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Yan Y, Zhu X, Qi H, Wang Y, Zhang H, He J. Rice seed storability: From molecular mechanisms to agricultural practices. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112215. [PMID: 39151802 DOI: 10.1016/j.plantsci.2024.112215] [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: 06/27/2024] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
The storability of rice seeds is crucial for ensuring flexible planting options, agricultural seed security, and global food safety. With the intensification of global climate change and the constant fluctuations in agricultural production conditions, enhancing the storability of rice seeds has become particularly important. Seed storability is a complex quantitative trait regulated by both genetic and environmental factors. This article reviews the main regulatory mechanisms of rice seed storability, including the accumulation of seed storage proteins, late embryogenesis abundant (LEA) proteins, heat shock proteins, sugar signaling, hormonal regulation by gibberellins and abscisic acid, and the role of the ubiquitination pathway. Additionally, this article explores the improvement of storability using wild rice genes, molecular marker-assisted selection, and gene editing techniques such as CRISPR/Cas9 in rice breeding. By providing a comprehensive scientific foundation and practical guidance, this review aims to promote the development of rice varieties with enhanced storability to meet evolving agricultural demands.
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Affiliation(s)
- Yuntao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Xiaoya Zhu
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Hui Qi
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China; Hunan Institute of Nuclear Agricultural Science and Space Breeding, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yan Wang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China.
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Xu L, Zhu X, Yi F, Liu Y, Sod B, Li M, Chen L, Kang J, Yang Q, Long R. A genome-wide study of the lipoxygenase gene families in Medicago truncatula and Medicago sativa reveals that MtLOX24 participates in the methyl jasmonate response. BMC Genomics 2024; 25:195. [PMID: 38373903 PMCID: PMC10875803 DOI: 10.1186/s12864-024-10071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Lipoxygenase (LOX) is a multifunctional enzyme that is primarily related to plant organ growth and development, biotic and abiotic stress responses, and production of flavor-associated metabolites. In higher plants, the LOX family encompasses several isozymes with varying expression patterns between tissues and developmental stages. These affect processes including seed germination, seed storage, seedling growth, fruit ripening, and leaf senescence. LOX family genes have multiple functions in response to hormones such as methyl jasmonate (MeJA) and salicylic acid. RESULTS In this study, we identified 30 and 95 LOX homologs in Medicago truncatula and Medicago sativa, respectively. These genes were characterized with analyses of their basic physical and chemical properties, structures, chromosomal distributions, and phylogenetic relationships to understand structural variations and their physical locations. Phylogenetic analysis was conducted for members of the three LOX subfamilies (9-LOX, type I 13-LOX, and type II 13-LOX) in Arabidopsis thaliana, Glycine max, M. truncatula, and M. sativa. Analysis of predicted promoter elements revealed several relevant cis-acting elements in MtLOX and MsLOX genes, including abscisic acid (ABA) response elements (ABREs), MeJA response elements (CGTCA-motifs), and antioxidant response elements (AREs). Cis-element data combined with transcriptomic data demonstrated that LOX gene family members in these species were most likely related to abiotic stress responses, hormone responses, and plant development. Gene expression patterns were confirmed via quantitative reverse transcription PCR. Several MtLOX genes (namely MtLOX15, MtLOX16, MtLOX20, and MtLOX24) belonging to the type I 13-LOX subfamily and other LOX genes (MtLOX7, MtLOX11, MsLOX23, MsLOX87, MsLOX90, and MsLOX94) showed significantly different expression levels in the flower tissue, suggesting roles in reproductive growth. Type I 13-LOXs (MtLOX16, MtLOX20, MtLOX21, MtLOX24, MsLOX57, MsLOX84, MsLOX85, and MsLOX94) and type II 13-LOXs (MtLOX5, MtLOX6, MtLOX9, MtLOX10, MsLOX18, MsLOX23, and MsLOX30) were MeJA-inducible and were predicted to function in the jasmonic acid signaling pathway. Furthermore, exogenous MtLOX24 expression in Arabidopsis verified that MtLOX24 was involved in MeJA responses, which may be related to insect-induced abiotic stress. CONCLUSIONS We identified six and four LOX genes specifically expressed in the flowers of M. truncatula and M. sativa, respectively. Eight and seven LOX genes were induced by MeJA in M. truncatula and M. sativa, and the LOX genes identified were mainly distributed in the type I and type II 13-LOX subfamilies. MtLOX24 was up-regulated at 8 h after MeJA induction, and exogenous expression in Arabidopsis demonstrated that MtLOX24 promoted resistance to MeJA-induced stress. This study provides valuable new information regarding the evolutionary history and functions of LOX genes in the genus Medicago.
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Affiliation(s)
- Lei Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiaoxi Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yajiao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bilig Sod
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Dong W, Jiao B, Wang J, Sun L, Li S, Wu Z, Gao J, Zhou S. Genome-Wide Identification and Expression Analysis of Lipoxygenase Genes in Rose ( Rosa chinensis). Genes (Basel) 2023; 14:1957. [PMID: 37895306 PMCID: PMC10606720 DOI: 10.3390/genes14101957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Lipoxygenases (LOX) play pivotal roles in plant resistance to stresses. However, no study has been conducted on LOX gene identification at the whole genome scale in rose (Rosa chinensis). In this study, a total of 17 RcLOX members were identified in the rose genome. The members could be classified into three groups: 9-LOX, Type I 13-LOX, and Type II 13-LOX. Similar gene structures and protein domains can be found in RcLOX members. The RcLOX genes were spread among all seven chromosomes, with unbalanced distributions, and several tandem and proximal duplication events were found among RcLOX members. Expressions of the RcLOX genes were tissue-specific, while every RcLOX gene could be detected in at least one tissue. The expression levels of most RcLOX genes could be up-regulated by aphid infestation, suggesting potential roles in aphid resistance. Our study offers a systematic analysis of the RcLOX genes in rose, providing useful information not only for further gene cloning and functional exploration but also for the study of aphid resistance.
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Affiliation(s)
- Wenqi Dong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China;
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Bo Jiao
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Jiao Wang
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Lei Sun
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Songshuo Li
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Zhiming Wu
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China;
| | - Shuo Zhou
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
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Hu F, Zhang Y, Guo J. Identification and characterization of lipoxygenase (LOX) genes involved in abiotic stresses in yellow horn. PLoS One 2023; 18:e0292898. [PMID: 37831731 PMCID: PMC10575502 DOI: 10.1371/journal.pone.0292898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Lipoxygenase (LOX) gene plays an essential role in plant growth, development, and stress response. 15 LOX genes were identified, which were unevenly distributed on chromosomes and divided into three subclasses in this study. In promoter region analysis, many cis-elements were identified in growth and development, abiotic stress response, hormonal response, and light response. qRT-PCR showed that the LOX gene showed tissue specificity in seven tissues, especially XsLOX1, 3, and 7 were relatively highly expressed in roots, stems, and axillary buds. The different expression patterns of LOX genes in response to abiotic stress and hormone treatment indicate that different XsLOX genes have different reactions to these stresses and play diversified roles. This study improves our understanding of the mechanism of LOX regulation in plant growth, development, and stress and lays a foundation for further analysis of biological functions.
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Affiliation(s)
- Fang Hu
- The College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yunxiang Zhang
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Jinzhong, Shanxi, China
| | - Jinping Guo
- The College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Jinzhong, Shanxi, China
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Gorina SS, Egorova AM, Lantsova NV, Toporkova YY, Grechkin AN. Discovery of α-Linolenic Acid 16( S)-Lipoxygenase: Cucumber ( Cucumis sativus L.) Vegetative Lipoxygenase 3. Int J Mol Sci 2023; 24:12977. [PMID: 37629162 PMCID: PMC10454662 DOI: 10.3390/ijms241612977] [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: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The GC-MS profiling of the endogenous oxylipins (Me/TMS) from cucumber (Cucumis sativus L.) leaves, flowers, and fruit peels revealed a remarkable abundance of 16-hydroxy-9,12,14-octadecatrienoic acid (16-HOT). Incubations of homogenates from these organs with α-linolenic acid yielded 16(S)-hydroperoxide (16-HPOT) as a predominant product. Targeted proteomic analyses of these tissues revealed the presence of several highly homologous isoforms of the putative "9S-lipoxygenase type 6". One of these isoenzymes (CsLOX3, an 877 amino acid polypeptide) was prepared by heterologous expression in E. coli and exhibited 16(S)- and 13(S)-lipoxygenase activity toward α-linolenic and linoleic acids, respectively. Furthermore, α-linolenate was a preferred substrate. The molecular structures of 16(S)-HOT and 16(S)-HPOT (Me or Me/TMS) were unequivocally confirmed by the mass spectral data, 1H-NMR, 2D 1H-1H-COSY, TOCSY, HMBC, and HSQC spectra, as well as enantiomeric HPLC analyses. Thus, the vegetative CsLOX3, biosynthesizing 16(S)-HPOT, is the first 16(S)-LOX and ω3-LOX ever discovered. Eicosapentaenoic and hexadecatrienoic acids were also specifically transformed to the corresponding ω3(S)-hydroperoxides by CsLOX3.
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Affiliation(s)
- Svetlana S Gorina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, P.O. Box 261, 420111 Kazan, Russia
| | - Alevtina M Egorova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, P.O. Box 261, 420111 Kazan, Russia
| | - Natalia V Lantsova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, P.O. Box 261, 420111 Kazan, Russia
| | - Yana Y Toporkova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, P.O. Box 261, 420111 Kazan, Russia
| | - Alexander N Grechkin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, P.O. Box 261, 420111 Kazan, Russia
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Fayaz M, Kundan M, Gani U, Sharma P, Wajid MA, Katoch K, Babu V, Gairola S, Misra P. Identification of Lipoxygenase gene repertoire of Cannabis sativa and functional characterization of CsLOX13 gene. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111780. [PMID: 37390920 DOI: 10.1016/j.plantsci.2023.111780] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/25/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Lipoxygenase (LOX) enzymes play a pivotal role in the biosynthesis of oxylipins. The phyto-oxilipins have been implicated in diverse aspects of plant biology, from regulating plant growth and development to providing tolerance against biotic and abiotic stresses. C. sativa is renowned for its bioactive secondary metabolites, namely cannabinoids. LOX route is assumed to be involved in the biosynthesis of hexanoic acid, which is one of the precursors of cannabinoids of C. sativa. For obvious reasons, the LOX gene family deserves thorough investigation in the C. sativa. Genome-wide analysis revealed the presence of 21 LOX genes in C. sativa, which can be further grouped into 13-LOX and 9-LOX depending upon their phylogeny as well as the enzyme activity. The promoter regions of the CsLOX genes were predicted to contain cis-acting elements involved in phytohormones responsiveness and stress response. The qRT-PCR-based expression analysis of 21 LOX genes revealed their differential expression in different plant parts (root, stem, young leaf, mature leaf, sugar leaf, and female flower). The majority of CsLOX genes displayed preferential expression in the female flower, which is the primary site for the biosynthesis of cannabinoids. The highest LOX activity and expression level of a jasmonate marker gene were reported in the female flowers among all the plant parts. Several CsLOX genes were found to be upregulated by MeJA treatment. Based on the transient expression in Nicotiana benthamiana and the development of stable Nicotiana tabacum transgenic lines, we demonstrate that CsLOX13 encodes functional lipoxygenase and play an important role in the biosynthesis of oxylipins.
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Affiliation(s)
- Mohd Fayaz
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Maridul Kundan
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
| | - Umar Gani
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India.
| | - Priyanka Sharma
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Mir Abdul Wajid
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kajal Katoch
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India
| | - Vikash Babu
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India
| | - Sumeet Gairola
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India
| | - Prashant Misra
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine Canal Road, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Wang Z, Luo Y, Yu J, Kou X, Xie L, Deng P, Li T, Chen C, Ji W, Liu X. Genome-wide identification and characterization of lipoxygenase genes related to the English grain aphid infestation response in wheat. PLANTA 2023; 257:84. [PMID: 36943494 DOI: 10.1007/s00425-023-04114-2] [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: 10/22/2022] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
44 wheat LOX genes were identified by silico genome-wide search method. TaLOX5, 7, 10, 24, 29, 33 were specifically expressed post aphid infestation, indicating their participation in wheat-aphid interaction. In plants, LOX genes play important roles in various biological progresses including seed germination, tuber development, plant vegetative growth and most crucially in plant signal transduction, stress response and plant defense against plant diseases and insects. Although LOX genes have been characterized in many species, the importance of the LOX family in wheat has still not been well understood, hampering further improvement of wheat under stress conditions. Here, we identified 44 LOX genes (TaLOXs) in the whole wheat genome and classified into three subfamilies (9-LOXs, Type I 13-LOXs and Type II 13-LOXs) according to phylogenetic relationships. The TaLOXs belonging to the same subgroup shared similar gene structures and motif organizations. Synteny analysis demonstrated that segmental duplication events mainly contributed to the expansion of the LOX gene family in wheat. The results of protein-protein interaction network (PPI) and miRNA-TaLOXs predictions revealed that three TaLOXs (TaLOX20, 22 and 37) interacted mostly with proteins related to methyl jasmonate (MeJA) signaling pathway. The expression patterns of TaLOXs in different tissues (root, stem, leaf, spike and grain) under diverse abiotic stresses (heat, cold, drought, drought and heat combined treatment, and salt) as well as under diverse biotic stresses (powdery mildew pathogen, Fusarium graminearum and stripe rust pathogen) were systematically analyzed using RNA-seq data. We obtained aphid-responsive candidate genes by RNA-seq data of wheat after the English grain aphid infestation. Aphid-responsive candidate genes, including TaLOX5, 7, 10, 24, 29 and 33, were up-regulated in the wheat aphid-resistant genotype (Lunxuan144), while they were little expressed in the susceptible genotype (Jimai22) during late response (48 h and 72 h) to the English grain aphid infestation. Meanwhile, qRT-PCR analysis was used to validate these aphid-responsive candidate genes. The genetic divergence and diversity of all the TaLOXs in bread wheat and its relative species were investigated by available resequencing data. Finally, the 3D structure of the TaLOX proteins was predicted based on the homology modeling method. This study not only systematically investigated the characteristics and evolutionary relationships of TaLOXs, but also provided potential candidate genes in response to the English grain aphid infestation and laid the foundation to further study the regulatory roles in the English grain aphid infestation of LOX family in wheat and beyond.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yufeng Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jiuyang Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xudan Kou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lincai Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
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Wang F, Xu H, Zhang L, Shi Y, Song Y, Wang X, Cai Q, He W, Xie H, Zhang J. The lipoxygenase OsLOX10 affects seed longevity and resistance to saline-alkaline stress during rice seedlings. PLANT MOLECULAR BIOLOGY 2023; 111:415-428. [PMID: 36867321 PMCID: PMC10089987 DOI: 10.1007/s11103-023-01334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/15/2023] [Indexed: 06/19/2023]
Abstract
Prolonged storage of rice seeds can lead to a decrease in seed vigor and seedling quality. The Lipoxygenase (LOX) gene family is widely distributed in plants, and LOX activity is closely related to seed viability and stress tolerance. In this study, the lipoxygenase OsLOX10 gene from the 9-lipoxygenase metabolic pathway was cloned from rice, and its roles in determining seed longevity and tolerance to saline-alkaline stress caused by Na2CO3 in rice seedlings were mainly investigated. CRISPR/Cas9 knockout of OsLOX10 increased seed longevity compared with the wild-type and OsLOX10 overexpression lines in response to artificial aging. The expression levels of other 9-lipoxygenase metabolic pathway related genes, such as LOX1, LOX2 and LOX3, were increased in the LOX10 overexpression lines. Quantitative real-time PCR and histochemical staining analysis showed that the expression of LOX10 was highest in seed hulls, anthers and the early germinating seeds. KI-I2 staining of starch showed that LOX10 could catalyze the degradation of linoleic acid. Furthermore, we found that the transgenic lines overexpressing LOX10 showed better tolerance to saline-alkaline stress than the wild-type and knockout mutant lines. Overall, our study demonstrated that the knockout LOX10 mutant increased seed longevity, whereas overexpression of LOX10 enhanced tolerance to saline-alkaline stress in rice seedlings.
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Affiliation(s)
- Fuxiang Wang
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Huibin Xu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Ling Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Yunrui Shi
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Yu Song
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Xinyue Wang
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Wei He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Huaan Xie
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China
| | - Jianfu Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- Rice Research Institute, Fujian Academy of Agricultural Sciences, 350018, Fuzhou, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Ministry of Agriculture and Affairs, 350003, Fuzhou, China.
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9
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Camargo PO, Calzado NF, Budzinski IGF, Domingues DS. Genome-Wide Analysis of Lipoxygenase (LOX) Genes in Angiosperms. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020398. [PMID: 36679110 PMCID: PMC9867167 DOI: 10.3390/plants12020398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
Lipoxygenases (LOXs) are enzymes that catalyze the addition of an oxygen molecule to unsaturated fatty acids, thus forming hydroperoxides. In plants, these enzymes are encoded by a multigene family found in several organs with varying activity patterns, by which they are classified as LOX9 or LOX13. They are involved in several physiological functions, such as growth, fruit development, and plant defense. Despite several studies on genes of the LOX family in plants, most studies are restricted to a single species or a few closely related species. This study aimed to analyze the diversity, evolution, and expression of LOX genes in angiosperm species. We identified 247 LOX genes among 23 species of angiosperms and basal plants. Phylogenetic analyses identified clades supporting LOX13 and two main clades for LOX9: LOX9_A and LOX9_B. Eudicot species such as Tarenaya hassleriana, Capsella rubella, and Arabidopsis thaliana did not present LOX9_B genes; however, LOX9_B was present in all monocots used in this study. We identified that there were potential new subcellular localization patterns and conserved residues of oxidation for LOX9 and LOX13 yet unexplored. In summary, our study provides a basis for the further functional and evolutionary study of lipoxygenases in angiosperms.
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Affiliation(s)
- Paula Oliveira Camargo
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro 13506-900, SP, Brazil
| | - Natália Fermino Calzado
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro 13506-900, SP, Brazil
| | - Ilara Gabriela Frasson Budzinski
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro 13506-900, SP, Brazil
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
| | - Douglas Silva Domingues
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro 13506-900, SP, Brazil
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
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10
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Zhang J, Ng C, Jiang Y, Wang X, Wang S, Wang S. Genome-wide identification and analysis of LOX genes in soybean cultivar “Zhonghuang 13”. Front Genet 2022; 13:1020554. [PMID: 36276975 PMCID: PMC9585170 DOI: 10.3389/fgene.2022.1020554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lipoxygenases (LOXs; EC1.13.11.12) are a family of iron- or manganese-containing dioxygenases that catalyze the oxygenation of polyunsaturated fatty acids (PUFAs) and play important roles in plant growth, development, and stress response. In this study, a total of 36 LOX gene family members were identified and annotated in Zhonghuang 13, a soybean cultivar bred by Chinese scientists in 2001. Sanger sequencing of the GmLOX1-coding sequence and colorimetric assays for the GmLOX1 protein showed that Zhonghuang 13 possessed the GmLOX1 gene. These LOX genes are divided into three subfamilies: 9-LOX, type Ⅰ 13-LOX and type II 13-LOX. In the 13-LOX group, the number of GmLOX members was the highest. These GmLOX genes are unevenly distributed on chromosomes 3, 7, 8, 10, 11, 12, 13, 15, 16, 19, and 20. Most of the 13-LOX genes exist in the form of gene clusters, indicating that these genes may originate from tandem duplications. The analysis of duplicated gene pairs showed that GmLOX genes underwent purifying selective pressure during evolution. The gene structures and conserved functional domains of these genes are quite similar. Compared to the orthologous gene pairs of LOX genes between wild soybean (Glycine soja W05) and Zhonghuang 13, the sequences of most gene pairs are relatively conserved. Many cis-elements are present in the promoter region and are involved in stress response, growth and development, hormone response and light response. The tissue-specific gene expression of GmLOX genes was evaluated. Represented by GmLOX1, GmLOX2, and GmLOX3, which were expressed at extremely high levels in seeds, they showed the characteristics of specific expression. This study provides detailed information on soybean lipoxygenase gene family members in Zhonghuang 13, which lays a foundation for further research.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Cheungchuk Ng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Yan Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xianxu Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- *Correspondence: Shaodong Wang, ; Sui Wang,
| | - Sui Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Shaodong Wang, ; Sui Wang,
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11
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Rocha ADJ, Soares JMDS, Nascimento FDS, Rocha ADS, de Amorim VBO, Ramos APDS, Ferreira CF, Haddad F, Amorim EP. Molecular, Histological and Histochemical Responses of Banana Cultivars Challenged with Fusarium oxysporum f. sp. cubense with Different Levels of Virulence. PLANTS (BASEL, SWITZERLAND) 2022; 11:2339. [PMID: 36145741 PMCID: PMC9500910 DOI: 10.3390/plants11182339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is the most limiting factor in the banana agribusiness worldwide. Therefore, studies regarding pathogen attack mechanisms, and especially host defense responses, in this pathosystem are of utmost importance for genetic breeding programs in the development of Foc-resistant banana cultivars. In this study, analysis at the molecular, histological and histochemical levels of the Musa spp. x Foc interaction was performed. Three Foc isolates representative of race 1 (R1), subtropical race 4 (ST4) and isolate 229A, which is a putative ST4, were inoculated in two Prata-type cultivars (Prata-Anã and BRS Platina) and one cultivar of the Cavendish type (Grand Naine). Of seven genes related to plant-pathogen interactions, five were overexpressed in 'BRS Platina' 12 h after inoculation (HAI) with Foc R1 and ST4 but had reduced or negative expression after inoculation with Foc 229A, according to RT-qPCR analyses. While hyphae, mycelia and spores of the Foc 229A isolate grow towards the central cylinder of the Grand Naine and Prata-Anã cultivars, culminating in the occlusion of the xylem vessels, the BRS Platina cultivar responds with increased presence of cellulose, phenolic compounds and calcium oxalate crystals, reducing colonization within 30 days after inoculation (DAI). In general, these data indicate that the cultivar BRS Platina has potential for use in banana-breeding programs focused on resistance to Foc tropical race 4 (TR4) and in aggregating information on the virulence relationships of the Foc pathogen and the defense responses of banana plants after infection.
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Affiliation(s)
- Anelita de Jesus Rocha
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Bahia, Brazil
| | - Julianna Matos da Silva Soares
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Bahia, Brazil
| | - Fernanda dos Santos Nascimento
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Bahia, Brazil
| | - Adailson dos Santos Rocha
- Departamento de Ciências Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Bahia, Brazil
| | | | | | | | - Fernando Haddad
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, Bahia, Brazil
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12
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Liao Z, Wang L, Li C, Cao M, Wang J, Yao Z, Zhou S, Zhou G, Zhang D, Lou Y. The lipoxygenase gene OsRCI-1 is involved in the biosynthesis of herbivore-induced JAs and regulates plant defense and growth in rice. PLANT, CELL & ENVIRONMENT 2022; 45:2827-2840. [PMID: 35538611 DOI: 10.1111/pce.14341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
The pathway mediated by jasmonic acid (JA), biosynthesized via 13-lipoxygenases (LOX), plays a central role in both plant development and defense. In rice, there are at least fourteen 13-LOXs. Yet, only two 13-LOXs have been known to be involved in the biosynthesis of JA and plant defenses in rice. Here we cloned a chloroplast-localized 13-LOX gene from rice, OsRCI-1, whose transcripts were upregulated following infestation by brown planthopper (BPH, Nilaparvata lugens), one of the most important pests in rice. Overexpression of OsRCI-1 (oeRCI lines) increased levels of BPH-induced JA, jasmonate-isoleucine, trypsin protease inhibitors and three volatile compounds, 2-heptanone, 2-heptanol and α-thujene. BPHs showed a decreased colonization, fecundity and mass, and developed slowly on oeRCI plants compared with wild-type (WT) plants. Moreover, BPH-infested oeRCI plants were more attractive to the egg parasitoid of BPH, Anagrus nilaparvatae than equally treated WT plants. The decreased attractiveness to BPH and enhanced attractiveness to the parasitoid of oeRCI plants correlated with higher levels of BPH-induced 2-heptanone and 2-heptanol, and 2-heptanone, respectively. Compared with oeRCI plants, WT plants had higher plant height and 1000-grain weight. These results indicate that OsRCI-1 is involved in herbivore-induced JA bursts and plays a role in plant defense and growth.
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Affiliation(s)
- Zhihong Liao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Lu Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Chengzhe Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Mengjiao Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
- The Promotion Station of Plant Protection, Fertilizer Utilization and Rural Energy Technology of Jiaxing, Jiaxing, Zhejiang, China
| | - Jiani Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Zhangliang Yao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Senya Zhou
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Guoxin Zhou
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Dayu Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Yonggen Lou
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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13
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Identification and Characterization of Jasmonic Acid Biosynthetic Genes in Salvia miltiorrhiza Bunge. Int J Mol Sci 2022; 23:ijms23169384. [PMID: 36012649 PMCID: PMC9409215 DOI: 10.3390/ijms23169384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Jasmonic acid (JA) is a vital plant hormone that performs a variety of critical functions for plants. Salvia miltiorrhiza Bunge (S. miltiorrhiza), also known as Danshen, is a renowned traditional Chinese medicinal herb. However, no thorough and systematic analysis of JA biosynthesis genes in S. miltiorrhiza exists. Through genome-wide prediction and molecular cloning, 23 candidate genes related to JA biosynthesis were identified in S. miltiorrhiza. These genes belong to four families that encode lipoxygenase (LOX), allene oxide synthase (AOS), allene oxide cyclase (AOC), and 12-OPDA reductase3 (OPR3). It was discovered that the candidate genes for JA synthesis of S. miltiorrhiza were distinct and conserved, in contrast to related genes in other plants, by evaluating their genetic structures, protein characteristics, and phylogenetic trees. These genes displayed tissue-specific expression patterns concerning to methyl jasmonate (MeJA) and wound tests. Overall, the results of this study provide valuable information for elucidating the JA biosynthesis pathway in S. miltiorrhiza by comprehensive and methodical examination.
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14
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Yan C, Jia K, Zhang J, Xiao Z, Sha X, Gao J, Yan H. Genome-wide identification and expression pattern analysis of lipoxygenase gene family in turnip ( Brassica rapa L. subsp. rapa). PeerJ 2022; 10:e13746. [PMID: 35898937 PMCID: PMC9310782 DOI: 10.7717/peerj.13746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/27/2022] [Indexed: 01/17/2023] Open
Abstract
Turnip (Brassica rapa L. subsp. rapa) is an important crop with edible and medicinal values, and various stresses, especially salt stress and drought stress, seriously threaten the yield of turnips. LOXs play important roles in regulating plant growth and development, signal transduction, and biotic and abiotic stress responses through secondary metabolites produced by the oxylipin metabolic pathway, and although the turnip genome has been published, however, the role of LOX family genes in various abiotic stress responses has not been systematically studied in turnips. In this study, a total of 15 LOX genes (BrrLOX) were identified in turnip, distributed on six chromosomes. Phylogenetic tree analysis classified these LOX genes into two classes: three 9-LOX proteins and 12 13-LOX type II proteins. Gene duplication analysis showed that tandem and segmental duplication were the main pathways for the expansion of the BrrLOX gene family. The Ka and Ks values of the duplicated genes indicate that the BrrLOX gene underwent strong purifying selection. Further analysis of the cis-acting elements of the promoters suggested that the expression of the BrrLOX gene may be influenced by stress and phytohormones. Transcriptome data analysis showed that 13 BrrLOX genes were expressed at one or more stages of turnip tuber development, suggesting that LOX genes may be involved in the formation of turnip fleshy roots. The qRT-PCR analysis showed that four stresses (salt stress, drought stress, cold stress, and heat stress) and three hormone treatments (methyl jasmonate, salicylic acid, and abscisic acid) affected the expression levels of BrrLOX genes and that different BrrLOX genes responded differently to these stresses. In addition, weighted gene co-expression network analysis (WGCNA) of BrrLOX revealed seven co-expression modules, and the genes in these co-expression modules are collectively involved in plant growth and development and stress response processes. Thus, our results provide valuable information for the functional identification and regulatory mechanisms of BrrLOX in turnip growth and development and stress response.
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Affiliation(s)
- Cunyao Yan
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Kai Jia
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jing Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Zhonglin Xiao
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiaomei Sha
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jie Gao
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Huizhuan Yan
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
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15
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Singh P, Arif Y, Miszczuk E, Bajguz A, Hayat S. Specific Roles of Lipoxygenases in Development and Responses to Stress in Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:979. [PMID: 35406959 PMCID: PMC9002551 DOI: 10.3390/plants11070979] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 05/24/2023]
Abstract
Lipoxygenases (LOXs), naturally occurring enzymes, are widely distributed in plants and animals. LOXs can be non-sulfur iron, non-heme iron, or manganese-containing dioxygenase redox enzymes. LOXs catalyze the oxidation of polyunsaturated fatty acids into fatty acid hydroperoxides. Linolenic acid, a precursor in the jasmonic acid (JA) biosynthesis, is converted to 12-oxo-phytodienoic acid through oxygenation with LOX, allene oxide synthase, and allene oxide cyclase. Moreover, JA participates in seed germination, fruit ripening, senescence, and many other physio-biochemical processes. LOXs also play crucial roles in defense responses against biotic stress, i.e., insects, pests, pathogenic attacks, and abiotic stress, such as wounding, UV-rays, extreme temperature, oxidative stress, and drought.
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Affiliation(s)
- Priyanka Singh
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (P.S.); (Y.A.); (S.H.)
| | - Yamshi Arif
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (P.S.); (Y.A.); (S.H.)
| | - Edyta Miszczuk
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland;
| | - Andrzej Bajguz
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland;
| | - Shamsul Hayat
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (P.S.); (Y.A.); (S.H.)
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16
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Mou Y, Sun Q, Yuan C, Zhao X, Wang J, Yan C, Li C, Shan S. Identification of the LOX Gene Family in Peanut and Functional Characterization of AhLOX29 in Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:832785. [PMID: 35356112 PMCID: PMC8959715 DOI: 10.3389/fpls.2022.832785] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Lipoxygenases (LOXs) are a gene family of nonheme iron-containing dioxygenases that play important roles in plant development and defense responses. To date, a comprehensive analysis of LOX genes and their biological functions in response to abiotic stresses in peanut has not been performed. In this study, a total of 72 putative LOX genes were identified in cultivated (Arachis hypogaea) and wild-type peanut (Arachis duranensis and Arachis ipaensis) and classified into three subfamilies: 9-LOX, type I 13-LOX and type II 13-LOX. The gene structures and protein motifs of these peanut LOX genes were highly conserved among most LOXs. We found that the chromosomal distribution of peanut LOXs was not random and that gene duplication played a crucial role in the expansion of the LOX gene family. Cis-acting elements related to development, hormones, and biotic and abiotic stresses were identified in the promoters of peanut LOX genes. The expression patterns of peanut LOX genes were tissue-specific and stress-inducible. Quantitative real-time PCR results further confirmed that peanut LOX gene expression could be induced by drought, salt, methyl jasmonate and abscisic acid treatments, and these genes exhibited diverse expression patterns. Furthermore, overexpression of AhLOX29 in Arabidopsis enhanced the resistance to drought stress. Compared with wide-type, AhLOX29-overexpressing plants showed significantly decreased malondialdehyde contents, as well as increased chlorophyll degradation, proline accumulation and superoxide dismutase activity, suggesting that the transgenic plants exhibit strengthened capacity to scavenge reactive oxygen species and prevent membrane damage. This systematic study provides valuable information about the functional characteristics of AhLOXs in the regulation of abiotic stress responses of peanut.
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17
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Meng Y, Liang Y, Liao B, He W, Liu Q, Shen X, Xu J, Chen S. Genome-Wide Identification, Characterization and Expression Analysis of Lipoxygenase Gene Family in Artemisia annua L. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050655. [PMID: 35270126 PMCID: PMC8912875 DOI: 10.3390/plants11050655] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 05/17/2023]
Abstract
Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without serious side effects. This study identified and analyzed LOX gene family members in the A. annua genome at the chromosomal level. Twenty LOX genes with various molecular weights, isoelectric points, and amino acid numbers were identified and named AaLOX, which were located in the cytoplasm or chloroplast. The average protein length of all AaLOX was 850 aa. Phylogenetic tree analysis revealed that the AaLOX was divided into two major groups, 9-LOX and 13-LOX. The exon numbers ranged from 1 to 12, indicating that different AaLOX genes have different functions. The secondary structure was mainly composed of alpha helix and random coil, and the tertiary structure was similar for most AaLOX. Upstream promoter region analysis revealed that a large number of cis-acting elements were closely related to plant growth and development, light response, hormone, and other stress responses. Transcriptome data analysis of different tissues suggested that the gene family was differently expressed in the roots, stems, leaves, and flowers of two A. annua strains HAN1 and LQ9. qRT-PCR confirmed that AaLOX5 and AaLOX17 had the highest expression in flowers and leaves. This study provides a theoretical basis for the further functional analysis of the AaLOX gene family.
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Affiliation(s)
- Ying Meng
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China;
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Yu Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Wenrui He
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610000, China
| | - Qianwen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
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Bollinedi H, Singh N, Gopala Krishnan S, Vinod KK, Bhowmick PK, Nagarajan M, Ellur RK, Singh AK. A novel LOX3-null allele (lox3-b) originated in the aromatic Basmati rice cultivars imparts storage stability to rice bran. Food Chem 2022; 369:130887. [PMID: 34461519 DOI: 10.1016/j.foodchem.2021.130887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/24/2021] [Accepted: 08/14/2021] [Indexed: 01/04/2023]
Abstract
Rapid deterioration of rice bran due to the LOX3 enzyme catalysed oxidation of PUFA is the major bottleneck for its utilization in various downstream applications. In the present study, we have identified a set of nine novel LOX3-null rice accessions carrying a deletion of C residue in the exon2 causing a frameshift mutation resulting in a truncated non-functional LOX3 protein. Our study, further manifested the predominance of C deletion based LOX3-null allele, named lox3-b, in the aromatic rice germplasm particularly in the Indian Basmati rice group. The LOX3-null genotypes exhibited significantly reduced rancidity, after six months of storage. They also showed significantly lower percentage reduction of linoleic acid (LA), higher γ-oryzanol content and lower hexanal content. A functional dCAPS marker designed based on the deletion polymorphism clearly differentiated LOX3 and lox3-b alleles, and has the potential application in marker assisted rice breeding programmes to develop cultivars with better bran storability.
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Affiliation(s)
- Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Neha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - P K Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - M Nagarajan
- ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, India
| | - R K Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - A K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India.
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Yu B, Wu Q, Li X, Zeng R, Min Q, Huang J. GLUTAMATE RECEPTOR-like gene OsGLR3.4 is required for plant growth and systemic wound signaling in rice (Oryza sativa). THE NEW PHYTOLOGIST 2022; 233:1238-1256. [PMID: 34767648 DOI: 10.1111/nph.17859] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/03/2021] [Indexed: 05/15/2023]
Abstract
Recent studies have revealed the physiological roles of glutamate receptor-like channels (GLRs) in Arabidopsis; however, the functions of GLRs in rice remain largely unknown. Here, we show that knockout of OsGLR3.4 in rice leads to brassinosteroid (BR)-regulated growth defects and reduced BR sensitivity. Electrophoretic mobility shift assays and transient transactivation assays indicated that OsGLR3.4 is the downstream target of OsBZR1. Further, agonist profile assays showed that multiple amino acids can trigger transient Ca2+ influx in an OsGLR3.4-dependent manner, indicating that OsGLR3.4 is a Ca2+ -permeable channel. Meanwhile, the study of internode cells demonstrated that OsGLR3.4-mediated Ca2+ flux is required for actin filament organization and vesicle trafficking. Following root injury, the triggering of both slow wave potentials (SWPs) in leaves and the jasmonic acid (JA) response are impaired in osglr3.4 mutants, indicating that OsGLR3.4 is required for root-to-shoot systemic wound signaling in rice. Brassinosteroid treatment enhanced SWPs and OsJAZ8 expression in root-wounded plants, suggesting that BR signaling synergistically regulates the OsGLR3.4-mediated systemic wound response. In summary, this article describes a mechanism of OsGLR3.4-mediated cell elongation and long-distance systemic wound signaling in plants and provides new insights into the contribution of GLRs to plant growth and responses to mechanical wounding.
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Affiliation(s)
- Bo Yu
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
| | - Qi Wu
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
| | - Xingxing Li
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
| | - Rongfeng Zeng
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
| | - Qian Min
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, 174 Shazheng Street, Chongqing, China
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20
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Hazman M. Gel express: a novel frugal method quantifies gene relative expression in conventional RT-PCR. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00194-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Real-time PCR system is a valuable scientific mainstream needed for quantifying specific gene expression. Nevertheless, compared with conventional PCR, the real-time PCR system is extremely expensive and not affordable for limited or mid-budget research laboratories. Here, a novel, doable and low-cost recipe (referred to as gel express) is developed to quantify gene expression using conventional RT-PCR assay. The novelty of the gel express method is based on replacing crossing point (CP) values with integrated density (IntDen) values of PCR amplicon bands in real-time PCR regular mathematical formulas.
Results
In this work, gene expression profiles of two different rice stress-marker genes (OsCYP94C2a and OsLOX8) were quantified in response to mechanical wounding at different time points (0, 30, 60, and 150 min). In the gel express method, the free software ImageJ was employed to measure integrated density (IntDen) values of PCR amplicon bands in agarose gel images. IntDen values were then used instead of crossing point (CP) values according to the following modified formula: [EIntDen(ref)/EIntDen(target)]sample ÷ [EIntDen(ref)/EIntDen(target)]control. Gene relative expression profiles (dynamic expression pattern) quantified by gel express method in both genes were highly comparable with real-time RT-PCR. R2 values were 0.9976 and 0.9975 in OsCYP94C2a and OsLOX, respectively. PCR amplification efficiency (E) for all studied genes could be calculated depending on IntDen values through experimentally designed calibration curves. PCR amplification efficiencies with all studied genes obtained by gel express were all in the accepted range. For better-visualized PCR amplicons thus detectable biological effects between treatments, the number of PCR cycles applied in gel express method (IntCyc) was experimentally estimated to be 29 cycles.
Conclusions
Gel express is a novel, cost-effective and feasible recipe for quantifying gene relative expression in conventional RT-PCR. The expression pattern quantified by gel express is highly comparable and fits the expression data revealed by the used real-time PCR system.
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21
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The Responses of the Lipoxygenase Gene Family to Salt and Drought Stress in Foxtail Millet ( Setaria italica). Life (Basel) 2021; 11:life11111169. [PMID: 34833045 PMCID: PMC8619181 DOI: 10.3390/life11111169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022] Open
Abstract
Plant lipoxygenases (LOXs), a kind of non-heme iron-containing dioxygenases, participate plant physiological activities (especially in response to biotic and abiotic stresses) through oxidizing various lipids. However, there was few investigations on LOXs in foxtail millet (Setaria italica). In this study, we identified the LOX gene family in foxtail millet, and divided the total 12 members into three sub-families on the basis of their phylogenetic relationships. Under salt and drought stress, LOX genes showed different expression patterns. Among them, only SiLOX7 showed up-regulated expression in Yugu1 (YG1) and Qinhuang2 (QH2), two stress-tolerant varieties, indicating that SiLOX7 may play an important role in responses to abiotic stress. Our research provides a basis for further investigation of the role of LOX genes in the adaptation to abiotic stresses and other possible biological functions in foxtail millet.
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Upadhyay RK, Shao J, Mattoo AK. Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses. PLANTA 2021; 254:108. [PMID: 34694486 PMCID: PMC8545783 DOI: 10.1007/s00425-021-03755-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH. Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant.
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Affiliation(s)
- Rakesh K Upadhyay
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.
| | - Jonathan Shao
- Bioinformatics-North East Area Office, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.
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23
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Kang Y, Liu W, Guan C, Guan M, He X. Evolution and functional diversity of lipoxygenase (LOX) genes in allotetraploid rapeseed (Brassica napus L.). Int J Biol Macromol 2021; 188:844-854. [PMID: 34416264 DOI: 10.1016/j.ijbiomac.2021.08.082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023]
Abstract
Lipoxygenase (LOX, EC 1.13.11.12) is a non-haeme iron-containing dioxygenase family that catalyzes the oxygenation of polyunsaturated fatty acids into bio-functionally fatty acid diverse (oxylipins) and plays vital role in plant growth and development and responses to abiotic and biotic stresses. Though LOX genes have been studied in many plant species, their roles in Brassicaceae species are still unknown. Here, a set of 14, 18, and 33 putative LOX genes were identified in Brassica rapa, Brassica oleracea and Brassica napus (allotetraploid rapeseed), respectively, which could be divided into 9-LOX (LOX1/5), 13-LOX type I (LOX3/4/6), and type II (LOX2) subgroups. There was an expansion of LOX2 orthologous genes in Brassicaceae. Most of the LOX genes are intron rich and conserved in gene structure, and the LOX proteins all have the conserved lipoxygenase and PLAT/LH2 domain. Ka/Ks ratio revealed that the majority of LOXs underwent purifying selection in Brassicaceae. The light-, ABA-, MeJA-related cis-elements and MYB-binding sites in the promoters of BnaLOXs were the most abundant. BnaLOXs displayed different spatiotemporal expression patterns and various abiotic/biotic stress responsive expression patterns. BnaLOX1/5 were slightly or no response to phytohormones and abiotic stresses. BnaLOX3/4/6 predominantly express in roots and were strongly up-regulated by salinity and PEG treatments, and BnaLOX3/4 were the methyl jasmonate (MeJA) and salicylic acid (SA) early response genes and strongly induced by infection of Sclerotinia sclerotiorum; while the BnaLOX2 members predominantly express in stamens, were MeJA and SA continuous response genes and strongly repressed by cold, heat and waterlogging treatments in leaves. Our results are useful for understanding the biological functions of the BnaLOX genes in allotetraploid rapeseed.
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Affiliation(s)
- Yu Kang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wei Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Mei Guan
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Xin He
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
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24
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Lv G, Tian Q, Zhang F, Chen J, Niaz M, Liu C, Hu H, Sun C, Chen F. Reduced expression of lipoxygenase genes improves flour processing quality in soft wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6247-6259. [PMID: 34097731 DOI: 10.1093/jxb/erab264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
Lipoxygenases (Loxs) are dioxygenases that play an important role in plant growth and defense. Loxs affect flour processing quality in common wheat (Triticum aestivum). We conducted a genome-wide association study (GWAS) that identified 306 significant single-nucleotide polymorphisms (SNPs) related to Lox activity in Chinese wheat accessions. Among them, a novel lipoxygenase-encoding (Lpx) gene, TaLpx-B4, was detected on chromosome 3B in a biparental population. Analysis of mutant wheat lines induced using ethyl methanesulfonate confirmed the role of TaLpx-B4 in modulating Lox activity. A phylogenetic tree of various plant Lpx genes indicated the predominance of the 9-Lpx type in common wheat. Further analysis revealed conserved intron number, exon length, and motif number in the TaLpx gene family. GWAS, linkage mapping, and gene annotation collectively showed that 14 out of 29 annotated TaLpx genes played a critical role in regulating Lox activity in the Chinese wheat accessions. Transgenic wheat grains with knockdown of Lpx family genes by RNAi showed significantly lower Lox activity than the wild type. One TaLpx-RNAi line had significantly reduced starch content and dough stability, and thus possessed relatively superior biscuit quality in soft wheat. Further analysis of the transcriptome, lipid components, and other metabolites revealed that knockdown of TaLpx genes significantly increased biscuit quality via changes in unsaturated fatty acid content as well as in starch, sucrose, and galactose metabolism. Our results provide new insights into the role of the TaLpx gene family that will be beneficial in improving soft wheat flour quality.
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Affiliation(s)
- Guoguo Lv
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Qiuzhen Tian
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Fuyan Zhang
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jianhui Chen
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Mohsin Niaz
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Chunyi Liu
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Huiting Hu
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Congwei Sun
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- CIMMYT-China Joint Center of Wheat and Maize Improvement / National Key Laboratory of Wheat and Maize Crop Science / Agronomy College, Henan Agricultural University, Zhengzhou, China
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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana. Sci Rep 2021; 11:9948. [PMID: 33976263 PMCID: PMC8113564 DOI: 10.1038/s41598-021-89211-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 01/19/2023] Open
Abstract
The LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.
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Bhunia RK, Sinha K, Kaur R, Kaur S, Chawla K. A Holistic View of the Genetic Factors Involved in Triggering Hydrolytic and Oxidative Rancidity of Rice Bran Lipids. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1915328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Rupam Kumar Bhunia
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
| | - Kshitija Sinha
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
- Department of Biotechnology, Sector-25, Panjab University, Chandigarh, India
| | - Ranjeet Kaur
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sumandeep Kaur
- Department of Biotechnology, Sector-25, Panjab University, Chandigarh, India
| | - Kirti Chawla
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
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Shrestha K, Pant S, Huang Y. Genome-wide identification and classification of Lipoxygenase gene family and their roles in sorghum-aphid interaction. PLANT MOLECULAR BIOLOGY 2021; 105:527-541. [PMID: 33387173 DOI: 10.1007/s11103-020-01107-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 05/29/2023]
Abstract
This report shows detailed characterization of LOX gene family in sorghum and provides new insight of sorghum LOX genes in genetic structure and their roles in plant response to infestation by sugarcane aphids. Lipoxygenases (LOXs) are monomeric, nonheme iron-containing dioxygenases that initiate the fatty acid oxidation pathway creating oxylipins and plant hormone jasmonate both have a key role in plant development and defense. To date, a comprehensive and systematic analysis of sorghum LOXs is still deficient. Thus, we performed a genome-wide analysis of the sorghum LOXs genome and identified nine LOXs genes. Detailed examination of protein sequences and phylogenetic analysis categorized the sorghum LOXs into two subclasses, 9-LOXs (SbLOX1, SbLOX3, SbLOX4, SbLOXm, and SbLOXo), 13-LOXs (SbLOX9, SbLOX5, and SbLOX2), and the unclassified SbLOX8. This classification was further supported by sequence similarity/identity matrix and subcellular localization analysis. The lipoxygenase domains, motifs, and vital amino acids were highly conserved in all sorghum LOX genes. In silico analysis of the promoter region of SbLOXs identified different hormones responsive cis-elements. Furthermore, to explore the roles of sorghum LOXs during sugarcane aphid feeding and exogenous MeJA application, expression analysis was conducted for all the eight LOXs in resistant (Tx2783) and susceptible (Tx7000) sorghum lines, respectively. As detailed in this report, the data generated from both genome-wide identification and expression analysis of lipoxygenase genes suggest the putative functions of two 13-LOXs (SbLOX9 and SbLOX5) and three 9-LOXs (SbLOX1, SbLOX3, and SbLOXo) in biosynthesis of jasmonic acid, green leaf volatiles and death acids, and all of them are involved in defense-related functions in plants. Furthermore, this report represents the first genome-wide analysis of the LOX gene family in sorghum, which will facilitate future studies to characterize the roles of each individual LOXs gene in aphid resistance and defense responses to other stresses.
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Affiliation(s)
- Kumar Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Shankar Pant
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Laboratory, USDA-ARS), Stillwater, OK, 74075, USA
| | - Yinghua Huang
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA.
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Laboratory, USDA-ARS), Stillwater, OK, 74075, USA.
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28
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Upadhyay RK, Edelman M, Mattoo AK. Identification, Phylogeny, and Comparative Expression of the Lipoxygenase Gene Family of the Aquatic Duckweed, Spirodela polyrhiza, during Growth and in Response to Methyl Jasmonate and Salt. Int J Mol Sci 2020; 21:E9527. [PMID: 33333747 PMCID: PMC7765210 DOI: 10.3390/ijms21249527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
Lipoxygenases (LOXs) (EC 1.13.11.12) catalyze the oxygenation of fatty acids and produce oxylipins, including the plant hormone jasmonic acid (JA) and its methyl ester, methyl jasmonate (MeJA). Little information is available about the LOX gene family in aquatic plants. We identified a novel LOX gene family comprising nine LOX genes in the aquatic plant Spirodela polyrhiza (greater duckweed). The reduced anatomy of S. polyrhiza did not lead to a reduction in LOX family genes. The 13-LOX subfamily, with seven genes, predominates, while the 9-LOX subfamily is reduced to two genes, an opposite trend from known LOX families of other plant species. As the 13-LOX subfamily is associated with the synthesis of JA/MeJA, its predominance in the Spirodela genome raises the possibility of a higher requirement for the hormone in the aquatic plant. JA-/MeJA-based feedback regulation during culture aging as well as the induction of LOX gene family members within 6 h of salt exposure are demonstrated.
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Affiliation(s)
- Rakesh K. Upadhyay
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA
| | - Marvin Edelman
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Autar K. Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA
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29
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Ji Q, Zhang T, Zhang D, Lv S, Tan A. Genome-wide identification and expression analysis of lipoxygenase genes in Tartary buckwheat. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1738956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Qiqi Ji
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering(CICMEAB), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, PR China
| | - Tianyuan Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering(CICMEAB), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, PR China
- National Data Center of Traditional Chinese Medicine of China, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Dong Zhang
- Chemical Laboratory, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Shiming Lv
- Basic Veterinary Laboratory, College of Animal Science, Guizhou University, Guiyang, Guizhou, PR China
| | - Aijuan Tan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering(CICMEAB), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, PR China
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Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K. Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. Sci Rep 2020; 10:683. [PMID: 31959799 PMCID: PMC6971257 DOI: 10.1038/s41598-020-57499-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/21/2019] [Indexed: 01/03/2023] Open
Abstract
Rice bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) implies substantial yield loss to rice. In times of climate change, increasing temperatures are observed and further acceleration is expected worldwide. Increasing temperature often turns into inhibition of host plant defense to pathogens. Recently, a reduced resistance in rice IRBB4 carrying Xa4, but an increase in resistance in IRBB7 carrying Xa7 resistance by increasing temperature has been reported. Influence of high temperature on both R genes (Xa4+Xa7) combined in IRBB67 was analyzed under growth chamber conditions and transcriptomic analysis performed. The pyramided line IRBB67 showed no differences in lesion length between both temperature regimes, demonstrating that non-effectiveness of Xa4 at high temperature did not affect IRBB67 resistance. Moreover, Xa4 complements Xa7 resistance with no Xoo spread in planta beyond the symptomatic area under both temperature regimes in IRBB67. Time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartments and point at a role of the cell wall involved in Xoo resistance and heat stress tolerance in both susceptible (IR24) and the resistant (IRBB67) NILs. Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature which may have enhanced its resistance. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plants cope with combined biotic and abiotic stresses.
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Affiliation(s)
- Gerbert Sylvestre Dossa
- International Rice Research Institute, Los Baños, Philippines.
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany.
- Food and Agriculture Organization, Sub Regional Office for Central Africa, PO. Box 2643, Libreville, Gabon.
| | - Ian Quibod
- International Rice Research Institute, Los Baños, Philippines
| | - Genelou Atienza-Grande
- International Rice Research Institute, Los Baños, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Edgar Maiss
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | | | - Kerstin Wydra
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
- Plant Production and Climate Change, Erfurt University of Applied Sciences, Erfurt, Germany
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31
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Dhanapal AP, York LM, Hames KA, Fritschi FB. Genome-Wide Association Study of Topsoil Root System Architecture in Field-Grown Soybean [ Glycine max (L.) Merr.]. FRONTIERS IN PLANT SCIENCE 2020; 11:590179. [PMID: 33643326 PMCID: PMC7902768 DOI: 10.3389/fpls.2020.590179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 05/09/2023]
Abstract
Water and nutrient acquisition is a critical function of plant root systems. Root system architecture (RSA) traits are often complex and controlled by many genes. This is the first genome-wide association study reporting genetic loci for RSA traits for field-grown soybean (Glycine max). A collection of 289 soybean genotypes was grown in three environments, root crowns were excavated, and 12 RSA traits assessed. The first two components of a principal component analysis of these 12 traits were used as additional aggregate traits for a total of 14 traits. Marker-trait association for RSA traits were identified using 31,807 single-nucleotide polymorphisms (SNPs) by a genome-wide association analysis. In total, 283 (non-unique) SNPs were significantly associated with one or more of the 14 root traits. Of these, 246 were unique SNPs and 215 SNPs were associated with a single root trait, while 26, four, and one SNPs were associated with two, three, and four root traits, respectively. The 246 SNPs marked 67 loci associated with at least one of the 14 root traits. Seventeen loci on 13 chromosomes were identified by SNPs associated with more than one root trait. Several genes with annotation related to processes that could affect root architecture were identified near these 67 loci. Additional follow-up studies will be needed to confirm the markers and candidate genes identified for RSA traits and to examine the importance of the different root characteristics for soybean productivity under a range of soil and environmental conditions.
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Affiliation(s)
| | - Larry M. York
- Noble Research Institute, LLC, Ardmore, OK, United States
| | - Kasey A. Hames
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Felix B. Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
- *Correspondence: Felix B. Fritschi
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Bioinformatics Analysis of the Lipoxygenase Gene Family in Radish ( Raphanus sativus) and Functional Characterization in Response to Abiotic and Biotic Stresses. Int J Mol Sci 2019; 20:ijms20236095. [PMID: 31816887 PMCID: PMC6928601 DOI: 10.3390/ijms20236095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in many developmental and stress-responsive processes in plants. However, little is known about the radish LOX gene family members and their functions in response to biotic and abiotic stresses. In this study, we completed a genome-wide analysis and expression profiling of RsLOX genes under abiotic and biotic stress conditions. We identified 11 RsLOX genes, which encoded conserved domains, and classified them in 9-LOX and 13-LOX categories according to their phylogenetic relationships. The characteristic structural features of 9-LOX and 13-LOX genes and the encoded protein domains as well as their evolution are presented herein. A qRT-PCR analysis of RsLOX expression levels in the roots under simulated drought, salinity, heat, and cold stresses, as well as in response to a Plasmodiophora brassicae infection, revealed three tandem-clustered RsLOX genes that are involved in responses to various environmental stresses via the jasmonic acid pathway. Our findings provide insights into the evolution and potential biological roles of RsLOXs related to the adaptation of radish to stress conditions.
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Sarde SJ, Bouwmeester K, Venegas‐Molina J, David A, Boland W, Dicke M. Involvement of sweet pepper CaLOX2 in jasmonate-dependent induced defence against Western flower thrips. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1085-1098. [PMID: 30450727 PMCID: PMC6850143 DOI: 10.1111/jipb.12742] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/12/2018] [Indexed: 05/25/2023]
Abstract
Insect herbivory can seriously hinder plant performance and reduce crop yield. Thrips are minute cell-content-feeding insects that are important vectors of viral plant pathogens, and are serious crop pests. We investigated the role of a sweet pepper (Capsicum annuum) lipoxygenase gene, CaLOX2, in the defense of pepper plants against Western flower thrips (Frankliniella occidentalis). This was done through a combination of in-silico, transcriptional, behavioral and chemical analyses. Our data show that CaLOX2 is involved in jasmonic acid (JA) biosynthesis and mediates plant resistance. Expression of the JA-related marker genes, CaLOX2 and CaPIN II, was induced by thrips feeding. Silencing of CaLOX2 in pepper plants through virus-induced gene silencing (VIGS) resulted in low levels of CaLOX2 transcripts, as well as significant reduction in the accumulation of JA, and its derivatives, upon thrips feeding compared to control plants. CaLOX2-silenced pepper plants exhibited enhanced susceptibility to thrips. This indicates that CaLOX2 mediates JA-dependent signaling, resulting in defense against thrips. Furthermore, exogenous application of JA to pepper plants increased plant resistance to thrips, constrained thrips population development and made plants less attractive to thrips. Thus, a multidisciplinary approach shows that an intact lipoxygenase pathway mediates various components of sweet pepper defense against F. occidentalis.
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Affiliation(s)
- Sandeep J Sarde
- Laboratory of EntomologyWageningen UniversityP.O. Box 166700 AA WageningenThe Netherlands
| | - Klaas Bouwmeester
- Laboratory of PhytopathologyWageningen UniversityP.O. Box 166700 AA, WageningenThe Netherlands
| | - Jhon Venegas‐Molina
- Laboratory of EntomologyWageningen UniversityP.O. Box 166700 AA WageningenThe Netherlands
| | - Anja David
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745 JenaGermany
| | - Wilhelm Boland
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745 JenaGermany
| | - Marcel Dicke
- Laboratory of EntomologyWageningen UniversityP.O. Box 166700 AA WageningenThe Netherlands
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Upadhyay RK, Handa AK, Mattoo AK. Transcript Abundance Patterns of 9- and 13-Lipoxygenase Subfamily Gene Members in Response to Abiotic Stresses (Heat, Cold, Drought or Salt) in Tomato ( Solanum lycopersicum L .) Highlights Member-Specific Dynamics Relevant to Each Stress. Genes (Basel) 2019; 10:genes10090683. [PMID: 31492025 PMCID: PMC6771027 DOI: 10.3390/genes10090683] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/31/2022] Open
Abstract
Lipoxygenases (LOXs; EC 1.13.11.12) catalyze the oxygenation of fatty acids to produce oxylipins including the jasmonate family of plant hormones. The involvement of jasmonates in plant growth and development and during abiotic stress has been documented, however, the response and regulation of each member of the LOX gene family under various abiotic stresses is yet to be fully deciphered. Previously, we identified fourteen members of the tomato LOX gene family, which were divisible into nine genes representing the 9-LOX family members and five others representing the 13-LOX family members based on the carbon oxidation position specificity of polyunsaturated fatty acids. Here, we have determined the transcript abundance patterns of all the 14 LOX genes in response to four independent abiotic stresses, namely, heat, cold, drought and salt. Our results show that each of these stresses leads to a time-dependent, variable or indifferent response of specific and different set(s) of LOX gene members of both subfamilies, differentiating functional relevance of the 14 LOX genes analyzed. Out of the 14 gene members, three LOX genes were expressed constitutively or were non-responsive to either heat (SlLOX9), cold (SlLOX9) or salt (SlLOX4) stress. An in-silico LOX gene promoter search for stress-responsive elements revealed that only some but not all of the LOX genes indeed are decorated with specific and known stress responsive cis-acting elements. Thus, these data implicate some other, yet to be discovered, cis-acting elements present in the LOX gene family members, which seemingly regulate tomato responses to defined abiotic stresses presented here.
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Affiliation(s)
- Rakesh K Upadhyay
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA.
- Department of Horticulture and Landscape Architecture, Purdue University, W. Lafayette, IN 47907-2010, USA.
| | - Avtar K Handa
- Department of Horticulture and Landscape Architecture, Purdue University, W. Lafayette, IN 47907-2010, USA.
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA.
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Berni R, Cai G, Xu X, Hausman JF, Guerriero G. Identification of Jasmonic Acid Biosynthetic Genes in Sweet Cherry and Expression Analysis in Four Ancient Varieties from Tuscany. Int J Mol Sci 2019; 20:E3569. [PMID: 31336562 PMCID: PMC6678830 DOI: 10.3390/ijms20143569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022] Open
Abstract
Sweet cherries are non-climacteric fruits whose early development is characterized by high levels of the phytohormone jasmonic acid (JA). Important parameters, such as firmness and susceptibility to cracking, can be affected by pre- and postharvest treatments of sweet cherries with JA. Despite the impact of JA on sweet cherry development and fruit characteristics, there are no studies (to the best of our knowledge) identifying the genes involved in the JA biosynthetic pathway in this species. We herein identify the sweet cherry members of the lipoxygenase family (13-LOX); allene oxide synthase, allene oxide cyclase and 12-oxo-phytodienoic acid reductase 3, as well as genes encoding the transcriptional master regulator MYC2. We analyze their expression pattern in four non-commercial Tuscan varieties ('Carlotta', 'Maggiola', 'Morellona', 'Crognola') having different levels of bioactives (namely phenolics). The highest differences are found in two genes encoding 13-LOX in the variety 'Maggiola' and one MYC2 isoform in 'Morellona'. No statistically-significant variations are instead present in the allene oxide synthase, allene oxide cyclase and 12-oxo-phytodienoic acid reductase 3. Our data pave the way to follow-up studies on the JA signaling pathway in these ancient varieties, for example in relation to development and post-harvest storage.
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Affiliation(s)
- Roberto Berni
- University of Siena, Department of Life Sciences, via P.A. Mattioli 4, 53100 Siena, Italy
- Trees and timber institute-National research council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy
| | - Giampiero Cai
- University of Siena, Department of Life Sciences, via P.A. Mattioli 4, 53100 Siena, Italy
| | - Xuan Xu
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Jean-Francois Hausman
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Gea Guerriero
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
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36
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Akbudak MA, Filiz E. Genome-wide analyses of ATP sulfurylase (ATPS) genes in higher plants and expression profiles in sorghum (Sorghum bicolor) under cadmium and salinity stresses. Genomics 2019; 111:579-589. [DOI: 10.1016/j.ygeno.2018.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/06/2018] [Accepted: 03/12/2018] [Indexed: 01/15/2023]
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Tandem 13-Lipoxygenase Genes in a Cluster Confers Yellow-Green Leaf in Cucumber. Int J Mol Sci 2019; 20:ijms20123102. [PMID: 31242619 PMCID: PMC6628033 DOI: 10.3390/ijms20123102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
Some lipoxygenase (LOX) isoenzymes can co-oxidize carotenoids. Carotenoids are collectors of light energy for photosynthesis and can protect plants from reactive oxygen species and coloration. This study isolated the cucumber (Cucumis sativus L.) yellow-green leaf mutant (ygl1), which had yellow-green leaves with decreased chlorophyll synthesis, increased relative carotenoid content, and delayed chloroplast development. Genetic analysis demonstrated that the phenotype of ygl1 was caused by a recessive mutation in a nuclear gene. The bulked segregants were resequenced, and the candidate ygl1 locus identified was mapped to the 9.2 kb region of the chromosome 4. Sequence analysis revealed that ygl1 encodes the tandem 13-LOX genes in a cluster. Four missense mutations were found in four tandem 13-LOX genes (Csa4M286960, Csa4M287550, Csa4M288070, and Csa4M288080) in the ygl1 mutant, and the four 13-LOX genes showed high similarity with one another. The transient RNA interference and virus-induced gene silencing of these genes simultaneously resulted in yellow-green leaves with a reduced amount of chloroplasts and increased relative carotenoid content, which were observed in the ygl1 mutant. This evidence supported the non-synonymous SNPs (Single Nucleotide Polymorphism) in the four tandem 13-LOX genes as being the causative mutation for the yellow-green leaves. Furthermore, this study provides a new allele for breeding cucumbers with yellow-green leaves and serves as an additional resource for studying carotenoid biosynthesis.
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38
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Development of expressed sequenced tags (EST) to identify some pathogen resistance genes expressed in Gossypium arboreum. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Li T, Wang YH, Liu JX, Feng K, Xu ZS, Xiong AS. Advances in genomic, transcriptomic, proteomic, and metabolomic approaches to study biotic stress in fruit crops. Crit Rev Biotechnol 2019; 39:680-692. [DOI: 10.1080/07388551.2019.1608153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Zhou B, Liu J, Kang R, Klionsky DJ, Kroemer G, Tang D. Ferroptosis is a type of autophagy-dependent cell death. Semin Cancer Biol 2019; 66:89-100. [PMID: 30880243 DOI: 10.1016/j.semcancer.2019.03.002] [Citation(s) in RCA: 556] [Impact Index Per Article: 111.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Macroautophagy (hereafter referred to as autophagy) involves an intracellular degradation and recycling system that, in a context-dependent manner, can either promote cell survival or accelerate cellular demise. Ferroptosis was originally defined in 2012 as an iron-dependent form of cancer cell death different from apoptosis, necrosis, and autophagy. However, this latter assumption came into question because, in response to ferroptosis activators (e.g., erastin and RSL3), autophagosomes accumulate, and because components of the autophagy machinery (e.g., ATG3, ATG5, ATG4B, ATG7, ATG13, and BECN1) contribute to ferroptotic cell death. In particular, NCOA4-facilitated ferritinophagy, RAB7A-dependent lipophagy, BECN1-mediated system xc- inhibition, STAT3-induced lysosomal membrane permeabilization, and HSP90-associated chaperone-mediated autophagy can promote ferroptosis. In this review, we summarize current knowledge on the signaling pathways involved in ferroptosis, while focusing on the regulation of autophagy-dependent ferroptotic cell death. The molecular comprehension of these phenomena may lead to the development of novel anticancer therapies.
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Affiliation(s)
- Borong Zhou
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510150, China.
| | - Jiao Liu
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510150, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France; Université Pierre et Marie Curie, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France; Department of Women's and Children's Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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41
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Upadhyay RK, Mattoo AK. Genome-wide identification of tomato (Solanum lycopersicum L.) lipoxygenases coupled with expression profiles during plant development and in response to methyl-jasmonate and wounding. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:318-328. [PMID: 30368230 DOI: 10.1016/j.jplph.2018.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 05/20/2023]
Abstract
Lipoxygenases (LOXs) (EC 1.13.11.12) catalyze the oxygenation of fatty acids and produce oxylipins including the plant hormone jasmonate (jasmonic acid/methyl jasmonate; MeJA). Little is known about the tomato LOX gene family members that impact tomato growth and development, and less so about their feed-back regulation in response to MeJA. We present genome wide identification of 14 LOX gene family members in tomato which map unevenly on 12 chromosomes. The characteristic structural features of 9-LOX and 13-LOX tomato gene family, their protein domains/features, and divergence are presented. Quantification of the expression patterns of all the 14 SlLOX gene members segregated the members based on differential association with growth, development, or fruit ripening. We also identified those SlLOX genes whose transcription responds to exogenous MeJA and/or wounding stress. MeJA-based feedback regulation that involves activation of specific members of LOX genes is defined. Specific nature of SlLOX gene regulation in tomato is defined. The novel data on dynamics of SlLOX gene expression should help catalyze future strategies to elucidate role(s) of each gene member in planta and for crop biotechnological intervention.
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Affiliation(s)
- Rakesh K Upadhyay
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA.
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA.
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42
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Sarde SJ, Kumar A, Remme RN, Dicke M. Genome-wide identification, classification and expression of lipoxygenase gene family in pepper. PLANT MOLECULAR BIOLOGY 2018; 98:375-387. [PMID: 30317456 PMCID: PMC6244800 DOI: 10.1007/s11103-018-0785-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/05/2018] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Lipoxygenases mediate important biological processes. Through comparative genomics, domain-scan analysis, sequence analysis, phylogenetic analysis, homology modelling and transcriptional analysis the lipoxygenase gene family of pepper (Capsicum annuum) has been identified. Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases playing a pivotal role in diverse biological processes in plants, including defence and development. Here, we exploited the recent sequencing of the pepper genome to investigate the LOX gene family in pepper. Two LOX classes are recognized, the 9- and 13-LOXs that oxygenate lipids at the 9th and 13th carbon atom, respectively. Using two main in-silico approaches, we identified a total of eight LOXs in pepper. Phylogenetic analysis classified four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Furthermore, sequence similarity/identity and subcellular localization analysis strengthen the classification predicted by phylogenetic analysis. Pivotal amino acids together with all domains and motifs are highly conserved in all pepper LOXs. Expression of 13-LOXs appeared to be more dynamic compared to 9-LOXs both in response to exogenous JA application and to thrips feeding. Bioinformatic and expression analyses predict the putative functions of two 13-LOXs, CaLOX6 and CaLOX7, in the biosynthesis of Green Leaf Volatiles, involved in indirect defence. The data are discussed in the context of LOX families in solanaceous plants and plants of other families.
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Affiliation(s)
- Sandeep J Sarde
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Abhishek Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Rahima N Remme
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
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Shaban M, Ahmed MM, Sun H, Ullah A, Zhu L. Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses. BMC Genomics 2018; 19:599. [PMID: 30092779 PMCID: PMC6085620 DOI: 10.1186/s12864-018-4985-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/31/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited. RESULTS A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii)). In the phylogenetic tree, these genes were clustered into three categories (9-LOX, 13-LOX type I, and 13-LOX type II). Segmental duplication of putative LOX genes was observed between homologues from A2 to At and D5 to Dt hinting at allopolyploidy in cultivated tetraploid species (G. hirsutum and G. barbadense). The structure and motif composition of GhLOX genes appears to be relatively conserved among the subfamilies. Moreover, many cis-acting elements related to growth, stresses, and phytohormone signaling were found in the promoter regions of GhLOX genes. Gene expression analysis revealed that all GhLOX genes were induced in at least two tissues and the majority of GhLOX genes were up-regulated in response to heat and salinity stress. Specific expressions of some genes in response to exogenous phytohormones suggest their potential roles in regulating growth and stress responses. In addition, functional characterization of two candidate genes (GhLOX12 and GhLOX13) using virus induced gene silencing (VIGS) approach revealed their increased sensitivity to salinity stress in target gene-silenced cotton. Compared with controls, target gene-silenced plants showed significantly higher chlorophyll degradation, higher H2O2, malondialdehyde (MDA) and proline accumulation but significantly reduced superoxide dismutase (SOD) activity, suggesting their reduced ability to effectively degrade accumulated reactive oxygen species (ROS). CONCLUSION This genome-wide study provides a systematic analysis of the cotton LOX gene family using bioinformatics tools. Differential expression patterns of cotton LOX genes in different tissues and under various abiotic stress conditions provide insights towards understanding the potential functions of candidate genes. Beyond the findings reported here, our study provides a basis for further uncovering the biological roles of LOX genes in cotton development and adaptation to stress conditions.
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Affiliation(s)
- Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
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Conrad M, Kagan VE, Bayir H, Pagnussat GC, Head B, Traber MG, Stockwell BR. Regulation of lipid peroxidation and ferroptosis in diverse species. Genes Dev 2018; 32:602-619. [PMID: 29802123 PMCID: PMC6004068 DOI: 10.1101/gad.314674.118] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review by Conrad et al. reviews the functions and regulation of lipid peroxidation, ferroptosis, and the antioxidant network in diverse species, including humans, other mammals and vertebrates, plants, invertebrates, yeast, bacteria, and archaea, and discusses the potential evolutionary roles of lipid peroxidation and ferroptosis. Lipid peroxidation is the process by which oxygen combines with lipids to generate lipid hydroperoxides via intermediate formation of peroxyl radicals. Vitamin E and coenzyme Q10 react with peroxyl radicals to yield peroxides, and then these oxidized lipid species can be detoxified by glutathione and glutathione peroxidase 4 (GPX4) and other components of the cellular antioxidant defense network. Ferroptosis is a form of regulated nonapoptotic cell death involving overwhelming iron-dependent lipid peroxidation. Here, we review the functions and regulation of lipid peroxidation, ferroptosis, and the antioxidant network in diverse species, including humans, other mammals and vertebrates, plants, invertebrates, yeast, bacteria, and archaea. We also discuss the potential evolutionary roles of lipid peroxidation and ferroptosis.
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Affiliation(s)
- Marcus Conrad
- Institute of Developmental Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Valerian E Kagan
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Department of Environmental Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Laboratory of Navigational Lipidomics of Cell Death and Regeneration, I.M. Sechenov First Moscow State Medical University, Moscow 119992, Russia
| | - Hülya Bayir
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Brian Head
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97330.,Molecular and Cell Biology Graduate Program, Oregon State University, Corvallis, Oregon 97330, USA
| | - Maret G Traber
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97330.,College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon 97330, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Chemistry, Columbia University, New York, New York 10027, USA
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Scholz SS, Schmidt-Heck W, Guthke R, Furch ACU, Reichelt M, Gershenzon J, Oelmüller R. Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales. Front Microbiol 2018; 9:217. [PMID: 29497409 PMCID: PMC5819561 DOI: 10.3389/fmicb.2018.00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/30/2018] [Indexed: 01/27/2023] Open
Abstract
Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 h induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense- and stress-responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. After 3 weeks, severe disease symptoms can be detected for wild-type plants while mutants impaired in jasmonate synthesis and perception perform much better. Thus, plant jasmonates have an important influence on the interaction, which is already visible at the mRNA level before hormone changes occur. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.
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Affiliation(s)
- Sandra S Scholz
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wolfgang Schmidt-Heck
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
| | - Reinhard Guthke
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany
| | - Alexandra C U Furch
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
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Sheshadri SA, Nishanth MJ, Harita N, Brindha P, Bindu S. Comparative genome based cis-elements analysis in the 5' upstream and 3' downstream region of cell wall invertase and Phenylalanine ammonia lyase in Nicotiana benthamiana. Comput Biol Chem 2018; 72:181-191. [PMID: 29329783 DOI: 10.1016/j.compbiolchem.2017.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 10/12/2017] [Accepted: 11/11/2017] [Indexed: 11/18/2022]
Abstract
Plant secondary metabolites are widely used in human disease treatment; though primary metabolism provides precursors for secondary metabolism, not much has been studied to unravel the link connecting both the processes. Most common form of gene regulation interconnecting diverse metabolism occurs at the transcriptional and/or posttranscriptional level mediated by regulatory cis-elements. The present study aims at understanding the common cis-elements network connecting the major primary metabolic enzyme, cell wall invertase (CWIN) and secondary metabolism genes in Nicotiana benthamiana (N. benthamiana). The CWIN and thirty one other gene sequences were extracted from N. benthamiana genome, followed by cis-element analysis of their 5' upstream and 3' downstream region using different programs (Genomatix software suite; PLACE and PlantCARe). Comparative cis-element analysis of CWIN (N. benthamiana and other plant species) and other primary, secondary metabolism and transcription factor genes (N. benthamiana) revealed the occurrence of common stress associated cis-elements. Predominantly, AHBP, L1BX, MYBL, MADS, MYBS, GTBX, DOFF and CCAF were found in the 5' upstream region of all genes, whereas AHBP, MYBL, L1BX, HEAT, CCAF and KAN1 were largely occurring in the 3' downstream region of all genes; indicating common function of these elements in transcriptional and posttranscriptional gene regulation. Further, genomic analysis using FGENESH, GenScan and homology based methods (BlastX and BlastN) was performed on the N. benthamiana contigs harboring CWIN and PAL, in an attempt to identify genomic neighborhood genes. The 5' upstream and 3' downstream region of genes in the genomic neighborhood of CWIN and PAL were also subjected to similar cis-element analysis, and the results indicated cis-elements profile similar to CWIN, PAL and other primary, secondary metabolism and transcription factor genes. The results of evolutionary studies confirmed that the 5' upstream region of NbCWINs significantly showed more proximity to secondary metabolism genes 4CL and the redox gene SOD, followed by the phenylpropanoid pathway gene CHI. The 3' downstream regions of NbCWINs were more closely related to other plant CWINs, followed by the redox gene, SOD and primary metabolism gene FBA. Thus, the commonly found stress responsive cis-elements in our study can play a vital role in modulating key pathways of both primary and secondary metabolism; thereby postulating their role in regulating plant growth and metabolisms under unfavourable growth conditions.
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Affiliation(s)
- S A Sheshadri
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - M J Nishanth
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - N Harita
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - P Brindha
- Centre for Advanced Research in Indian System of Medicine (CARISM), SASTRA University, Thanjavur, 613401 India
| | - S Bindu
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India.
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Calingacion M, Mumm R, Tan K, Quiatchon-Baeza L, Concepcion JCT, Hageman JA, Prakash S, Fitzgerald M, Hall RD. A Multidisciplinary Phenotyping and Genotyping Analysis of a Mapping Population Enables Quality to Be Combined with Yield in Rice. Front Mol Biosci 2017; 4:32. [PMID: 28589124 PMCID: PMC5438996 DOI: 10.3389/fmolb.2017.00032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/04/2017] [Indexed: 12/21/2022] Open
Abstract
In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography—Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher) yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.
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Affiliation(s)
- Mariafe Calingacion
- Grain Quality and Nutrition Centre, International Rice Research InstituteLaguna, Philippines.,Laboratory of Plant Physiology, Wageningen University and ResearchWageningen, Netherlands
| | - Roland Mumm
- Wageningen Plant Research, Wageningen University and ResearchWageningen, Netherlands.,Netherlands Metabolomics CentreLeiden, Netherlands
| | - Kevin Tan
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Lenie Quiatchon-Baeza
- Grain Quality and Nutrition Centre, International Rice Research InstituteLaguna, Philippines
| | - Jeanaflor C T Concepcion
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Jos A Hageman
- Biometris, Wageningen University and ResearchWageningen, Netherlands
| | - Sangeeta Prakash
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Melissa Fitzgerald
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Robert D Hall
- Laboratory of Plant Physiology, Wageningen University and ResearchWageningen, Netherlands.,Wageningen Plant Research, Wageningen University and ResearchWageningen, Netherlands.,Netherlands Metabolomics CentreLeiden, Netherlands
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48
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Borrego EJ, Kolomiets MV. Synthesis and Functions of Jasmonates in Maize. PLANTS (BASEL, SWITZERLAND) 2016; 5:E41. [PMID: 27916835 PMCID: PMC5198101 DOI: 10.3390/plants5040041] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 02/02/2023]
Abstract
Of the over 600 oxylipins present in all plants, the phytohormone jasmonic acid (JA) remains the best understood in terms of its biosynthesis, function and signaling. Much like their eicosanoid analogues in mammalian system, evidence is growing for the role of the other oxylipins in diverse physiological processes. JA serves as the model plant oxylipin species and regulates defense and development. For several decades, the biology of JA has been characterized in a few dicot species, yet the function of JA in monocots has only recently begun to be elucidated. In this work, the synthesis and function of JA in maize is presented from the perspective of oxylipin biology. The maize genes responsible for catalyzing the reactions in the JA biosynthesis are clarified and described. Recent studies into the function of JA in maize defense against insect herbivory, pathogens and its role in growth and development are highlighted. Additionally, a list of JA-responsive genes is presented for use as biological markers for improving future investigations into JA signaling in maize.
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Affiliation(s)
- Eli J Borrego
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA.
| | - Michael V Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA.
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50
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Sheshadri SA, Nishanth MJ, Simon B. Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta. FRONTIERS IN PLANT SCIENCE 2016; 7:1725. [PMID: 27933071 PMCID: PMC5122738 DOI: 10.3389/fpls.2016.01725] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/02/2016] [Indexed: 05/07/2023]
Abstract
Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants.
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Affiliation(s)
| | | | - Bindu Simon
- School of Chemical and Biotechnology, SASTRA UniversityThanjavur, India
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