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Cui Z, Huang H, Du T, Chen J, Huang S, Dai Q. Integrated transcriptome and metabolome revealed the drought responsive metabolic pathways in Oriental Lily (Lilium L.). PeerJ 2023; 11:e16658. [PMID: 38130923 PMCID: PMC10734436 DOI: 10.7717/peerj.16658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Objective Lily is an essential ornamental flowering species worldwide. Drought stress is a major constraint affecting the morphology and physiology and lily leaves and flowers. Therefore, understanding the molecular mechanism underlying lily response to drought stress is important. Method Transcriptome and metabolome analysis were performed on Oriental Lily subjected to drought stress. Result Most transcription factors and metabolites yielded by the conjoint analysis displayed a downregulated expression pattern. Differential genes and metabolites mainly co-enriched in glycolic pathways related to sugars, such as galactose, and sucrose, glycolysis and gluconeogenesis, indicating that drought stress reduced the sugar metabolism level of Oriental Lily. Combined with transcriptome and metabolome data, nine pairs of differentially expressed metabolites and the genes (p < 0.05) were obtained. Interestingly, a gene named TRINITY_DN2608 (encoding a type of alpha-D-glucose) cloned and its overexpression lines in Arabidopsis thaliana was generated. Overexpression of TRINITY_DN2608 gene elevated the susceptibility to drought stress possibly by suppressing the glucose level. Conclusion The enrichment of sugar-related pathways advocates the potential role of glucose metabolism in drought stress. Our study provides theoretical information related to the glucose-mediated drought response and would be fruitful in future lily breeding programs.
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Affiliation(s)
- Zhenkui Cui
- Department of Landscape Architecture, Fujian Forestry Vocational & Technical College, Nanping, Fujian, China
| | - Huaming Huang
- Department of Landscape Architecture, Fujian Forestry Vocational & Technical College, Nanping, Fujian, China
| | - Tianqing Du
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jianfeng Chen
- Department of Landscape Architecture, Fujian Forestry Vocational & Technical College, Nanping, Fujian, China
| | - Shuyan Huang
- Department of Landscape Architecture, Fujian Forestry Vocational & Technical College, Nanping, Fujian, China
| | - Qushun Dai
- Department of Landscape Architecture, Fujian Forestry Vocational & Technical College, Nanping, Fujian, China
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Zhou X, Zhang Q, Zhao Y, Ding S, Yu GH. Integrated Multi-Omics Analyses Reveal That Autophagy-Mediated Cellular Metabolism Is Required for the Initiation of Pollen Germination. Int J Mol Sci 2023; 24:15014. [PMID: 37834462 PMCID: PMC10573924 DOI: 10.3390/ijms241915014] [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: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Autophagy is an evolutionarily conserved mechanism for degrading and recycling various cellular components, functioning in both normal development and stress conditions. This process is tightly regulated by a set of autophagy-related (ATG) proteins, including ATG2 in the ATG9 cycling system and ATG5 in the ATG12 conjugation system. Our recent research demonstrated that autophagy-mediated compartmental cytoplasmic deletion is essential for pollen germination. However, the precise mechanisms through which autophagy regulates pollen germination, ensuring its fertility, remain largely unknown. Here, we applied multi-omics analyses, including transcriptomic and metabolomic approaches, to investigate the downstream pathways of autophagy in the process of pollen germination. Although ATG2 and ATG5 play similar roles in regulating pollen germination, high-throughput transcriptomic analysis reveals that silencing ATG5 has a greater impact on the transcriptome than silencing ATG2. Cross-comparisons of transcriptome and proteome analysis reveal that gene expression at the mRNA level and protein level is differentially affected by autophagy. Furthermore, high-throughput metabolomics analysis demonstrates that pathways related to amino acid metabolism and aminoacyl-tRNA biosynthesis were affected by both ATG2 and ATG5 silencing. Collectively, our multi-omics analyses reveal the central role of autophagy in cellular metabolism, which is critical for initiating pollen germination and ensuring pollen fertility.
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Affiliation(s)
| | | | | | | | - Guang-Hui Yu
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (X.Z.)
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Caeiro A, Jarak I, Correia S, Canhoto J, Carvalho R. Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo ( Solanum betaceum Cav.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2869. [PMID: 37571022 PMCID: PMC10420837 DOI: 10.3390/plants12152869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
Tamarillo is a solanaceous tree that has been extensively studied in terms of in vitro clonal propagation, namely somatic embryogenesis. In this work, a protocol of indirect somatic embryogenesis was applied to obtain embryogenic and non-embryogenic callus from leaf segments. Nuclear magnetic resonance spectroscopy was used to analyze the primary metabolome of these distinct calli to elucidate possible differentiation mechanisms from the common genetic background callus. Standard multivariate analysis methods were then applied, and were complemented by univariate statistical methods to identify differentially expressed primary metabolites and related metabolic pathways. The results showed carbohydrate and lipid metabolism to be the most relevant in all the calli assayed, with most discriminant metabolites being fructose, glucose and to a lesser extent choline. The glycolytic rate was higher in embryogenic calli, which shows, overall, a higher rate of sugar catabolism and a different profile of phospholipids with a choline/ethanolamine analysis. In general, our results show that a distinct primary metabolome between embryogenic and non-embryogenic calli occurs and that intracellular levels of fructose and sucrose and the glucose to sucrose ratio seem to be good candidates as biochemical biomarkers of embryogenic competence.
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Affiliation(s)
- André Caeiro
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
| | - Ivana Jarak
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo, Allen 208, 4200-393 Porto, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
- InnovPlanProtect CoLab, 7350-478 Elvas, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
| | - Rui Carvalho
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, 3000-456 Coimbra, Portugal
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Liao J, Zhang Z, Shang Y, Jiang Y, Su Z, Deng X, Pu X, Yang R, Zhang L. Anatomy and Comparative Transcriptome Reveal the Mechanism of Male Sterility in Salvia miltiorrhiza. Int J Mol Sci 2023; 24:10259. [PMID: 37373407 DOI: 10.3390/ijms241210259] [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: 04/20/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Salvia miltiorrhiza Bunge is an important traditional herb. Salvia miltiorrhiza is distributed in the Sichuan province of China (here called SC). Under natural conditions, it does not bear seeds and its sterility mechanism is still unclear. Through artificial cross, there was defective pistil and partial pollen abortion in these plants. Electron microscopy results showed that the defective pollen wall was caused by delayed degradation of the tapetum. Due to the lack of starch and organelle, the abortive pollen grains showed shrinkage. RNA-seq was performed to explore the molecular mechanisms of pollen abortion. KEGG enrichment analysis suggested that the pathways of phytohormone, starch, lipid, pectin, and phenylpropanoid affected the fertility of S. miltiorrhiza. Moreover, some differentially expressed genes involved in starch synthesis and plant hormone signaling were identified. These results contribute to the molecular mechanism of pollen sterility and provide a more theoretical foundation for molecular-assisted breeding.
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Affiliation(s)
- Jinqiu Liao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhizhou Zhang
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yukun Shang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Yuanyuan Jiang
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zixuan Su
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Xuexue Deng
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiang Pu
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Ruiwu Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Li Zhang
- Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
- College of Science, Sichuan Agricultural University, Ya'an 625014, China
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He P, Zhang J, Lv Z, Cui P, Xu X, George MS, Lu G. Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato. BMC PLANT BIOLOGY 2023; 23:300. [PMID: 37270475 DOI: 10.1186/s12870-023-04272-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/07/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants' developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified. RESULTS In this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes. CONCLUSION A total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs.
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Affiliation(s)
- Peiwen He
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jingzhen Zhang
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Zunfu Lv
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Cui
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ximing Xu
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Melvin Sidikie George
- Crop Science Department, Njala University, Njala Campus. Private Mail bag, Freetown, 999127, Sierra Leone
| | - Guoquan Lu
- Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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Pers-Kamczyc E, Kamczyc J. Study of the Pollen Grain Metabolome under Deposition of Nitrogen and Phosphorus in Taxus baccata L. and Juniperus communis L. Int J Mol Sci 2022; 23:ijms232214105. [PMID: 36430583 PMCID: PMC9692909 DOI: 10.3390/ijms232214105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Nitrogen plays an important role in both quantitative and qualitative aspects of plant reproduction, including pollen grain compounds and seed production. Recent studies have pointed out that pollen grains produced by male plants of T. baccata and J. communis subjected to a long period of fertilizer supplementation have lower in vitro germination ability and higher nitrogen content. To gain molecular insights into these observations, we conducted GC-MS analysis of both species to characterize the metabolomes of dry, mature pollen grains, which allowed for the identification and quantification of more than 200 metabolites. The results demonstrated that fertilizer supplementation impacts the relative content of 14 metabolites in J. communis (9 downregulated and 5 upregulated) and 21 in T. baccata (6 downregulated and 15 upregulated). Although plants showed little similarity in patterns, in metabolite profiles, both up and down fold-changes were observed. This is the first report on the gymnosperm pollen grain metabolomic profile and changes induced by long-term nitrogen and phosphorus supplementation. Pollen grains produced by fertilizer-supplemented male individuals had significantly lower relative content of linolenic acid, 5,6-dihydrouracil, maltotriose, galactonic acid, D-xylulose, and glycerol-α-phosphate but higher content of sorbitol, glucosamine, and 1,5-anhydro-D-glucitol as well as n-acetyl-d-hexosamine, dimethyl phthalate, glycine, galactose-6-phosphate, D-fructose-6-phosphate, pyroglutamic acid, and 3-(3-hydroxyphenyl)-3-hydroxypropionic acid. Thus, in pollen grain samples earlier shown to have different germination abilities, the presence of different metabolites indicates a significant environmental impact on the quality of gymnosperm pollen grains.
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Affiliation(s)
- Emilia Pers-Kamczyc
- Department of Genetics and Environmental Interactions, Institute of Dendrology, Polish Academy of Sciences, 5 Parkowa Str., 62-035 Kórnik, Poland
- Correspondence:
| | - Jacek Kamczyc
- Department of Game Management and Forest Protection, Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, 71 Wojska Polskiego Str., 60-625 Poznań, Poland
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Wang J, Xue X, Zeng H, Li J, Chen L. Sucrose rather than GA transported by AtSWEET13 and AtSWEET14 supports pollen fitness at late anther development stages. THE NEW PHYTOLOGIST 2022; 236:525-537. [PMID: 35811428 PMCID: PMC9795879 DOI: 10.1111/nph.18368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/05/2022] [Indexed: 05/31/2023]
Abstract
Both sugar and the hormone gibberellin (GA) are essential for anther-enclosed pollen development and thus for plant productivity in flowering plants. Arabidopsis (Arabidopsis thaliana) AtSWEET13 and AtSWEET14, which are expressed in anthers and associated with seed yield, transport both sucrose and GA. However, it is still unclear which substrate transported by them directly affects anther development and seed yield. Histochemical staining, cross-sectioning and microscopy imaging techniques were used to investigate and interpret the phenotypes of the atsweet13;14 double mutant during anther development. Genetic complementation of atsweet13;14 using AtSWEET9, which transports sucrose but not GA, and the GA transporter AtNPF3.1, respectively, was conducted to test the substrate preference relevant to the biological process. The loss of both AtSWEET13 and AtSWEET14 resulted in reduced pollen viability and therefore decreased pollen germination. AtSWEET9 fully rescued the defects in pollen viability and germination of atsweet13;14, whereas AtNPF3.1 failed to do so, indicating that AtSWEET13/14-mediated sucrose rather than GA is essential for pollen fertility. AtSWEET13 and AtSWEET14 function mainly at the anther wall during late anther development stages, and they probably are responsible for sucrose efflux into locules to support pollen development to maturation, which is vital for subsequent pollen viability and germination.
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Affiliation(s)
- Jiang Wang
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Xueyi Xue
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Houqing Zeng
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou311121China
| | - Jiankun Li
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Li‐Qing Chen
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
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