1
|
Zhou H, Ma J, Liu H, Zhao P. Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. Int J Mol Sci 2023; 25:25. [PMID: 38203199 PMCID: PMC10778614 DOI: 10.3390/ijms25010025] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.
Collapse
Affiliation(s)
- Huijuan Zhou
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an 710061, China;
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| |
Collapse
|
2
|
Zheng H, Meng K, Liu J, Lin Z, Peng Q, Xie G, Wu P, Elsheery NI. Identification and expression of bifunctional acid urea-degrading enzyme/urethanase from Enterobacter sp. R-SYB082 and its application in degradation of ethyl carbamate in Chinese rice wine (Huangjiu). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:4599-4608. [PMID: 35179235 DOI: 10.1002/jsfa.11818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/08/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Ethyl carbamate (EC) is a potential carcinogen existing in fermented foods such as Chinese rice wine (Huangjiu). Since urea is an important precursor of EC, the degradation of urea could be an effective way to reduce EC in foods. RESULTS In this study, an Enterobacter sp. R-SYB082 with acid urea degradation characteristics was obtained through microbial screening. Further research isolated a new acid urea-degrading enzyme from R-SYB082 strain - ureidoglycolate amidohydrolase (UAH) - which could degrade EC directly. The cloning and expression of UAH in Escherichia coli BL21 (DE3) suggested that the activity of urea-degrading enzyme reached 3560 U L-1 , while urethanase activity reached 2883 U L-1 in the optimal fermentation condition. The enzyme had the dual ability of degrading substrate urea and product EC. The removal rate of EC in Chinese rice wine could reach 90.7%. CONCLUSION This study provided a new method for the integrated control of EC in Chinese rice wine and other fermented foods. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Huajun Zheng
- National Engineering Research Center for Chinese Huangjiu (Branch Center), Shaoxing University, Shaoxing, China
- School of Life Science, Shaoxing University, Shaoxing, China
| | - Kai Meng
- National Engineering Research Center for Chinese Huangjiu (Branch Center), Shaoxing University, Shaoxing, China
- School of Life Science, Shaoxing University, Shaoxing, China
| | - Jun Liu
- Thermo Fisher Scientific (China) Co. Ltd, Shanghai, China
| | - Zichen Lin
- National Engineering Research Center for Chinese Huangjiu (Branch Center), Shaoxing University, Shaoxing, China
- School of Life Science, Shaoxing University, Shaoxing, China
| | - Qi Peng
- National Engineering Research Center for Chinese Huangjiu (Branch Center), Shaoxing University, Shaoxing, China
- School of Life Science, Shaoxing University, Shaoxing, China
- California Institute of Food and Agricultural Research, University of California, Davis, CA, USA
| | - Guangfa Xie
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Peng Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | | |
Collapse
|
3
|
Jiao C. PpCBF6 Is Involved in Phytosulfokine α-Retarded Chilling Injury by Suppressing the Expression of PpLOX5 in Peach Fruit. FRONTIERS IN PLANT SCIENCE 2022; 13:874338. [PMID: 35574078 PMCID: PMC9100813 DOI: 10.3389/fpls.2022.874338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The involvement of PpCBF6 in phytosulfokine α (PSKα)-ameliorated chilling injury (CI) by suppressing the expression of lipoxygenase 5 (LOX5) in peach fruit was revealed. The peaches were immersed in distilled water and PSKα solution. PSKα application inhibited the progression of CI index and weight loss, and the reduction of firmness and total soluble solids content in peaches. The endogenous PSKα accumulation and gene expression of PSK receptor 1 (PSKR1) and PSKR2 were up regulated by PSKα application. The superoxide anion (O2 -) production rate, hydrogen peroxide (H2O2) production and reactive oxygen species (ROS) content decreased by PSKα application. Furthermore, PSKα application reduced the gene expression of 12 PpLOXs and LOX activity. The gene expression of 6 PpCBFs was enhanced by PSKα application. Importantly, after PSKα application, among 12 PpLOXs, the decrease in gene expression of PpLOX5 was the lowest, and among 6 PpCBFs, the increase in gene expression of PpCBF6 was the highest. Further results suggested that PpCBF6 bound to the C-repeat/dehydration responsive element (CRT/DRE) motif in PpLOX5 promoter, and repressed its transcription. Thus, PpCBF6 was involved in the PSKα-retarded CI by inhibiting the expression of PpLOX5 in peaches.
Collapse
Affiliation(s)
- Caifeng Jiao
- School of Horticulture, Anhui Agricultural University, Hefei, China
| |
Collapse
|
4
|
Lyu J, Cai Z, Li Y, Suo H, Yi R, Zhang S, Nian H. The Floral Repressor GmFLC-like Is Involved in Regulating Flowering Time Mediated by Low Temperature in Soybean. Int J Mol Sci 2020; 21:E1322. [PMID: 32075331 PMCID: PMC7072909 DOI: 10.3390/ijms21041322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/09/2023] Open
Abstract
Soybean is an important crop that is grown worldwide. Flowering time is a critical agricultural trait determining successful reproduction and yields. For plants, light and temperature are important environmental factors that regulate flowering time. Soybean is a typical short-day (SD) plant, and many studies have elucidated the fine-scale mechanisms of how soybean responds to photoperiod. Low temperature can delay the flowering time of soybean, but little is known about the detailed mechanism of how temperature affects soybean flowering. In this study, we isolated GmFLC-like from soybean, which belongs to the FLOWERING LOCUS C clade of the MADS-box family and is intensely expressed in soybean leaves. Heterologous expression of GmFLC-like results in a delayed-flowering phenotype in Arabidopsis. Additional experiments revealed that GmFLC-like is involved in long-term low temperature-triggered late flowering by inhibiting FT gene expression. In addition, yeast one-hybrid, dual-luciferase reporter assay, and electrophoretic mobility shift assay revealed that the GmFLC-like protein could directly repress the expression of FT2a by physically interacting with its promoter region. Taken together, our results revealed that GmFLC-like functions as a floral repressor involved in flowering time during treatments with various low temperature durations. As the only the FLC gene in soybean, GmFLC-like was meaningfully retained in the soybean genome over the course of evolution, and this gene may play an important role in delaying flowering time and providing protective mechanisms against sporadic and extremely low temperatures.
Collapse
Affiliation(s)
- Jing Lyu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Zhandong Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Yonghong Li
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Haicui Suo
- Crop Research Institute, Guangdong Academy of Agriculture, Guangzhou 510642, China;
| | - Rong Yi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shuai Zhang
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
5
|
Zhang Y, Li W, Lin Y, Zhang L, Wang C, Xu R. Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing. BMC Genomics 2018; 19:641. [PMID: 30157757 PMCID: PMC6116504 DOI: 10.1186/s12864-018-5035-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 08/23/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Soybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq). RESULTS SLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, 'Huapidou', and a cultivated soybean, 'Qihuang26', which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively. CONCLUSIONS With SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.
Collapse
Affiliation(s)
- Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Yanhui Lin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 China
| |
Collapse
|
6
|
A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice. Funct Integr Genomics 2018; 18:241-259. [PMID: 29470681 PMCID: PMC5908820 DOI: 10.1007/s10142-017-0585-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/12/2023]
Abstract
The wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae), is an important pest of wheat and other cereals, threatening the quality and quantity of grain production. WSS larvae feed and develop inside the stem where they are protected from the external environment; therefore, pest management strategies primarily rely on host plant resistance. A major locus on the long arm of wheat chromosome 3B underlies most of the variation in stem solidness; however, the impact of stem solidness on WSS feeding has not been completely characterized. Here, we used a multiomics approach to examine the response to WSS in both solid- and semi-solid-stemmed wheat varieties. The combined transcriptomic, proteomic, and metabolomic data revealed that two important molecular pathways, phenylpropanoid and phosphate pentose, are involved in plant defense against WSS. We also detected a general downregulation of several key defense transcripts, including those encoding secondary metabolites such as DIMBOA, tricetin, and lignin, which suggested that the WSS larva might interfere with plant defense. We comparatively analyzed the stem solidness genomic region known to be associated with WSS tolerance in wild emmer, durum, and bread wheats, and described syntenic regions in the close relatives barley, Brachypodium, and rice. Additionally, microRNAs identified from the same genomic region revealed potential regulatory pathways associated with the WSS response. We propose a model outlining the molecular responses of the WSS–wheat interactions. These findings provide insight into the link between stem solidness and WSS feeding at the molecular level.
Collapse
|
7
|
Irani S, Todd CD. Ureide metabolism under abiotic stress in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2016; 199:87-95. [PMID: 27302009 DOI: 10.1016/j.jplph.2016.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/21/2023]
Abstract
Ureides are nitrogenous compounds derived from purine catabolism which contribute to nitrogen recycling in plants. Accumulation of ureide compounds has been reported in a number of plant species under stress conditions, suggesting their involvement in plants' response to stress. In this research a biochemical and molecular approach was applied to address the ureide accumulation under abiotic stress conditions in Arabidopsis thaliana. Ureide concentration and changes in expression of ureide metabolic genes were examined in response to drought, NaCl and mannitol treatments. Additionally, an Arabidopsis allantoinase (ALN) mutant with constitutive accumulation of a ureide compound, allantoin, was used to investigate the impact of high levels of this compound on drought and NaCl stress responses. In the leaf tissue of adult plants allantoin accumulated in response to soil drying. Transcription of urate oxidase (UO), involved in allantoin production, was highly up-regulated under the same conditions. Allantoin and allantoate also accumulated in seedlings following treatment with NaCl or mannitol. aln mutants with enhanced levels of allantoin exhibited higher tolerance to drought and NaCl. Hydrogen peroxide and superoxide did not accumulate in the aln mutant leaves to the same degree in response to drought when compared to the wild-type. Our results suggest that ureide metabolism and accumulation contribute to the abiotic stress response which is regulated, at least in part, at the transcriptional level. Higher concentrations of allantoin in the mutant elevates abiotic stress tolerance, possibly by reducing oxidative damage.
Collapse
Affiliation(s)
- Solmaz Irani
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada.
| |
Collapse
|