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Xue C, Zhu S, Li Y, Chen X, Lu L, Su P, Zhang Q, Liu X, Guan R, Liu Z, Zhao Z, Tang S, Chen J, Zhang J, Zhang W, Lu H, Luo W. Cold exposure accelerates lysine catabolism to promote cold acclimation via remodeling hepatic histone crotonylation. ENVIRONMENT INTERNATIONAL 2024; 192:109015. [PMID: 39312841 DOI: 10.1016/j.envint.2024.109015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 08/29/2024] [Accepted: 09/14/2024] [Indexed: 09/25/2024]
Abstract
BACKGROUND Cold environments pose serious threats on human health, with increased risk for myocardial infarction, stroke, frostbite, and hypothermia. Acquired cold acclimation is required to minimize cold-induced injures and to improve metabolic health. However, the underlying mechanisms remain to be fully elucidated. OBJECTIVE We aimed to identify critical amino acids involved in cold acclimation and unmask the regulatory mechanisms. METHODS A total of twenty male participants were recruited and followed up after 3 months' natural cold exposure. Cold-induced vasodilation (CIVD) tests and clinical biochemical analysis were performed at baseline and after 3-months cold exposure, whilst blood samples were collected, and plasma amino acids were analyzed by targeted metabolomics. To further confirm the effect of lysine on cold tolerance and explain the latent mechanism, mice were challenged with chronic cold exposure for 7 days with lysine supplement, then core and local surface temperature as well as thermogenesis activity were detected. RESULTS Continuous cold exposure shortened the CIVD onset time and increased the average finger temperature. Levels of the plasma lysine and glycine were decreased in both humans and mice. Venn analysis from three datasets revealed that lysine was the only significantly changed plasma amino acid, which strongly correlated with the altered CIVD. Moreover, mice sustained a relatively higher core temperature and surface temperature in the back, tail and paws upon lysine supplementation. Furthermore, lysine supplementation increased the level of histone H3K18cr and promoted the gene and protein expression of Cpt1a, Cpt2 and Cyp27a1 in liver. CONCLUSION Our work identified lysine as a critical amino acid for the remodeling of hepatic histone crotonylation that facilitates cold acclimation.
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Affiliation(s)
- Chong Xue
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Sijin Zhu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Yang Li
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaoming Chen
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Liang Lu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Peng Su
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Qian Zhang
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Xinqin Liu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Ruili Guan
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Zongcai Liu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Zhiwei Zhao
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Shan Tang
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Jingyuan Chen
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Jianbin Zhang
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China.
| | - Wenbin Zhang
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China.
| | - Huanyu Lu
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China.
| | - Wenjing Luo
- Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China.
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Bulgakov VP, Fialko AV, Yugay YA. Involvement of epigenetic factors in flavonoid accumulation during plant cold adaptation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109096. [PMID: 39250844 DOI: 10.1016/j.plaphy.2024.109096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/11/2024]
Abstract
Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation.
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Affiliation(s)
- Victor P Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia; Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5 Radio Str., Vladivostok, 690041, Russia.
| | - Alexandra V Fialko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia; Institute of Automation and Control Processes, Far Eastern Branch of the Russian Academy of Sciences, 5 Radio Str., Vladivostok, 690041, Russia
| | - Yulia A Yugay
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia
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Zhang J, Dong KL, Ren MZ, Wang ZW, Li JH, Sun WJ, Zhao X, Fu XX, Ye JF, Liu B, Zhang DM, Wang MZ, Zeng G, Niu YT, Lu LM, Su JX, Liu ZJ, Soltis PS, Soltis DE, Chen ZD. Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae). HORTICULTURE RESEARCH 2024; 11:uhae077. [PMID: 38779140 PMCID: PMC11109519 DOI: 10.1093/hr/uhae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/08/2024] [Indexed: 05/25/2024]
Abstract
How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kai-Lin Dong
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Zhen Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Jian-Hua Li
- Biology Department, Hope College, Holland, MI 49423, USA
| | - Wen-Jing Sun
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Xin-Xing Fu
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China
| | - Jian-Fei Ye
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Da-Ming Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Mo-Zhu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Gang Zeng
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Yan-Ting Niu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Li-Min Lu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jun-Xia Su
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611-7800, USA
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Šola I, Gmižić D, Pinterić M, Tot A, Ludwig-Müller J. Adjustments of the Phytochemical Profile of Broccoli to Low and High Growing Temperatures: Implications for the Bioactivity of Its Extracts. Int J Mol Sci 2024; 25:3677. [PMID: 38612494 PMCID: PMC11011926 DOI: 10.3390/ijms25073677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Climate change causes shifts in temperature patterns, and plants adapt their chemical content in order to survive. We compared the effect of low (LT) and high (HT) growing temperatures on the phytochemical content of broccoli (Brassica oleracea L. convar. botrytis (L.) Alef. var. cymosa Duch.) microgreens and the bioactivity of their extracts. Using different spectrophotometric, LC-MS/MS, GC-MS, and statistical methods, we found that LT increased the total phenolics and tannins in broccoli. The total glucosinolates were also increased by LT; however, they were decreased by HT. Soluble sugars, known osmoprotectants, were increased by both types of stress, considerably more by HT than LT, suggesting that HT causes a more intense osmotic imbalance. Both temperatures were detrimental for chlorophyll, with HT being more impactful than LT. HT increased hormone indole-3-acetic acid, implying an important role in broccoli's defense. Ferulic and sinapic acid showed a trade-off scheme: HT increased ferulic while LT increased sinapic acid. Both stresses decreased the potential of broccoli to act against H2O2 damage in mouse embryonal fibroblasts (MEF), human keratinocytes, and liver cancer cells. Among the tested cell types treated by H2O2, the most significant reduction in ROS (36.61%) was recorded in MEF cells treated with RT extracts. The potential of broccoli extracts to inhibit α-amylase increased following both temperature stresses; however, the inhibition of pancreatic lipase was increased by LT only. From the perspective of nutritional value, and based on the obtained results, we conclude that LT conditions result in more nutritious broccoli microgreens than HT.
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Affiliation(s)
- Ivana Šola
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Daria Gmižić
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Marija Pinterić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Ana Tot
- Andrija Štampar Teaching Institute of Public Health, Mirogojska 16, 10000 Zagreb, Croatia
| | - Jutta Ludwig-Müller
- Faculty of Biology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
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5
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Bhupenchandra I, Chongtham SK, Gangarani Devi A, Dutta P, Lamalakshmi E, Mohanty S, Choudhary AK, Das A, Sarika K, Kumar S, Yumnam S, Sagolsem D, Rupert Anand Y, Bhutia DD, Victoria M, Vinodh S, Tania C, Dhanachandra Sharma A, Deb L, Sahoo MR, Seth CS, Swapnil P, Meena M. Harnessing weedy rice as functional food and source of novel traits for crop improvement. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38436101 DOI: 10.1111/pce.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.
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Affiliation(s)
- Ingudam Bhupenchandra
- ICAR-Farm Science Centre Tamenglong, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, Manipur, India
| | - Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Ayam Gangarani Devi
- ICAR Research Complex for North Eastern Hill Region, Tripura Centre Lembucherra, Tripura, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Elangbam Lamalakshmi
- ICAR Research Complex for North Eastern Hill Region, Sikkim Centre, Tadong, Sikkim, India
| | - Sansuta Mohanty
- Molecular Biology and Biotechnology Department, Faculty of Agricultural Sciences, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Anil K Choudhary
- Division of Crop Production, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Anup Das
- ICAR Research Complex for North Eastern Hill Region, Lembucherra, Tripura, India
| | - Konsam Sarika
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, Madhya Pradesh, India
| | - Sonika Yumnam
- All India Coordinated Research Project on Chickpea, Central Agricultural University, Imphal, Manipur, India
| | - Diana Sagolsem
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Y Rupert Anand
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Dawa Dolma Bhutia
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - M Victoria
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - S Vinodh
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Chongtham Tania
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Prashant Swapnil
- Department of Botany, School of Basic Science, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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Konecny T, Nikoghosyan M, Binder H. Machine learning extracts marks of thiamine's role in cold acclimation in the transcriptome of Vitis vinifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1303542. [PMID: 38126012 PMCID: PMC10731266 DOI: 10.3389/fpls.2023.1303542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Introduction The escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine. Methods We used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific "portraits" of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied. Results Our analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines. Discussion Application of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.
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Affiliation(s)
- Tomas Konecny
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Maria Nikoghosyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Bioinformatics Group, Institute of Molecular Biology Institute of National Academy of Sciences RA, Yerevan, Armenia
| | - Hans Binder
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
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Yu Z, Huang X, Wen S, Cao H, Wang N, Shen S, Ding M. Alternative Splicing under Cold Stress in Paper Mulberry. PLANTS (BASEL, SWITZERLAND) 2023; 12:3950. [PMID: 38068587 PMCID: PMC10707748 DOI: 10.3390/plants12233950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 05/19/2024]
Abstract
The paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intricate landscape of AS events. We have detected all seven types of AS events, with the alternative 3' splice site (A3) having the most. We observed that many genes that underwent differential AS were significantly enriched in starch and sucrose metabolism and circadian rhythm pathways. Moreover, a considerable proportion of differentially spliced genes (DSGs) also showed differential expression, with 20.38% and 25.65% under 12 h and 24 h cold treatments, respectively. This suggests a coordinated regulation between gene AS and expression, playing a pivotal role in the paper mulberry's adaptation to cold stress. We further investigated the regulatory mechanisms of AS, identifying 41 serine/arginine-rich (SR) splicing factors, among which 11 showed differential expression under cold treatment, while 29 underwent alternative splicing. Additionally, genes undergoing AS displayed significantly higher DNA methylation levels under cold stress, while normal splicing (non-AS) genes exhibited relatively lower methylation levels. These findings suggest that methylation may play an important role in governing gene AS. Finally, our research will provide useful information on the role of AS in the cold acclimation tolerance of the paper mulberry.
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Affiliation(s)
- Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Xia Huang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Haijuan Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Nan Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
| | - Shihua Shen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China; (Z.Y.); (X.H.); (S.W.); (H.C.); (N.W.)
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8
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Ku YS. Be sweet, be strong, and be tolerant: ERDL4 regulates sugar transport and promotes cold tolerance in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:1727-1728. [PMID: 37607254 PMCID: PMC10602601 DOI: 10.1093/plphys/kiad463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Affiliation(s)
- Yee-Shan Ku
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
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Jahed KR, Saini AK, Sherif SM. Coping with the cold: unveiling cryoprotectants, molecular signaling pathways, and strategies for cold stress resilience. FRONTIERS IN PLANT SCIENCE 2023; 14:1246093. [PMID: 37649996 PMCID: PMC10465183 DOI: 10.3389/fpls.2023.1246093] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Low temperature stress significantly threatens crop productivity and economic sustainability. Plants counter this by deploying advanced molecular mechanisms to perceive and respond to cold stress. Transmembrane proteins initiate these responses, triggering a series of events involving secondary messengers such as calcium ions (Ca2+), reactive oxygen species (ROS), and inositol phosphates. Of these, calcium signaling is paramount, activating downstream phosphorylation cascades and the transcription of cold-responsive genes, including cold-regulated (COR) genes. This review focuses on how plants manage freeze-induced damage through dual strategies: cold tolerance and cold avoidance. Tolerance mechanisms involve acclimatization to decreasing temperatures, fostering gradual accumulation of cold resistance. In contrast, avoidance mechanisms rely on cryoprotectant molecules like potassium ions (K+), proline, glycerol, and antifreeze proteins (AFPs). Cryoprotectants modulate intracellular solute concentration, lower the freezing point, inhibit ice formation, and preserve plasma membrane fluidity. Additionally, these molecules demonstrate antioxidant activity, scavenging ROS, preventing protein denaturation, and subsequently mitigating cellular damage. By forming extensive hydrogen bonds with water molecules, cryoprotectants also limit intercellular water movement, minimizing extracellular ice crystal formation, and cell dehydration. The deployment of cryoprotectants is a key adaptive strategy that bolsters plant resilience to cold stress and promotes survival in freezing environments. However, the specific physiological and molecular mechanisms underlying these protective effects remain insufficiently understood. Therefore, this review underscores the need for further research to elucidate these mechanisms and assess their potential impact on crop productivity and sustainability, contributing to the progressive discourse in plant biology and environmental science.
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Affiliation(s)
| | | | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
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10
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Jarambasa T, Regon P, Jyoti SY, Gupta D, Panda SK, Tanti B. Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses. Genetica 2023; 151:225-239. [PMID: 37269422 DOI: 10.1007/s10709-023-00190-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
AP2/ERF (APETALA2/Ethylene Response Factor) is a family of transcription factors that play essential roles in regulating gene expression in response to various environmental stimuli, including biotic and abiotic stresses, hormone signaling, and developmental processes. Pisum sativum (L.), commonly known as garden pea, is a winter crop sensitive to high temperatures and can also be affected by extreme cold and drought conditions. This study performed a genome-wide analysis of AP2/ERF genes and identified 153 AP2/ERF genes in P. sativum. Based on the conserved AP2/ERF domain and sequence homology, they were classified into AP2 (APETALA2), ERF (Ethylene Response Factor), DREB (Dehydration responsive element-binding), RAV (Related to Abscisic Acid Insensitive 3/ Viviparous 1) and Soloist subfamily. The DREB and ERF subfamily were further divided into groups A1-6 and B1-B6. Tandem and segmental duplication events were more frequent in the ERF subfamily, which can have important implications for their evolution and functional diversification. Under cold stress, the expression of DREB1A was highly induced in leaves, whereas DREB1B was suppressed. Similarly, the DREB2A, DREB2C, DREB2E, and DREB2F were induced in leaves under drought stress. The putative target genes of AP2/ERF transcription factors are highly diversified, suggesting that they play essential roles in various physiological responses in plants, including responses to biotic and abiotic stresses as well as developmental processes. Thus, this study of AP2/ERF genes and their functions provides valuable insight into how P. sativum responds to different environmental conditions, including cold and drought stresses.
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Affiliation(s)
- Trishna Jarambasa
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati, Assam, 781014, India
| | - Preetom Regon
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati, Assam, 781014, India
| | - Sabnoor Yeasrin Jyoti
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati, Assam, 781014, India
| | - Divya Gupta
- Department of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India
| | - Sanjib Kumar Panda
- Department of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati, Assam, 781014, India.
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11
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Vera Hernández PF, Mendoza Onofre LE, Rosas Cárdenas FDF. Responses of sorghum to cold stress: A review focused on molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1124335. [PMID: 36909409 PMCID: PMC9996117 DOI: 10.3389/fpls.2023.1124335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.
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Affiliation(s)
- Pedro Fernando Vera Hernández
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
| | | | - Flor de Fátima Rosas Cárdenas
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
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12
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Goswami AK, Maurya NK, Goswami S, Bardhan K, Singh SK, Prakash J, Pradhan S, Kumar A, Chinnusamy V, Kumar P, Sharma RM, Sharma S, Bisht DS, Kumar C. Physio-biochemical and molecular stress regulators and their crosstalk for low-temperature stress responses in fruit crops: A review. FRONTIERS IN PLANT SCIENCE 2022; 13:1022167. [PMID: 36578327 PMCID: PMC9790972 DOI: 10.3389/fpls.2022.1022167] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Low-temperature stress (LTS) drastically affects vegetative and reproductive growth in fruit crops leading to a gross reduction in the yield and loss in product quality. Among the fruit crops, temperate fruits, during the period of evolution, have developed the mechanism of tolerance, i.e., adaptive capability to chilling and freezing when exposed to LTS. However, tropical and sub-tropical fruit crops are most vulnerable to LTS. As a result, fruit crops respond to LTS by inducing the expression of LTS related genes, which is for climatic acclimatization. The activation of the stress-responsive gene leads to changes in physiological and biochemical mechanisms such as photosynthesis, chlorophyll biosynthesis, respiration, membrane composition changes, alteration in protein synthesis, increased antioxidant activity, altered levels of metabolites, and signaling pathways that enhance their tolerance/resistance and alleviate the damage caused due to LTS and chilling injury. The gene induction mechanism has been investigated extensively in the model crop Arabidopsis and several winter kinds of cereal. The ICE1 (inducer of C-repeat binding factor expression 1) and the CBF (C-repeat binding factor) transcriptional cascade are involved in transcriptional control. The functions of various CBFs and aquaporin genes were well studied in crop plants and their role in multiple stresses including cold stresses is deciphered. In addition, tissue nutrients and plant growth regulators like ABA, ethylene, jasmonic acid etc., also play a significant role in alleviating the LTS and chilling injury in fruit crops. However, these physiological, biochemical and molecular understanding of LTS tolerance/resistance are restricted to few of the temperate and tropical fruit crops. Therefore, a better understanding of cold tolerance's underlying physio-biochemical and molecular components in fruit crops is required under open and simulated LTS. The understanding of LTS tolerance/resistance mechanism will lay the foundation for tailoring the novel fruit genotypes for successful crop production under erratic weather conditions.
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Affiliation(s)
- Amit Kumar Goswami
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Kumar Maurya
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suneha Goswami
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kirti Bardhan
- Department of Basic Sciences and Humanities, Navsari Agricultural University, Navsari, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jai Prakash
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Satyabrata Pradhan
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amarjeet Kumar
- Multi Testing Technology Centre and Vocational Training Centre, Selesih, Central Agricultural University, Imphal, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prabhat Kumar
- Department of Agriculture and Farmers Welfare, Ministry of Agriculture & Farmers Welfare, Govt. of India, Krishi Bhavan, New Delhi, India
| | - Radha Mohan Sharma
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Stuti Sharma
- Department of Plant Breeding and Genetics, Jawaharlal Nehru Krishi Vishwavidyalaya, Jabalpur, Madhya Pradesh, India
| | | | - Chavlesh Kumar
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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