228 , 2024 Jan doi: 10.1111/pce.14816
A transcriptional regulation of ERF15 contributes to ABA-mediated cold tolerance in tomato.
Hainan Institute, Zhejiang University, Sanya, China.; Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China.
Cold stress is a major meteorological threat to crop growth and yield. Abscisic acid (ABA) plays important roles in plant cold tolerance by activating the expression of cold-responsive genes; however, the underlying transcriptional regulatory module remains unknown. Here, we demonstrated that the cold- and ABA-responsive transcription factor ETHYLENE RESPONSE FACTOR 15 (ERF15) positively regulates ABA-mediated cold tolerance in tomato. Exogenous ABA treatment significantly enhanced cold tolerance in wild-type tomato plants but failed to rescue erf15 mutants from cold stress. Transcriptome analysis showed that ERF15 was associated with the expression of cold-responsive transcription factors such as CBF1 and WRKY6. Further RT-qPCR assays confirmed that the ABA-induced increased in CBF1 and WRKY6 transcripts was suppressed in erf15 mutants when the plants were subjected to cold treatment. Moreover, yeast one-hybrid assays, dual-luciferase assays and electrophoretic mobility shift assays demonstrated that ERF15 activated the transcription of CBF1 and WRKY6 by binding their promoters. Silencing CBF1 or WRKY6 significantly decreased cold tolerance. Overall, our study identified the role of ERF15 in conferring ABA-mediated cold tolerance in tomato plants by activating CBF1 and WRKY6 expression. This study not only broadens our knowledge of the mechanism of ABA-mediated cold tolerance in plants but also highlights ERF15 as an ideal target gene for cold-tolerant crop breeding.
PMID: 38221812
Plant Cell Environ , IF:7.228 , 2024 Jan doi: 10.1111/pce.14796
ERF54 regulates cold tolerance in Rosa multiflora through DREB/COR signalling pathways.
Discipline of Ornamental Horticulture, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, Zhejiang, China.; Discipline of Landscape Architecture, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, Henan, China.
Ethylene-responsive factors (ERFs) participate in a wide range of physiological and biological processes. However, many of the functions of ERFs in cold stress responses remain unclear. We, therefore, characterised the cold responses of RmERF54 in Rosa multiflora, a rose-related cold-tolerant species. Overexpression of RmERF54, which is a nuclear transcription factor, increases the cold resistance of transgenic tobacco and rose somatic embryos. In contrast, virus-induced gene silencing (VIGS) of RmERF54 increased cold susceptibility of R. multiflora. The overexpression of RmERF54 resulted in extensive transcriptional reprogramming of stress response and antioxidant enzyme systems. Of these, the levels of transcripts encoding the PODP7 peroxidase and the cold-related COR47 protein showed the largest increases in the somatic embryos with ectopic expression of RmERF54. RmERF54 binds to the promoters of the RmPODP7 and RmCOR47 genes and activates expression. RmERF54-overexpressing lines had higher antioxidant enzyme activities and considerably lower levels of reactive oxygen species. Opposite effects on these parameters were observed in the VIGS plants. RmERF54 was identified as a target of Dehydration-Responsive-Element-Binding factor (RmDREB1E). Taken together, provide new information concerning the molecular mechanisms by which RmERF54 regulates cold tolerance.
PMID: 38164066
J Exp Bot , IF:6.992 , 2024 Jan doi: 10.1093/jxb/erae007
PlantC2U: Deep learning of cross-species sequence landscapes predict plastid C-to-U RNA editing in plants.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361104, China.
In plants, C-to-U RNA editing is mainly occurred in the plastids and mitochondria transcripts, which contributes to complex transcriptional regulatory network. More evidences reveal that RNA editing plays critical roles in plant growth and development. However, RNA editing sites accurately detected by transcriptome sequencing data alone are still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves over 95% sensitivity and 99% specificity, which outperforms PREPACT tool, random forest, and support vector machine. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce the possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in cold stress response of K. obovata, suggesting their potential regulatory roles in the plants stress adaption. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB would help researchers explore the RNA editing events in plants and thus would be of broad utility for the plant research community.
PMID: 38190348
Int J Biol Macromol , IF:6.953 , 2024 Feb , V257 (Pt 1) : P128617 doi: 10.1016/j.ijbiomac.2023.128617
Genome-wide identification and expression profiling of the WRKY gene family reveals abiotic stress response mechanisms in Platycodon grandiflorus.
College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China.; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China. Electronic address: zlp_ahtcm@126.com.; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei, China; Anhui Province Key Laboratory of Pharmaceutical Technology and Application, Anhui University of Chinese Medicine, Hefei, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China. Electronic address: guishy0520@ahtcm.edu.cn.
The WRKY family of transcription factors (TFs) is an important gene family involved in abiotic stress responses. Although the roles of WRKY TFs in plant abiotic stress responses are well studied, little is known about the stress-induced changes in WRKY family in Platycodon grandiflorus. 42 PgWRKY genes in seven subgroups were identified in the P. grandiflorus genome. The content of eight platycodins in P. grandiflorus was investigated under cold, heat, and drought stresses. Platycodin D levels significantly increased under three abiotic stresses, while the content changes of other platycodins varied. Transcriptome analysis showed that different WRKY family members exhibited varied expression patterns under different abiotic stresses. PgWRKY20, PgWRKY26, and PgWRKY39 were identified as three key candidates for temperature and drought stress responses, and were cloned and analysed for sequence characteristics, gene structure, subcellular localisation, and expression patterns. The RT-qPCR results showed that PgWRKY26 expression significantly increased after heat stress for 48 h, cold stress for 6 h, and drought stress for 2 d (DS_2 d). The PgWRKY39 expression level significantly increased at DS_2 d. This study provides a theoretical basis for clarifying the molecular mechanism of the abiotic stress responses of the WRKY gene family in P. grandiflorus.
PMID: 38070802
Int J Biol Macromol , IF:6.953 , 2024 Jan , V256 (Pt 1) : P128063 doi: 10.1016/j.ijbiomac.2023.128063
WRKY transcription factors in passion fruit analysis reveals key PeWRKYs involved in abiotic stress and flavonoid biosynthesis.
Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.; Yunnan Agricultural University, Yunnan 650201, China.; Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China. Electronic address: songs@catas.cn.; Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China. Electronic address: xuyi@catas.cn.
WRKY transcription factors (TFs) are a superfamily of regulators involved in plant responses to pathogens and abiotic stress. Passion fruit is famous for its unique flavor and nutrient-rich juice, but its growth is limited by environmental factors and pathogens. In this study, 55 WRKY genes were identified from the Passiflora edulis genome. The structure and evolutionary characteristics of PeWRKYs were analyzed using a bioinformatics approach. PeWRKYs were classified into seven subgroups (I, IIa, IIb, IIc, IId, IIe, III) according to their homologs in Arabidopsis thaliana. Group IIa PeWRKY48 gene was highly up-regulated under cold stress by RNA expression analysis, and transgenic PeWRKY48 in yeast and Arabidopsis showed resistance exposure to cold, salt, and drought stress. Metabolome and transcriptome co-expression analysis of two different disease resistance genotypes of P. edulis identified PeWRKY30 as a key TF co-expressed with flavonoid accumulation in yellow fruit P. edulis, which may contribute to biotic or abiotic resistance. The qRT-PCR verified the expression of key genes in different tissues of P. edulis and in different species of Passiflora. This study provides a set of WRKY candidate genes that will facilitate the genetic improvement of disease and abiotic tolerance in passion fruit.
PMID: 37963507
Int J Biol Macromol , IF:6.953 , 2024 Jan , V254 (Pt 2) : P127778 doi: 10.1016/j.ijbiomac.2023.127778
ROS scavenging enzyme-encoding genes play important roles in the desert moss Syntrichia caninervis response to extreme cold and desiccation stresses.
State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830000 Urumqi, China.; State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830000 Urumqi, China. Electronic address: lixs@ms.xjb.ac.cn.
Abiotic stress is one of the major environmental constraints limiting plant growth. Syntrichia caninervis is one of the unique plant models that can cope with harsh environments. Reactive oxygen species (ROS) are a vital signaling molecule for protecting plants from oxidative stress, but research on ROS in S. caninervis is limited. Here, we identified 112 ROS genes in S. caninervis, including 40 GSTs, 51 PODs, 9 SODs, 6 CATs, 3 GPXs and 3 APXs families. GO and KEGG analyses showed that ROS genes are involved in responses to various stimuli and phenylpropanoid biosynthesis. ROS genes contain many stress-responsive and hormonal cis-elements in their promoter regions. More ROS genes were induced by cold stress than desiccation stress, and both conditions changed the transcript abundances of several ROS genes. CAT and POD, H(2)O(2), MDA, and GSH were also induced under biotic stress, specifically CAT activity. The results indicated that the ScCAT genes and their activities could be strongly associated with the regulation of ROS production. This is the first systematic identification of ROS genes in S. caninervis and our findings contribute to further research into the roles of ScROS adjustment under abiotic stress while also providing excellent genetic resources for plant breeding.
PMID: 37926320
Int J Biol Macromol , IF:6.953 , 2023 Dec , V253 (Pt 7) : P127442 doi: 10.1016/j.ijbiomac.2023.127442
Genome-wide analyses of calmodulin and calmodulin-like proteins in the halophyte Nitraria sibirica reveal their involvement in response to salinity, drought and cold stress.
State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.; Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, Inner Mongolia, China.; College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: lulu2020@njfu.edu.cn.
The calmodulin (CaM) and calmodulin-like (CML) proteins are major calcium sensors that play a critical role in environmental stimulus response in plants. Nevertheless, the CaM/CML proteins from the specific plants with extreme tolerance to abiotic stresses remained so far uncharacterized. In this study, 66 candidate proteins (three NsCaMs and sixty-three NsCMLs) were identified from the halophyte Nitraria sibirica, which can withstand an extreme salinity. Bioinformatic analysis of upstream cis-acting elements predicted the potential involvement of NsCaM/CMLs in abiotic stress responses and various hormone responses. Additionally, the Nitraria sibirica transcriptome revealed that 17 and 7 NsCMLs were significantly upregulated under 100 mM or 400 mM NaCl treatment. Transcription of most salt-responsive genes was similarly upregulated under cold stress, yet downregulated under drought treatment. Moreover, predictive subcellular localization analysis suggested that the stress-responsive NsCML proteins mainly localize at the cellular membrane and within the nucleus. Furthermore, transgenic overexpression of two NsCMLs (NISI03G1136 and NISI01G1645) was found to mitigate H(2)O(2) accumulation caused by salt stress. These results provide insights into the potential function of Nitraria sibirica CaM/CML proteins, which could aid the investigation of molecular mechanisms of extreme tolerance to abiotic stresses in halophytes.
PMID: 37844818
Int J Biol Macromol , IF:6.953 , 2023 Dec , V253 (Pt 2) : P126701 doi: 10.1016/j.ijbiomac.2023.126701
Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses.
Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China.; Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China.; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China.; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China. Electronic address: zmeng@sdnu.edu.cn.; Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China; Research team of plant pathogen microbiology and immunology, College of Life Science, Shandong Normal University, Jinan, China. Electronic address: zhangquan@sdnu.edu.cn.
ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.
PMID: 37673165
Plant J , IF:6.417 , 2024 Jan doi: 10.1111/tpj.16624
Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis.
Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China.; Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China.; Department of Plant Biology, Department of Horticulture, Michigan State University AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA.
Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.
PMID: 38184780
Plant J , IF:6.417 , 2024 Jan , V117 (1) : P72-91 doi: 10.1111/tpj.16470
The OsTIL1 lipocalin protects cell membranes from reactive oxygen species damage and maintains the 18:3-containing glycerolipid biosynthesis under cold stress in rice.
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.; Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan.; Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, USA.; Department of Mathematics, University of North Texas, Denton, Texas, 76203, USA.
Lipocalins constitute a conserved protein family that binds to and transports a variety of lipids while fatty acid desaturases (FADs) are required for maintaining the cell membrane fluidity under cold stress. Nevertheless, it remains unclear whether plant lipocalins promote FADs for the cell membrane integrity under cold stress. Here, we identified the role of OsTIL1 lipocalin in FADs-mediated glycerolipid remodeling under cold stress. Overexpression and CRISPR/Cas9 mediated gene edition experiments demonstrated that OsTIL1 positively regulated cold stress tolerance by protecting the cell membrane integrity from reactive oxygen species damage and enhancing the activities of peroxidase and ascorbate peroxidase, which was confirmed by combined cold stress with a membrane rigidifier dimethyl sulfoxide or a H(2) O(2) scavenger dimethyl thiourea. OsTIL1 overexpression induced higher 18:3 content, and higher 18:3/18:2 and (18:2 + 18:3)/18:1 ratios than the wild type under cold stress whereas the gene edition mutant showed the opposite. Furthermore, the lipidomic analysis showed that OsTIL1 overexpression led to higher contents of 18:3-mediated glycerolipids, including galactolipids (monoglactosyldiacylglycerol and digalactosyldiacylglycerol) and phospholipids (phosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol) under cold stress. RNA-seq and enzyme linked immunosorbent assay analyses indicated that OsTIL1 overexpression enhanced the transcription and enzyme abundance of four omega-3 FADs (OsFAD3-1/3-2, 7, and 8) under cold stress. These results reveal an important role of OsTIL1 in maintaining the cell membrane integrity from oxidative damage under cold stress, providing a good candidate gene for improving cold tolerance in rice.
PMID: 37753661
Ecotoxicol Environ Saf , IF:6.291 , 2024 Jan , V269 : P115737 doi: 10.1016/j.ecoenv.2023.115737
DgHDA6 enhances the cold tolerance in chrysanthemum by improving ROS scavenging capacity.
Department of Ornamental Horticulture, 211 Huimin Road, Chengdu 611130, China.; Department of Ornamental Horticulture, 211 Huimin Road, Chengdu 611130, China. Electronic address: qingllinliu@126.com.
Histone deacetylases have been demonstrated to play an important role in responding to low-temperature stress, but the related response mechanism in chrysanthemum remains unclear. In this study, we isolated a cold-induced gene, DgHDA6, from chrysanthemum (Chrysanthemum morifolium Ramat). DgHDA6 contains 474 amino acids and shares a typical deacetylation domain with RPD3/HDA1 family members. The overexpression of DgHDA6 enhanced cold resistance in chrysanthemums. After low-temperature stress, the overexpression lines showed a higher survival rate. The contents of proline, soluble proteins and sugars, and the activities of antioxidant enzymes were significantly increased while the contents of H(2)O(2), O(2)(-) and MDA were lower. Moreover, cold-stress-responding genes such as DgCuZnSOD, DgCAT, DgP5CS, and DgFAD were upregulated after cold stress. These results suggest that the overexpression of DgHDA6 can improve cold tolerance in chrysanthemum by enhancing ROS scavenging capacity.
PMID: 38029581
Int J Mol Sci , IF:5.923 , 2024 Jan , V25 (2) doi: 10.3390/ijms25021115
Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean (Glycine max) under Various Abiotic Stresses.
College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.
PMID: 38256188
Int J Mol Sci , IF:5.923 , 2024 Jan , V25 (2) doi: 10.3390/ijms25020929
Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale.
Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China.; MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China.
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
PMID: 38256002
Int J Mol Sci , IF:5.923 , 2024 Jan , V25 (2) doi: 10.3390/ijms25020918
The Roles of Circadian Clock Genes in Plant Temperature Stress Responses.
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea.; Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea.
Plants monitor day length and memorize changes in temperature signals throughout the day, creating circadian rhythms that support the timely control of physiological and metabolic processes. The DEHYDRATION-RESPONSE ELEMENT-BINDING PROTEIN 1/C-REPEAT BINDING FACTOR (DREB1/CBF) transcription factors are known as master regulators for the acquisition of cold stress tolerance, whereas PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is involved in plant adaptation to heat stress through thermomorphogenesis. Recent studies have shown that circadian clock genes control plant responses to temperature. Temperature-responsive transcriptomes show a diurnal cycle and peak expression levels at specific times of throughout the day. Circadian clock genes play essential roles in allowing plants to maintain homeostasis by accommodating temperature changes within the normal temperature range or by altering protein properties and morphogenesis at the cellular level for plant survival and growth under temperature stress conditions. Recent studies revealed that the central oscillator genes CIRCADIAN CLOCK ASSOCIATED 1/LATE ELONGATED HYPOCOTYL (CCA1/LHY) and PSEUDO-RESPONSE REGULATOR5/7/9 (PRR5/7/9), as well as the EVENING COMPLEX (EC) genes REVEILLE4/REVEILLE8 (REV4/REV8), were involved in the DREB1 pathway of the cold signaling transcription factor and regulated the thermomorphogenesis gene PIF4. Further studies showed that another central oscillator, TIMING OF CAB EXPRESSION 1 (TOC1), and the regulatory protein ZEITLUPE (ZTL) are also involved. These studies led to attempts to utilize circadian clock genes for the acquisition of temperature-stress resistance in crops. In this review, we highlight circadian rhythm regulation and the clock genes involved in plant responses to temperature changes, as well as strategies for plant survival in a rapidly changing global climate.
PMID: 38255990
Front Plant Sci , IF:5.753 , 2023 , V14 : P1280251 doi: 10.3389/fpls.2023.1280251
The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L.
Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States.; Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States.; Cooperative Agricultural Research Center, College of Agriculture & Human Sciences, Prairie View A&M University, Prairie View, TX, United States.
INTRODUCTION: With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered. METHODS: The soybean plants were exposed to cold stress (8-10 degrees C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated. RESULTS AND DISCUSSION: We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.
PMID: 38269137
Front Plant Sci , IF:5.753 , 2023 , V14 : P1242948 doi: 10.3389/fpls.2023.1242948
Estimating the frost damage index in lettuce using UAV-based RGB and multispectral images.
College of Information Technology, Shanghai Ocean University, Shanghai, China.; Institute of Agricultural Science and Technology Information, Shanghai Academy of Agricultural Sciences, Shanghai, China.; Key Laboratory of Intelligent Agricultural Technology (Yangtze River Delta), Ministry of Agriculture and Rural Affairs, Shanghai, China.; Jinshan Experimental Station, Shanghai Agrobiological Gene Center, Shanghai, China.; School of Computer and Artificial Intelligence, Wuhan University of Technology, Wuhan, China.
INTRODUCTION: The cold stress is one of the most important factors for affecting production throughout year, so effectively evaluating frost damage is great significant to the determination of the frost tolerance in lettuce. METHODS: We proposed a high-throughput method to estimate lettuce FDI based on remote sensing. Red-Green-Blue (RGB) and multispectral images of open-field lettuce suffered from frost damage were captured by Unmanned Aerial Vehicle platform. Pearson correlation analysis was employed to select FDI-sensitive features from RGB and multispectral images. Then the models were established for different FDI-sensitive features based on sensor types and different groups according to lettuce colors using multiple linear regression, support vector machine and neural network algorithms, respectively. RESULTS AND DISCUSSION: Digital number of blue and red channels, spectral reflectance at blue, red and near-infrared bands as well as six vegetation indexes (VIs) were found to be significantly related to the FDI of all lettuce groups. The high sensitivity of four modified VIs to frost damage of all lettuce groups was confirmed. The average accuracy of models were improved by 3% to 14% through a combination of multisource features. Color of lettuce had a certain impact on the monitoring of frost damage by FDI prediction models, because the accuracy of models based on green lettuce group were generally higher. The MULTISURCE-GREEN-NN model with R(2) of 0.715 and RMSE of 0.014 had the best performance, providing a high-throughput and efficient technical tool for frost damage investigation which will assist the identification of cold-resistant green lettuce germplasm and related breeding.
PMID: 38239223
Front Plant Sci , IF:5.753 , 2023 , V14 : P1272986 doi: 10.3389/fpls.2023.1272986
Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics.
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy.
Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.
PMID: 38235207
Int J Food Microbiol , IF:5.277 , 2024 Jan , V410 : P110479 doi: 10.1016/j.ijfoodmicro.2023.110479
Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment.
FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria. Electronic address: nadja.pracser@ffoqsi.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: andreas.zaiser@vetmeduni.ac.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.; Austrian National Reference Laboratory for Listeria monocytogenes, Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Beethovenstrasse 6, 8010 Graz, Austria. Electronic address: ariane.pietzka@ages.at.; FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: martin.wagner@vetmeduni.ac.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: kathrin.rychli@vetmeduni.ac.at.
Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 degrees C and 10 degrees C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content. The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.
PMID: 37977080
Rice (N Y) , IF:4.783 , 2024 Jan , V17 (1) : P5 doi: 10.1186/s12284-023-00682-9
OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice.
College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.; Yuelushan Laboratory, Changsha, 410128, China.; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China. tangwenbang@163.com.; Yuelushan Laboratory, Changsha, 410128, China. tangwenbang@163.com.; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China. luxuedan1@126.com.; Yuelushan Laboratory, Changsha, 410128, China. luxuedan1@126.com.
Chilling is a major abiotic stress affecting rice growth, development and geographical distribution. Plant vacuolar processing enzymes (VPEs) contribute to the seed storage protein processing and mediate the programmed cell death by abiotic and biotic stresses. However, little is known about the roles of plant VPEs in cold stress responses and tolerance regulation. Here, we found that OsVPE2 was a chilling-responsive gene. The early-indica rice variety Xiangzaoxian31 overexpressing OsVPE2 was more sensitive to chilling stress, whereas the OsVPE2-knockout mutants generated by the CRISPR-Cas9 technology exhibited significantly enhanced chilling tolerance at the seedling stage without causing yield loss. Deficiency of OsVPE2 reduces relative electrolyte leakage, accumulation of toxic compounds such as reactive oxygen species and malondialdehyde, and promotes antioxidant enzyme activities under chilling stress conditions. It was indicated that OsVPE2 mediated the disintegration of vacuoles under chilling stress, accompanied by the entry of swollen mitochondria into vacuoles. OsVPE2 suppressed the expression of genes that have a positive regulatory role in antioxidant process. Moreover, haplotype analysis suggested that the natural variation in the OsVPE2 non-coding region may endow OsVPE2 with different expression levels, thereby probably conferring differences in cold tolerance between japonica and indica sub-population. Our results thus reveal a new biological function of the VPE family in regulating cold resistance, and suggest that the gene editing or natural variations of OsVPE2 can be used to create cold tolerant rice varieties with stable yield.
PMID: 38194166
Plant Cell Rep , IF:4.57 , 2024 Jan , V43 (2) : P34 doi: 10.1007/s00299-023-03117-3
A novel R2R3-MYB transcription factor PbMYB1L of Pyrus bretschneideri regulates cold tolerance and anthocyanin accumulation.
College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.; College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China. zhyong@sicau.edu.cn.
PbMYB1L enhances the cold tolerance and anthocyanin accumulation of transgenic Arabidopsis by regulating the expression of genes related to the cold-responsive genes pathway and anthocyanin synthesis pathway. MYB transcription factors (TFs) have been demonstrated to play diverse roles in plant growth and development. In the present study, we identified a novel R2R3-MYB transcription factor, PbMYB1L, from the peel of 'Red Zaosu' pear (Pyrus bretschneideri), which was induced by cold stress and acted as a positive regulator in anthocyanin biosynthesis. Notably, the transgenic Arabidopsis lines exhibited enhanced tolerance to cold stress. Compared to the Arabidopsis wild-type plants, the transgenic lines displayed longer primary roots and reduced reactive oxygen species (ROS) levels including O(2-), hydrogen peroxide (H(2)O(2)), and malondialdehyde (MDA). Furthermore, significant upregulation of key cold-responsive genes AtCBF1, AtCBF2, AtCBF3, AtCBF4, and AtKIN1 was observed in the transgenic plants under cold stress conditions compared to wild type. Arabidopsis plants overexpressing PbMYB1L had significant anthocyanin accumulation in leaves after cold treatment with quantitative results indicating higher expression of anthocyanin structural genes compared to wild type. These findings suggest that PbMYB1L not only plays a vital role in conferring cold tolerance but also acts as a crucial regulator of anthocyanin biosynthesis.
PMID: 38200377
Plant Cell Rep , IF:4.57 , 2024 Jan , V43 (2) : P38 doi: 10.1007/s00299-023-03116-4
Cellular dynamics in the maize leaf growth zone during recovery from chilling depends on the leaf developmental stage.
Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium. cindy.laine@uantwerpen.be.; Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium.; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt.; Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, Antwerp University, Groenenborgerlaan 171, 2020, Antwerp, Belgium. gerrit.beemster@uantwerpen.be.
A novel non-steady-state kinematic analysis shows differences in cell division and expansion determining a better recovery from a 3-day cold spell in emerged compared to non-emerged maize leaves. Zea mays is highly sensitive to chilling which frequently occurs during its seedling stage. Although the direct effect of chilling is well studied, the mechanisms determining the subsequent recovery are still unknown. Our goal is to determine the cellular basis of the leaf growth response to chilling and during recovery of leaves exposed before or after their emergence. We first studied the effect of a 3-day cold spell on leaf growth at the plant level. Then, we performed a kinematic analysis to analyse the dynamics of cell division and elongation during recovery of the 4th leaf after exposure to cold before or after emergence. Our results demonstrated cold more strongly reduced the final length of non-emerged than emerged leaves (- 13 vs. - 18%). This was not related to growth differences during cold, but a faster and more complete recovery of the growth of emerged leaves. This difference was due to a higher cell division rate on the 1st and a higher cell elongation rate on the 2nd day of recovery, respectively. The dynamics of cell division and expansion during recovery determines developmental stage-specific differences in cold tolerance of maize leaves.
PMID: 38200224
Plant Physiol Biochem , IF:4.27 , 2024 Jan , V207 : P108341 doi: 10.1016/j.plaphy.2024.108341
CsLHY positively regulates cold tolerance by activating CsSWEET17 in tea plants.
Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China.; Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China. Electronic address: wanglu317@tricaas.com.
Low temperature is one of the most important environmental factors limiting tea plants' geographic distribution and severely affects spring tea's yield and quality. Circadian components contribute to plant responses to low temperatures; however, comparatively little is known about these components in tea plants. In this study, we identified a core clock component the LATE ELONGATED HYPOCOTYL, CsLHY, which is mainly expressed in tea plants' mature leaves, flowers, and roots. Notably, CsLHY maintained its circadian rhythmicity of expression in summer, but was disrupted in winter and held a high expression level. Meanwhile, we found that CsLHY expression rhythm was not affected by different photoperiods but was quickly broken by cold, and the low temperature induced and kept CsLHY expression at a relatively high level. Yeast one-hybrid and dual-luciferase assays confirmed that CsLHY can bind to the promoter of Sugars Will Eventually be Exported Transporters 17 (CsSWEET17) and function as a transcriptional activator. Furthermore, suppression of CsLHY expression in tea leaves not only reduced CsSWEET17 expression but also impaired the freezing tolerance of leaves compared to the control. Our results demonstrate that CsLHY plays a positive role in the low-temperature response of tea plants by regulating CsSWEET17 when considered together.
PMID: 38266557
BMC Plant Biol , IF:4.215 , 2024 Jan , V24 (1) : P12 doi: 10.1186/s12870-023-04698-7
Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress.
College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China.; College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China. zengbin@xjau.edu.cn.
ABC (ATP-binding cassette) transporter proteins are one of the most extensive protein families known to date and are ubiquitously found in animals, plants, and microorganisms. ABCs have a variety of functions, such as plant tissue development regulation, hormone transport, and biotic and abiotic stress resistance. However, the gene characterization and function of the ABC gene family in almond (Prunus dulcis) have not been thoroughly studied. In this study, we identified 117 PdABC genes using the whole genome of 'Wanfeng' almond obtained by sequencing and explored their protein characterization. The PdABC family members were classified into eight subfamilies. The members of the same subfamily had conserved motifs but poorly conserved numbers of exons and introns and were unevenly distributed among the eight subfamilies and on the eight chromosomes. Expression patterns showed that PdABC family members were significantly differentially expressed during almond development, dormant freezing stress, and salt stress. We found that PdABC59 and PdABC77 had extremely high expression levels in pollen. PdABC63 and PdABC64 had high expression levels during almond petal development and multiple stages of flower development. PdABC98 was highly expressed in annual dormant branches after six temperature-freezing stress treatments. PdABC29, PdABC69, and PdABC98 were highly expressed under different concentrations of salt stress. This study preliminarily investigated the expression characteristics of ABC genes in different tissues of almond during flower development, freezing stress and salt stress, and the results will provide a reference for further in-depth research and breeding of almond in the future.
PMID: 38163883
BMC Genomics , IF:3.969 , 2024 Jan , V25 (1) : P101 doi: 10.1186/s12864-024-09995-5
Genome-wide identification, evolution, and role of SPL gene family in beet (Beta vulgaris L.) under cold stress.
College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China.; College of Food Science and Engineering, Xinjiang Institute of Technology, 843199, Aksu, People's Republic of China.; College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China. chenggy508@sohu.com.
BACKGROUND: SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world's main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available. RESULTS: Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy. CONCLUSION: Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.
PMID: 38262939
BMC Genomics , IF:3.969 , 2024 Jan , V25 (1) : P18 doi: 10.1186/s12864-023-09926-w
Genome-wide identification, characterization, and expression analysis of m6A readers-YTH domain-containing genes in alfalfa.
School of Resources and Environmental Engineering, Ludong University, Yantai, China.; School of Resources and Environmental Engineering, Ludong University, Yantai, China. yinyl0605@163.com.; School of Resources and Environmental Engineering, Ludong University, Yantai, China. yzhaosoils@gmail.com.
Eukaryotic messenger RNAs (mRNAs) are often modified with methyl groups at the N6 position of adenosine (m6A), and these changes are interpreted by YTH domain-containing proteins to regulate the metabolism of m6A-modified mRNAs. Although alfalfa (Medicago sativa) is an established model organism for forage development, the understanding of YTH proteins in alfalfa is still limited. In the present investigation, 53 putative YTH genes, each encoding a YT521 domain-containing protein, were identified within the alfalfa genome. These genes were categorized into two subfamilies: YTHDF (49 members) and YTHDC (four members). Each subfamily demonstrates analogous motif distributions and domain architectures. Specifically, proteins encoded by MsYTHDF genes incorporate a single domain structure, while those corresponding to MsYTH5, 8, 12, 16 who are identified as members of the MsYTHDC subfamily, exhibit CCCH-type zinc finger repeats at their N-termini. It is also observed that the predicted aromatic cage pocket that binds the m6A residue of MsYTHDC consists of a sequence of two tryptophan residues and one tyrosine residue (WWY). Conversely, in MsYTHDF, the binding pocket comprises two highly conserved tryptophan residues and either one tryptophan residue (WWW) or tyrosine residue (WWY) in MsYTHDF.Through comparative analysis of qRT-PCR data, we observed distinct expression patterns in specific genes under abiotic stress, indicating their potential regulatory roles. Notably, five genes (MsYTH2, 14, 26, 27, 48) consistently exhibit upregulation, and two genes (MsYTH33, 35) are downregulated in response to both cold and salt stress. This suggests a common mechanism among these YTH proteins in response to various abiotic stressors in alfalfa. Further, integrating qRT-PCR with RNA-seq data revealed that MsYTH2, MsYTH14, and MsYTH16 are highly expressed in leaves at various development stages, underscoring their potential roles in regulating the growth of these plant parts. The obtained findings shed further light on the biological functions of MsYTH genes and may aid in the selection of suitable candidate genes for future genetic enhancement endeavors aimed at improving salt and cold tolerance in alfalfa.
PMID: 38166738
BMC Genomics , IF:3.969 , 2024 Jan , V25 (1) : P22 doi: 10.1186/s12864-023-09919-9
Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans.
Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. miranda100816@126.com.; The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China. miranda100816@126.com.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. you123chui@163.com.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. you123chui@163.com.; The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China. you123chui@163.com.
BACKGROUND: Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported. RESULTS: In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells. CONCLUSIONS: These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.
PMID: 38166591
BMC Genomics , IF:3.969 , 2024 Jan , V25 (1) : P83 doi: 10.1186/s12864-024-09966-w
Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe.
College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.; Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.; College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China. echozhang@yangtzeu.edu.cn.; College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China. liung906@163.com.; Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China. liung906@163.com.
BACKGROUND: Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS: In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS: Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
PMID: 38245685
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (2) doi: 10.3390/plants13020203
Structural and Functional Strategies in Cenchrus Species to Combat Environmental Extremities Imposed by Multiple Abiotic Stresses.
Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan.; Department of Botany, The Government Sadiq College Women University, Bahawalpur 63100, Pakistan.; Department of Botany, University of Poonch Rawalakot, Rawalakot 12350, Azad Jammu and Kashmir, Pakistan.; Department of Botany, Division of Science and Technology, University of Education, Lahore 54700, Pakistan.; Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 1451, Saudi Arabia.; Facultad de Ciencias Agrotecnologicas, Universidad Autonoma de Chihuahua, Chihuahua 31350, Mexico.; Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia.
Multiple abiotic stresses such as drought, salinity, heat, and cold stress prevailing in natural habitats affect plant growth and development. Different species modify their structural and functional traits to combat these abiotic stresses while growing in stressful environments. Cenchrus species, i.e., Cenchrus pennisetiformis, C. setiger, and C. prieurii are widely distributed grasses found growing all over the world. Samples from natural populations were collected from different ecological regions in the Punjab and Khyber Pakhtoonkhwa that were exposed to aridity, salinity, and cold, while one site was designated as normal control. In the present study, structural and functional modifications of three Cenchrus species under abiotic stresses were evaluated. It was expected that each Cenchrus species may evolve different strategies to cope with multiple abiotic stresses. All Cenchrus species responded differently whether growing in normal environment or stressful conditions. The most remarkable feature for survival in C. pennisetiformis under cold stress was increased inflorescence and increased stem and root lignification. C. prieurii showed better tolerance to saline and cold environments. C. setiger showed better development of leaf sheath anatomical traits. The structural and functional modifications in Cenchrus species such as development of mechanical tissues provided structural support, while dermal and parenchymatous tissues increased water storage capacity and minimized water loss. An increase in the concentration of organic osmolytes and ionic content aids turgor pressure maintenance and ionic content crucial for plant growth and development. It was concluded that structural and functional alterations in all Cenchrus species were very specific and critical for survival under different environmental stresses. The ecological fitness of these species relied on maintenance of growth and biomass production, and the development of mechanical, vascular, dermal and parenchyma tissues under stressful environmental conditions. Moreover, accumulation of beneficial ions (K(+) and Ca(2+)) and organic osmolytes were critical in turgor maintenance, hence survival of Cenchrus spp.
PMID: 38256756
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (2) doi: 10.3390/plants13020154
Comprehensive Identification of the beta-Amylase (BAM) Gene Family in Response to Cold Stress in White Clover.
Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.; International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.; National Engineering Research Center for Ornamental Horticulture, Yunnan Flower Breeding Key Laboratory, Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.
White clover (Trifolium repens L.) is an allopolyploid plant and an excellent perennial legume forage. However, white clover is subjected to various stresses during its growth, with cold stress being one of the major limiting factors affecting its growth and development. Beta-amylase (BAM) is an important starch-hydrolyzing enzyme that plays a significant role in starch degradation and responses to environmental stress. In this study, 21 members of the BAM gene family were identified in the white clover genome. A phylogenetic analysis using BAMs from Arabidopsis divided TrBAMs into four groups based on sequence similarity. Through analysis of conserved motifs, gene duplication, synteny analysis, and cis-acting elements, a deeper understanding of the structure and evolution of TrBAMs in white clover was gained. Additionally, a gene regulatory network (GRN) containing TrBAMs was constructed; gene ontology (GO) annotation analysis revealed close interactions between TrBAMs and AMY (alpha-amylase) and DPE (4-alpha-glucanotransferase). To determine the function of TrBAMs under various tissues and stresses, RNA-seq datasets were analyzed, showing that most TrBAMs were significantly upregulated in response to biotic and abiotic stresses and the highest expression in leaves. These results were validated through qRT-PCR experiments, indicating their involvement in multiple gene regulatory pathways responding to cold stress. This study provides new insights into the structure, evolution, and function of the white clover BAM gene family, laying the foundation for further exploration of the functional mechanisms through which TrBAMs respond to cold stress.
PMID: 38256708
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (1) doi: 10.3390/plants13010127
Class III Peroxidases in the Peach (Prunus persica): Genome-Wide Identification and Functional Analysis.
Federal State Funded Institution of Science "The Labor Red Banner Order Nikita Botanical Gardens-National Scientific Center of the RAS", Nikita, 298648 Yalta, Russia.; A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia.
Class III peroxidases are plant-specific and play a key role in the response to biotic and abiotic stresses, as well as in plant growth and development. In this study, we investigated 60 POD genes from Prunus persica based on genomic and transcriptomic data available in NCBI and analysed the expression of individual genes with qPCR. Peroxidase genes were clustered into five subgroups using the phylogenetic analysis. Their exon-intron structure and conserved motifs were analysed. Analysis of the transcriptomic data showed that the expression of PpPOD genes varied significantly in different tissues, at different developmental stages and under different stress treatments. All genes were divided into low- and high-expressed genes, and the most highly expressed genes were identified for individual tissues (PpPOD12 and PpPOD42 in flower buds and PpPOD73, PpPOD12, PpPOD42, and PpPOD31 in fruits). The relationship between cold tolerance and the level of peroxidase expression was revealed. These studies were carried out for the first time in the peach and confirmed that chilling tolerance may be related to the specificity of antioxidant complex gene expression.
PMID: 38202438
Gene , IF:3.688 , 2024 Feb , V896 : P148041 doi: 10.1016/j.gene.2023.148041
Low-temperature perception and modulations in Ocimum basilicum commercial cultivar CIM-Shishir: Biosynthetic potential with insight towards climate-smart resilience.
CSIR- Human Resource Development Centre Campus, Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India.; Biotechnology Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226016, India. Electronic address: sunita.dhawan@cimap.res.in.; Genetics and Plant Breeding Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India.; Analytical Chemistry Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India.
The newly released interspecific hybrid variety CIM-Shishir, resulting from a cross between Ocimum basilicum and Ocimum kilimandscharicum claims to be a multicut, lodging resistant, cold tolerant, high essential oil yielding with linalool rich variety. It has a purple-green stem and has a unique feature and advantage of better survival in the winter season than other O. basilicum varieties, illustrating its physiological mechanisms for cold tolerance. In this study, we subjected both the CIM-Shishir variety and a control plant to cold stress to investigate the impact of low temperatures on various physiological, trichome developments, secondary metabolite constitution aspects related to essential oil production, and gene expression. The analysis revealed a significantly higher density and altered morphology of trichomes on the leaf surface of the variety subjected to low temperatures, indicating its adaptation to cold conditions. Furthermore, when comparing the treated plants under low-temperature stress, it was observed that the relative electrolyte leakage and Malondialdehyde (MDA) contents substantially increased in the control in contrast to the CIM-Shishir variety. This finding suggests that CIM-Shishir exhibits superior cold tolerance. Additionally, an increase in proline content was noted in the variety exposed to low temperatures compared to the control. Moreover, the chlorophyll and anthocyanin content gradually increased with prolonged exposure to low-temperature stress in the newly developed variety, indicating its ability to maintain photosynthetic capacity and adapt to cold conditions. The activities of superoxide dismutase (SOD) also increased under low-temperature conditions in the CIM-Shishir variety, further highlighting its cold tolerance behaviour. In our research, we investigated the comprehensive molecular mechanisms of cold response in Ocimum. We analyzed the expression of key genes associated with cold tolerance in two plant groups: the newly developed hybrid variety known as CIM-Shishir Ocimum, which exhibits cold tolerance, and the control plants susceptible to cold climates that include WRKY53, ICE1, HOS1, COR47, LOS15, DREB5, CBF4, LTI6, KIN, and ERD2. These genes exhibited significantly higher expression levels in the CIM-Shishir variety compared to the control, shedding light on the genetic basis of its cold tolerance. The need for climate-smart, resilient high-yielding genotype is of high importance due to varied climatic conditions as this will hit the yield drastically and further to the economic sectors including farmers and many industries that are dependent on the bioactive constituents of Ocimum.
PMID: 38036074
Gene , IF:3.688 , 2024 Jan , V893 : P147908 doi: 10.1016/j.gene.2023.147908
Identification and expression analysis of miR396 and its target genes in Jerusalem artichoke under temperature stress.
College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: zszhou@njau.edu.cn.
The highly conserved miR396 plays a pivotal role in the growth, development, and responses to abiotic and biotic stresses in plants. However, research on miR396 and its targets in Jerusalem artichoke remains largely unexplored. In this study, we employed bioinformatics and experimental techniques, such as cloning and qRT-PCR, to investigate the regulatory role of miR396 on its targets, leveraging our lab's transcriptomic and degradomic data of Jerusalem artichoke. Specifically, we initially cloned and characterized the precursors (htu-MIR396a/b/c) and mature sequences (htu-miR396a/b/c) of three miR396 isoforms. Subsequently, we identified nine target genes, including seven Growth-Regulating Factors (GRFs) (HtGRF3/4/6/9/10/12/13), one WRKY transcription factor (HtWRKY40), and one Scarecrow-like (SCL) transcription factor (HtSCL33). Finally, we conducted an analysis of their expression patterns across various tissues and their responses to temperature stress. Notably, htu-MIR396s exhibited high expression in seedling stems, while htu-miR396s predominantly expressed in seedling leaves. Moreover, HtWRKY40 and HtSCL33 displayed higher expression levels than HtGRFs in most tissues, except leaves. Remarkably, HtGRF4/6/10/12/13 exhibited higher expression in leaves than in roots and stems during seedling growth. Furthermore, during tuber development, HtGRF4/6/10, HtWRKY40, and HtSCL33 were highly expressed, while HtGRF3/9/12/13 showed relatively lower expression levels. Under heat stress (42℃), htu-MIR396 expression was up-regulated, and htu-miR396 showed dynamic expression patterns in seedlings, resulting in the induction of HtGRF4/6/10/12/13 in leaves and HtSCL33 in roots, while HtWRKY40 in leaves was repressed. Conversely, under cold stress (4℃), htu-MIR396s showed fluctuating expression levels, and htu-miR396s were up-regulated in seedlings. Notably, HtGRF4/13 and HtSCL33 in seedlings were reduced, whereas HtGRF6 in roots and HtWRKY40 in leaves were enhanced. These findings offer valuable insights into the functional roles of miR396-target interactions under abiotic stress in Jerusalem artichoke.
PMID: 37858744
PLoS One , IF:3.24 , 2024 , V19 (1) : Pe0297473 doi: 10.1371/journal.pone.0297473
Phylogenomic curation of Ovate Family Proteins (OFPs) in the U's Triangle of Brassica L. indicates stress-induced growth modulation.
Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan.; Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan.; Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan.; Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China.; College of Tropical Crops, Hainan University, Haikou, China.
The Ovate Family Proteins (OFPs) gene family houses a class of proteins that are involved in regulating plant growth and development. To date, there is no report of the simultaneous functional characterization of this gene family in all members of U's Triangle of Brassica. Here, we retrieved a combined total of 256 OFP protein sequences and analyzed their chromosomal localization, gene structure, conserved protein motif domains, and the pattern of cis-acting regulatory elements. The abundance of light-responsive elements like G-box, MRE, and GT1 motif suggests that OFPs are sensitive to the stimuli of light. The protein-protein interaction network analysis revealed that OFP05 and its orthologous genes were involved in regulating the process of transcriptional repression through their interaction with homeodomain transcription factors like KNAT and BLH. The presence of domains like DNA binding 2 and its superfamily speculated the involvement of OFPs in regulating gene expression. The biotic and abiotic stress, and the tissue-specific expression analysis of the RNA-seq datasets revealed that some of the genes such as BjuOFP30, and BnaOFP27, BolOFP11, and BolOFP10 were highly upregulated in seed coat at the mature stage and roots under various chemical stress conditions respectively which suggests their crucial role in plant growth and development processes. Experimental validation of prominent BnaOFPs such as BnaOFP27 confirmed their involvement in regulating gene expression under salinity, heavy metal, drought, heat, and cold stress. The GO and KEGG pathway enrichment analysis also sheds light on the involvement of OFPs in regulating plant growth and development. These findings have the potential to serve as a forerunner for future studies in terms of functionally diverse analysis of the OFP gene family in Brassica and other plant species.
PMID: 38277374
Can J Microbiol , IF:2.419 , 2024 Jan , V70 (1) : P15-31 doi: 10.1139/cjm-2023-0030
Pseudomonas mosselii improves cold tolerance of Asian rice (Oryza sativa L.) in a genotype-dependent manner by increasing proline in japonica and reduced glutathione in indica varieties.
Marquette University, Biological Sciences Department, Milwaukee, WI, USA. RINGGOLD: 5505
Cold stress is an important factor limiting rice production and distribution. Identifying factors that contribute to cold tolerance in rice is of primary importance. While some plant specific genetic factors involved in cold tolerance have been identified, the role of the rice microbiome remains unexplored. In this study, we evaluated the influence of plant growth promoting bacteria (PGPB) with the ability of phosphate solubilization on rice cold tolerance and survival. To reach this goal, inoculated and uninoculated 2-week-old seedlings were cold stressed and evaluated for survival and other phenotypes such as electrolyte leakage (EL) and necessary elements for cold tolerance. The results of this study showed that of the five bacteria, Pseudomonas mosselii, improved both indica and japonica varietal plants' survival and decreased EL, indicating increased membrane integrity. We observed different possible cold tolerance mechanisms in japonica and indica plants such as increases in proline and reduced glutathione levels, respectively. This bacterium also improved the shoot growth of cold exposed indica plants during the recovery period. This study confirmed the host genotype dependent activity of P. mosselii and indicated that there is an interaction between specific plant genes and bacterial genes that causes different plant responses to cold stress.
PMID: 37699259
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2285169 doi: 10.1080/15592324.2023.2285169
Cold acclimation alleviates photosynthetic inhibition and oxidative damage induced by cold stress in citrus seedlings.
Nanchang Key Laboratory of Germplasm Innovation and Utilization of Fruit and Tea, Jiangxi Academy of Agricultural Sciences, Nanchang, P. R. China.; Institute of Environment and Sustainable Development in Agriculture, CAAS, Beijing, P. R. China.
Cold stress seriously inhibits plant growth and development, geographical distribution, and yield stability of plants. Cold acclimation (CA) is an important strategy for modulating cold stress, but the mechanism by which CA induces plant resistance to cold stress is still not clear. The purpose of this study was to investigate the effect of CA treatment on the cold resistance of citrus seedlings under cold stress treatment, and to use seedlings without CA treatment as the control (NA). The results revealed that CA treatment increased the content of photosynthetic pigments under cold stress, whereas cold stress greatly reduced the value of gas exchange parameters. CA treatment also promoted the activity of Rubisco and FBPase, as well as led to an upregulation of the transcription levels of photosynthetic related genes (rbcL and rbcS)，compared to the NA group without cold stress. In addition, cold stress profoundly reduced photochemical chemistry of photosystem II (PSII), especially the maximum quantum efficiency (F(v)/F(m)) in PSII. Conversely, CA treatment improved the chlorophyll a fluorescence parameters, thereby improving electron transfer efficiency. Moreover, under cold stress, CA treatment alleviated oxidative stress damage to cell membranes by inhibiting the concentration of H(2)O(2) and MDA, enhancing the activities of superoxide dismutase (SOD), catalase (CAT), ascorbic acid peroxidase (APX) and glutathione reductase (GR), accompanied by an increase in the expression level of antioxidant enzyme genes (CuZnSOD1, CAT1, APX and GR). Additionally, CA also increased the contents of abscisic acid (ABA) and salicylic acid (SA) in plants under cold stress. Overall, we concluded that CA treatment suppressed the negative effects of cold stress by enhancing photosynthetic performance, antioxidant enzymes functions and plant hormones contents.
PMID: 38015652
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2250891 doi: 10.1080/15592324.2023.2250891
Identification, expression analysis of quinoa betalain biosynthesis genes and their role in seed germination and cold stress.
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.; College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China.
Betalains provide Chenopodium quinoa bright color, and the key enzyme genes for betalain biosynthesis include CYP76AD, DODA, and GTs. In this study, 59 CqCYP76AD, CqDODA and CqGTs genes in quinoa were identified and characterized by gene structural characteristics, phylogenetic relationships and gene expression patterns. The CqCYP76AD genes were divided into a, beta and gamma types, CqDODA into a and beta types, and CqGTs into CqcDOPA5GT, CqB5GT and CqB6GT types according to phylogenetic relationships. The analysis of co-linearity identified eight pairs of duplicated genes which were subjected to purifying selection during evolution. CqCYP76AD and CqDODA, as well as CqcDOPA5GT and CqB5GT may have been evolutionarily linked in genetic inheritance, based on gene location and gene structure study. The tissue expression specificity of CqCYP76AD, CqDODA, and CqGTs genes in response to seed germination and cold stress was studied by RNA-Seq data. The genes CqCYP76AD, CqDODA, and CqGTs were involved in betalain biosynthesis and cold stress. CqCYP76AD, CqDODA, CqcDOPA5GT and CqB5GT gene sequences were consistent in the eight quinoa samples and showed significant variations in expression. In contrast, the inconsistency between changes in gene expression and betalain accumulation indicates that other factors may influence betalain biosynthesis in quinoa. This study offers the theoretical basis for the roles of the CqCYP76AD, CqDODA, and CqGTs genes in betalain biosynthesis and cold stress in quinoa, as well as a guide for the full utilization of betalains in quinoa plants.
PMID: 37616475
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2213924 doi: 10.1080/15592324.2023.2213924
Genome-wide analysis of the CDPK gene family and their important roles response to cold stress in white clover.
Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China.; International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China.; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China.; Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China.
Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.
PMID: 37202838
Sheng Wu Gong Cheng Xue Bao , 2024 Jan , V40 (1) : P190-210 doi: 10.13345/j.cjb.230191
[Identification of banana ADA1 gene family members and their expression profiles under biotic and abiotic stresses].
Institute of Horticultural Plant Bioengineering, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
The Spt-Ada-Gcn5-acetyltransferase (SAGA) is an ancillary transcription initiation complex which is highly conserved. The ADA1 (alteration/deficiency in activation 1, also called histone H2A functional interactor 1, HFI1) is a subunit in the core module of the SAGA protein complex. ADA1 plays an important role in plant growth and development as well as stress resistance. In this paper, we performed genome-wide identification of banana ADA1 gene family members based on banana genomic data, and analyzed the basic physicochemical properties, evolutionary relationships, selection pressure, promoter cis-acting elements, and its expression profiles under biotic and abiotic stresses. The results showed that there were 10, 6, and 7 family members in Musa acuminata, Musa balbisiana and Musa itinerans. The members were all unstable and hydrophilic proteins, and only contained the conservative SAGA-Tad1 domain. Both MaADA1 and MbADA1 have interactive relationship with Sgf11 (SAGA-associated factor 11) of core module in SAGA. Phylogenetic analysis revealed that banana ADA1 gene family members could be divided into 3 classes. The evolution of ADA1 gene family members was mostly influenced by purifying selection. There were large differences among the gene structure of banana ADA1 gene family members. ADA1 gene family members contained plenty of hormonal elements. MaADA1-1 may play a prominent role in the resistance of banana to cold stress, while MaADA1 may respond to the Panama disease of banana. In conclusion, this study suggested ADA1 gene family members are highly conserved in banana, and may respond to biotic and abiotic stress.
PMID: 38258641
Biochem Biophys Rep , 2024 Mar , V37 : P101620 doi: 10.1016/j.bbrep.2023.101620
Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress.
Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.; Faculty of Agriculture (Meshgin-Shahr Campus), University of Mohaghegh Ardabili, Ardabil, Iran.
Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2(+) related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.
PMID: 38155945
Methods Mol Biol , 2024 , V2730 : P3-23 doi: 10.1007/978-1-0716-3503-2_1
Identifying Ice-Binding Proteins in Nature.
Department of Evolution, Behavior and Ecology, University of Illinois, Urbana Champaign, Urbana, IL, USA. adevries@illinois.edu.
Organisms inhabiting freezing terrestrial, polar, and alpine environments survive because they have evolved adaptations to tolerate sub-freezing temperatures. Among these adaptations are ice-binding proteins (IBPs) which in the case of fishes and some insects have antifreeze properties which allow them to avoid freezing even at their lowest environmental temperatures. Other organisms, including some insects, microorganisms, and plants, tolerate freezing and also contain IBPs. Unlike fish and insects, their antifreeze properties (hysteresis) are minimal, but most are potent ice recrystallization inhibitors (IRIs). Microbes secrete IBPs into their immediate environment where they are thought to modify ice growth in a way that ensures a liquidous habitat in the ice and also reduces ice recrystallization. With plants, IBPs are found in the small amount of apoplastic fluid associated with the extracellular spaces and show a weak hysteresis but are potent IRIs.Techniques are described for drawing blood and hemolymph from fish and insects, respectively, in order to determine whether there is a hysteresis present (separation of the freezing and melting points) indicative of an antifreeze protein. For microbes, which secrete very small amounts of IBPs into their environment, a technique is described where their spent growth media causes the pitting of the basal plane of an ice crystal at a temperature slightly below the media freezing point. In plants, IBPs are isolated from the apoplastic fluids of the leaves by vacuum infiltration of a fluid into the extracellular spaces and then recovering the fluid by centrifugation.The pitting of the basal plane again can be used to verify the presence of IBPs in the concentrated apoplastic fluid.The techniques describe how to collect fluids from a variety of organisms to determine if IBPs are present using nanoliter osmometry or using the ice basal plane pitting technique.
PMID: 37943447