1
|
Parakkunnel R, K BN, Vanishree G, George A, Kv S, Yr A, K UB, Anandan A, Kumar S. Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops. BMC Genomics 2024; 25:653. [PMID: 38956471 PMCID: PMC11218257 DOI: 10.1186/s12864-024-10527-4] [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: 02/12/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Oil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism providing energy to the germinating seeds. Major LD-associated proteins are lipoxygenases, phospholipaseD, oleosins, TAG-lipases, steroleosins, caleosins and SEIPINs; involved in facilitating germination and enhancing peroxidation resulting in off-flavours. However, how natural selection is balancing contradictory processes in lipid-rich seeds remains evasive. The present study was aimed at the prediction of selection signatures among orthologous clades in major oilseeds and the correlation of selection effect with gene expression. RESULTS The LD-associated genes from the major oil-bearing crops were analyzed to predict natural selection signatures in phylogenetically close-knit ortholog clusters to understand adaptive evolution. Positive selection was the major force driving the evolution and diversification of orthologs in a lineage-specific manner. Significant positive selection effects were found in 94 genes particularly in oleosin and TAG-lipases, purifying with excess of non-synonymous substitution in 44 genes while 35 genes were neutral to selection effects. No significant selection impact was noticed in Brassicaceae as against LOX genes of oil palm. A heavy load of deleterious mutations affecting selection signatures was detected in T-lineage oleosins and LOX genes of Arachis hypogaea. The T-lineage oleosin genes were involved in mainly anther, tapetum and anther wall morphogenesis. In Ricinus communis and Sesamum indicum > 85% of PLD genes were under selection whereas selection pressures were low in Brassica juncea and Helianthus annuus. Steroleosin, caleosin and SEIPINs with large roles in lipid droplet organization expressed mostly in seeds and were under considerable positive selection pressures. Expression divergence was evident among paralogs and homeologs with one gene attaining functional superiority compared to the other. The LOX gene Glyma.13g347500 associated with off-flavor was not expressed during germination, rather its paralog Glyma.13g347600 showed expression in Glycine max. PLD-α genes were expressed on all the tissues except the seed,δ genes in seed and meristem while β and γ genes expressed in the leaf. CONCLUSIONS The genes involved in seed germination and lipid metabolism were under strong positive selection, although species differences were discernable. The present study identifies suitable candidate genes enhancing seed oil content and germination wherein directional selection can become more fruitful.
Collapse
Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India.
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Anjitha George
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sripathy Kv
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Aruna Yr
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - A Anandan
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, 275103, Uttar Pradesh, India
| |
Collapse
|
2
|
Zhang Y, Zhao Z, Liu Z, Yao J, Yin K, Yan C, Zhang Y, Liu J, Li J, Zhao N, Zhao R, Zhou X, Chen S. Populus euphratica PeNADP-ME interacts with PePLDδ to mediate sodium and ROS homeostasis under salinity stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108600. [PMID: 38593488 DOI: 10.1016/j.plaphy.2024.108600] [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: 10/12/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Populus euphratica phospholipase Dδ (PePLDδ) is transcriptionally regulated and mediates reactive oxygen species (ROS) and ion homeostasis under saline conditions. The purpose of this study is to explore the post-transcriptional regulation of PePLDδ in response to salt environment. P. euphratica PePLDδ was shown to interact with the NADP-dependent malic enzyme (NADP-ME) by screening the yeast two-hybrid libraries. The transcription level of PeNADP-ME increased upon salt exposure to NaCl (200 mM) in leaves and roots of P. euphratica. PeNADP-ME had a similar subcellular location with PePLDδ in the cytoplasm, and the interaction between PeNADP-ME and PePLDδ was further verified by GST pull-down and yeast two-hybrid. To clarify whether PeNADP-ME interacts with PePLDδ to enhance salt tolerance, PePLDδ and PeNADP-ME were overexpressed singly or doubly in Arabidopsis thaliana. Dual overexpression of PeNADP-ME and PePLDδ resulted in an even more pronounced improvement in salt tolerance compared with single transformants overexpressing PeNADP-ME or PePLDδ alone. Greater Na+ limitation and Na+ efflux in roots were observed in doubly overexpressed plants compared with singly overexpressed plants with PeNADP-ME or PePLDδ. Furthermore, NaCl stimulation of SOD, APX, and POD activity and transcription were more remarkable in the doubly overexpressed plants. It is noteworthy that the enzymic activity of NADP-ME and PLD, and total phosphatidic acid (PA) concentrations were significantly higher in the double-overexpressed plants than in the single transformants. We conclude that PeNADP-ME interacts with PePLDδ in Arabidopsis to promote PLD-derived PA signaling, conferring Na+ extrusion and ROS scavenging under salt stress.
Collapse
Affiliation(s)
- Ying Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ziyan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhe Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Kexin Yin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Caixia Yan
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanli Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jian Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jing Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Nan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Rui Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoyang Zhou
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shaoliang Chen
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
3
|
Guo X, Zhu W, Wang F, Wang H. Genome-Wide Investigation of the PLD Gene Family in Tomato: Identification, Analysis, and Expression. Genes (Basel) 2024; 15:326. [PMID: 38540385 PMCID: PMC10970076 DOI: 10.3390/genes15030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Phospholipase Ds (PLDs) are important phospholipid hydrolases in plants that play crucial roles in the regulation of plant growth, development, and stress tolerance. In this study, 14 PLD genes were identified in the tomato genome and were localized on eight chromosomes, and one tandem-duplicated gene pair was identified. According to a phylogenetic analysis, the genes were categorized into four subtypes: SlPLDα, β, and δ belonged to the C2-PLD subfamily, while SlPLDζ belonged to the PXPH-PLD subfamily. The gene structure and protein physicochemical properties were highly conserved within the same subtype. The promoter of all the SlPLD genes contained hormone-, light-, and stress-responsive cis-acting regulatory elements, but no significant correlation between the number, distribution, and type of cis-acting elements was observed among the members of the same subtype. Transcriptome data showed that the expression of the SlPLD genes was different in multiple tissues. A quantitative RT-PCR analysis revealed that the SlPLD genes responded positively to cold, salt, drought, and abscisic acid treatments, particularly to salt stress. Different expression patterns were observed for different genes under the same stress, and for the same gene under different stresses. The results provide important insights into the functions of SlPLD genes and lay a foundation for further studies of the response of SlPLD genes to abiotic stresses.
Collapse
Affiliation(s)
| | | | | | - Hui Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (X.G.)
| |
Collapse
|
4
|
Zhang Y, Yin K, Yao J, Zhao Z, Liu Z, Yan C, Zhang Y, Liu J, Li J, Zhao N, Zhao R, Zhou X, Chen S. Populus euphratica GLABRA3 Binds PLDδ Promoters to Enhance Salt Tolerance. Int J Mol Sci 2023; 24:ijms24098208. [PMID: 37175914 PMCID: PMC10179125 DOI: 10.3390/ijms24098208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
High NaCl (200 mM) increases the transcription of phospholipase Dδ (PLDδ) in roots and leaves of the salt-resistant woody species Populus euphratica. We isolated a 1138 bp promoter fragment upstream of the translation initiation codon of PePLDδ. A promoter-reporter construct, PePLDδ-pro::GUS, was introduced into Arabidopsis plants (Arabidopsis thaliana) to demonstrate the NaCl-induced PePLDδ promoter activity in root and leaf tissues. Mass spectrometry analysis of DNA pull-down-enriched proteins in P. euphratica revealed that PeGLABRA3, a basic helix-loop-helix transcription factor, was the target transcription factor for binding the promoter region of PePLDδ. The PeGLABRA3 binding to PePLDδ-pro was further verified by virus-induced gene silencing, luciferase reporter assay (LRA), yeast one-hybrid assay, and electrophoretic mobility shift assay (EMSA). In addition, the PeGLABRA3 gene was cloned and overexpressed in Arabidopsis to determine the function of PeGLABRA3 in salt tolerance. PeGLABRA3-overexpressed Arabidopsis lines (OE1 and OE2) had a greater capacity to scavenge reactive oxygen species (ROS) and to extrude Na+ under salinity stress. Furthermore, the EMSA and LRA results confirmed that PeGLABRA3 interacted with the promoter of AtPLDδ in transgenic plants. The upregulated AtPLDδ in PeGLABRA3-transgenic lines resulted in an increase in phosphatidic acid species under no-salt and saline conditions. We conclude that PeGLABRA3 activated AtPLDδ transcription under salt stress by binding to the AtPLDδ promoter region, conferring Na+ and ROS homeostasis control via signaling pathways mediated by PLDδ and phosphatidic acid.
Collapse
Affiliation(s)
- Ying Zhang
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kexin Yin
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Ziyan Zhao
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhe Liu
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Caixia Yan
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yanli Zhang
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jian Liu
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jing Li
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nan Zhao
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Rui Zhao
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiaoyang Zhou
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shaoliang Chen
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
5
|
Kong J, Yin K, Zhang C, Liu X, Yang N. PLDδ, auxin, and H 2O 2 mediated the allelopathic effect of cycloastragenol on root growth in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2023; 282:153929. [PMID: 36724592 DOI: 10.1016/j.jplph.2023.153929] [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: 10/25/2022] [Revised: 01/06/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Cycloastragenol (CAG) is a tetra-cyclic triterpenoid allelochemical. It has been widely studied in animals but rarely in plants. Here, we reported that a model allelochemical CAG inhibited primary root elongation of Arabidopsis by reducing the sizes of both the meristem and elongation zones. Phospholipase Dδ(PLDδ), hydrogen peroxide (H2O2), and auxin affected this process. After treatment with CAG, the expression of PLDδ and the activity of the Phospholipase D(PLD) enzyme increased in WT. Mutants analysis demonstrated that PLDδ negatively regulated the primary root elongation by CAG treatment. CAG treatment stimulated the accumulation of H2O2 in roots. The production of H2O2 was derived from cell wall peroxidase. Mutants analysis showed that PLDδ positively regulated the production of H2O2 by CAG treatment. CAG also decreased auxin content in the root tip by affecting the expression of auxin synthesis-related genes. PLDδ was involved in the auxin reduction mediated by CAG, but H2O2 did not participate in this process. In conclusion, PLDδ, auxin, and H2O2 mediated the inhibition of primary root growth by CAG in Arabidopsis.
Collapse
Affiliation(s)
- Juantao Kong
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Kai Yin
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Cuixia Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Xuan Liu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Ning Yang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China.
| |
Collapse
|
6
|
Zhu Y, Zhao M, Li T, Wang L, Liao C, Liu D, Zhang H, Zhao Y, Liu L, Ge X, Li B. Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt. FRONTIERS IN PLANT SCIENCE 2023; 14:1174281. [PMID: 37152175 PMCID: PMC10161258 DOI: 10.3389/fpls.2023.1174281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.
Collapse
Affiliation(s)
- Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| | - Mei Zhao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Taotao Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Lianzhe Wang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Chunli Liao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Dongxiao Liu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Huamin Zhang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Yanpeng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| |
Collapse
|