Mol Plant , IF:12.084 , 2020 Dec doi: 10.1016/j.molp.2020.11.022

Transcriptional Activation and Phosphorylation of OsCNGC9 Confer Enhanced Chilling Tolerance in Rice.

Wang, Jiachang and Ren, Yulong and Liu, Xi and Luo, Sheng and Zhang, Xiao and Liu, Xin and Lin, Qibing and Zhu, Shanshan and Wan, Hua and Yang, Yang and Zhang, Yu and Lei, Bin and Zhou, Chunlei and Pan, Tian and Wang, Yongfei and Wu, Mingming and Jing, Ruonan and Xu, Yang and Han, Meng and Wu, Fuqing and Lei, Cailin and Guo, Xiuping and Cheng, Zhijun and Zheng, Xiaoming and Wang, Yihua and Zhao, Zhigang and Jiang, Ling and Zhang, Xin and Wang, Haiyang and Wan, Jianmin

National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.; National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.; National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.; National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: wanjm@njau.edu.cn.

Low temperature is a major environmental factor limiting plant growth and productivity. Although transient elevation of cytoplasmic calcium has long been recognized as a critical signal for plant cold tolerance, the calcium channels responsible for this process have remained largely elusive. Here, we reported that OsCNGC9, a cyclic nucleotide-gated channel, positively regulates chilling tolerance by mediating cytoplasmic calcium elevation in rice (Oryza sativa). We showed that the loss-of-function mutant of OsCNGC9 is defective in cold-induced calcium influx and more sensitive to prolonged cold treatment while OsCNGC9 overexpression confers enhanced cold tolerance. Mechanistically, we showed that in response to chilling stress, OsSAPK8, a homolog of Arabidopsis thaliana OST1, phosphorylates and activates OsCNGC9 to trigger Ca(2+) influx. In addition, transcription of OsCNGC9 is activated by a rice dehydration responsive element binding transcription factor, OsDREB1A. Together, our results suggested that OsCNGC9 enhances chilling tolerance in rice through regulating cold-induced calcium influx and cytoplasmic calcium elevation.

PMID: 33278597

Plant Biotechnol J , IF:8.154 , 2020 Dec doi: 10.1111/pbi.13533

Lysine crotonylation of DgTIL1 at K72 modulates cold tolerance by enhancing DgnsLTP stability in chrysanthemum.

Huang, Qiuxiang and Liao, Xiaoqin and Yang, Xiaohan and Luo, Yunchen and Lin, Ping and Zeng, Qinhan and Bai, Huiru and Jiang, Beibei and Pan, Yuanzhi and Zhang, Fan and Zhang, Lei and Jia, Yin and Liu, Qinglin

Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China.

Lysine crotonylation of proteins is a recently identified post-translational modification (PTM) in plants. However, the function of lysine crotonylated proteins in response to abiotic stress in plants has not been reported. In this study, we identified a temperature-induced lipocalin-1-like gene (DgTIL1) from chrysanthemum and showed that it was notably induced in response to cold stress. Overexpression of DgTIL1 enhanced cold tolerance in transgenic chrysanthemum. Ubiquitin membrane yeast two-hybrid (MYTH) system and bimolecular fluorescence complementation (BIFC) assays showed that DgTIL1 interacts with a nonspecific lipid transfer protein (DgnsLTP), which can promote peroxidase (POD) expression and POD activity to reduce the accumulation of reactive oxygen species (ROS) and improve resistance to cold stress in DgnsLTP transgenic chrysanthemum. In addition, we found that DgTIL1 was lysine crotonylated at K72 in response to low temperature in chrysanthemum. Moreover, lysine crotonylation of DgTIL1 prevented DgnsLTP protein degradation in tobacco and chrysanthemum. Inhibition of DgnsLTP degradation by lysine crotonylation of DgTIL1 further enhanced POD expression and POD activity, reduced the accumulation of ROS under cold stress in DgTIL1 transgenic chrysanthemum, thus promoting the cold-resistance of chrysanthemum.

PMID: 33368971

Genomics , IF:6.205 , 2020 Dec , V113 (1 Pt 1) : P245-256 doi: 10.1016/j.ygeno.2020.12.022

Genomics, expression, and function analyses of XB3 family genes in cotton.

Ge, Dongdong and Jiang, Jiuhua and An, Xiaohui and Wang, Longjie and Pan, Ting and Liu, Kang and Sun, Jing and Hong, Delin

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, China. Electronic address: Kangliu@njau.edu.c.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: delinhong@njau.edu.cn.

XANTHOMONAS RESISTANCE 21-binding protein3 (XB3) is the first characterized XA21 interacting protein required for plant immunity. We isolated GhXB32A that is similar to XBAT32 and was induced during inoculation of Verticillium dahliae in cotton. 32 putative XB3 family genes were identified in G. hirsutum, G. arboreum, and G. raimondii. Cis-Acting elements related to growth, stresses, and phytohormone were detected in the promoter regions. GhXB3s were ubiquitously expressed in different cotton tissues with different patterns. Most GhXB3s were down-regulated by cold stress, but up-regulated by heat, salt, PEG, V. dahliae, ethylene, and some were up-regulated by SA or MeJA. Silencing GhXB32A and GhXB32D greatly improved resistance to Verticillium wilt, while silencing GhXB35A(D) or GhXB37A(D) made them more susceptible to V. dahliae. The interacting proteins of GhXB32A and GhXB32D were functionally enriched in response to abiotic and/or biotic stresses, and photosynthesis. XB3 family genes are potential stress resistance genes for cotton improvement.

PMID: 33340692

Plant J , IF:6.141 , 2020 Dec doi: 10.1111/tpj.15127

The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine.

Wang, Yi and Xin, Haiping and Fan, Peige and Zhang, Jisen and Liu, Yongbo and Dong, Yang and Wang, Zemin and Yang, Yingzhen and Zhang, Qing and Ming, Ray and Zhong, Gan-Yuan and Li, Shaohua and Liang, Zhenchang

Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, PR China.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China.; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.; US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, USA.; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.

Vitis amurensis (Shanputao) is the most cold tolerant Vitis species and so is of great interest to grape breeders and producers in areas with low winter temperatures. Here, we report its high-quality, chromosome-level genome assembly based on a combination of sequence data from Illumina and PacBio platforms, BioNano optical mapping and high-throughput chromosome conformation Capture (Hi-C) mapping. The 604.56 Mb genome contains 32,885 protein coding genes. Shanputao was found to share a common ancestor with PN40024 (V. vinifera) approximately 2.17 - 2.91MYA, and gene expansion observed in Shanputao might contribute to the enhancement of cold tolerance. Transcriptome analysis revealed seventeen genes involved in cold signal transduction, suggesting that there were different response mechanism to chilling temperature and freezing conditions. Furthermore, a genome wide association study uncovered a phosphoglycerate kinase gene that may contribute to the freezing resistance of buds in the winter. The Shanputao genome sequence not only represents a valuable resource for grape breeders, but also is important for clarifying the molecular mechanisms involved in cold tolerance.

PMID: 33300184

Int J Biol Macromol , IF:5.162 , 2020 Dec , V169 : P264-273 doi: 10.1016/j.ijbiomac.2020.12.102

Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum).

Sagar, Sushma and Deepika and Biswas, Dipul Kumar and Chandrasekar, Ramsankar and Singh, Amarjeet

National Institute of Plant Genome Research, New Delhi 110067, India.; National Institute of Plant Genome Research, New Delhi 110067, India. Electronic address: amarjeet.singh@nipgr.ac.in.

Phospholipases D (PLDs) are phospholipid hydrolyzing enzymes and crucial components of lipid signaling in plants. PLDs are implicated in stress responses in different plants however, characterization of PLDs in chickpea is missing. Here, we identify 13 PLD genes in the chickpea genome. PLD family could be divided into alpha, beta, delta, epsilon and zeta isoforms based on sequence and structure. Protein remodeling described that chickpea PLDs are composed of defined arrangements of alpha-helix, beta-sheets and short loops. Phylogenetic analysis suggested evolutionary conservation of chickpea PLD family with dicots. In-planta subcellular localization showed the plasma membrane localization of chickpea PLDs. All PLD promoters had hormone and stress related cis-regulatory elements, which suggested overlapping function of PLDs in hormone and abiotic stress signaling. The qRT-PCR expression analysis revealed that most PLD genes are differentially expressed in multiple abiotic stresses (drought, salt and cold stress). Moreover, several PLD genes had overlapping expression in abiotic stress and ABA and JA treatment. These observations indicate the involvement of PLD gene family in cross-talk of phytohormone and abiotic stress signaling in chickpea. Thus, present study opens new avenues of utilizing PLD related information for understanding hormone-regulated abiotic stress signaling in legume crops.

PMID: 33338528

Int J Mol Sci , IF:4.556 , 2020 Dec , V21 (24) doi: 10.3390/ijms21249380

Structural Diversity and Highly Specific Host-Pathogen Transcriptional Regulation of Defensin Genes Is Revealed in Tomato.

Nikoloudakis, Nikolaos and Pappi, Polyxeni and Markakis, Emmanouil A and Charova, Spyridoula N and Fanourakis, Dimitrios and Paschalidis, Konstantinos and Delis, Costas and Tzortzakakis, Emmanuel A and Tsaniklidis, Georgios

Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus.; Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Crete, Greece.; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013 Heraklion, Crete, Greece.; Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece.; Giannakakis SA, Export Fruits and Vegetables, 70200 Tympaki, Crete, Greece.; School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, 71004 Heraklion, Crete, Greece.; Department of Agricultural Technology, School of Agricultural Technology and Food Technology and Nutrition, University of Peloponnese, 24100 Antikalamos, Kalamata, Greece.

Defensins are small and rather ubiquitous cysteine-rich anti-microbial peptides. These proteins may act against pathogenic microorganisms either directly (by binding and disrupting membranes) or indirectly (as signaling molecules that participate in the organization of the cellular defense). Even though defensins are widespread across eukaryotes, still, extensive nucleotide and amino acid dissimilarities hamper the elucidation of their response to stimuli and mode of function. In the current study, we screened the Solanum lycopersicum genome for the identification of defensin genes, predicted the relating protein structures, and further studied their transcriptional responses to biotic (Verticillium dahliae, Meloidogyne javanica, Cucumber Mosaic Virus, and Potato Virus Y infections) and abiotic (cold stress) stimuli. Tomato defensin sequences were classified into two groups (C8 and C12). Our data indicate that the transcription of defensin coding genes primarily depends on the specific pathogen recognition patterns of V. dahliae and M. javanica. The immunodetection of plant defensin 1 protein was achieved only in the roots of plants inoculated with V. dahliae. In contrast, the almost null effects of viral infections and cold stress, and the failure to substantially induce the gene transcription suggest that these factors are probably not primarily targeted by the tomato defensin network.

PMID: 33317090

Sci Rep , IF:3.998 , 2020 Dec , V10 (1) : P21861 doi: 10.1038/s41598-020-78873-3

A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species.

Wong, Changi and Ling, Yee Soon and Wee, Julia Lih Suan and Mujahid, Aazani and Muller, Moritz

Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Malaysia.; Water Research Unit, Faculty of Science and Natural Resources, University Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.; Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 93400, Kota Samarahan, Sarawak, Malaysia.; Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.; Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Malaysia. mmueller@swinburne.edu.my.

Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.

PMID: 33318532

Am J Bot , IF:3.038 , 2020 Dec , V107 (12) : P1693-1709 doi: 10.1002/ajb2.1584

Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium).

Jaikumar, Nikhil S and Dorn, Kevin M and Baas, Dean and Wilke, Brook and Kapp, Christian and Snapp, Sieglinde S

Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.; United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 1701 Centre Ave, Fort Collins, CO, 80526, USA.; Michigan State University Extension, 612 E. Main Street, Centreville, MI, 49032, USA.; Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI, 49060, USA.; Upper Peninsula Research and Extension Center, Michigan State University, E3774 University Drive, Chatham, MI, 49816, USA.; Department of Plant, Soil and Microbial Science, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824, USA.; Center for Global Change and Earth Observations, Michigan State University, 1405 S Harrison Rd., East Lansing, MI, 48823, USA.

PREMISE: Nucleic acid integrity can be compromised under many abiotic stresses. To date, however, few studies have considered whether nucleic acid damage and damage repair play a role in cold-stress adaptation. A further insufficiently explored question concerns how age affects cold stress adaptation among mature perennials. As a plant ages, the optimal trade-off between growth and stress tolerance may shift. METHODS: Oxidative damage to RNA and expression of genes involved in DNA repair were compared in multiple mature cohorts of Thinopyrum intermedium (an emerging perennial cereal) and in wheat and barley under intermittent freezing stress and under nonfreezing conditions. Activity of glutathione peroxidase (GPX) and four other antioxidative enzymes was also measured under these conditions. DNA repair genes included photolyases involved in repairing ultraviolet-induced damage and two genes involved in repairing oxidatively induced damage (ERCC1, RAD23). RESULTS: Freezing stress was accompanied by large increases in photolyase expression and ERCC1 expression (in wheat and Thinopyrum) and in GPX and GR activity (particularly in Thinopyrum). This is the first report of DNA photolyases being overexpressed under freezing stress. Older Thinopyrum had lower photolyase expression and less freezing-induced overexpression of ERCC1. Younger Thinopyrum plants sustained more oxidative damage to RNA. CONCLUSIONS: Overexpression of DNA repair genes is an important aspect of cold acclimation. When comparing adult cohorts, aging was associated with changes in the freezing stress response, but not with overall increases or decreases in stress tolerance.

PMID: 33340368