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Zhu F, Han J, Hong J, Cai F, Tang Q, Yu Q, Ma S, Liu X, Huo S, Chen K. Characterization of the UDP-glycosyltransferase UGT33D1 in silkworm Bombyx mori. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38956869 DOI: 10.1111/imb.12935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024]
Abstract
Uridine diphosphate (UDP)-glycosyltransferases (UGTs) are important metabolizing enzymes functioning by adding a sugar moiety to a small lipophilic substrate molecule and play critical roles in drug/toxin metabolism for all realms of life. In this study, the silkworm Bombyx mori UGT33D1 gene was characterized in detail. UGT33D1 was found localized in the endoplasmic reticulum (ER) compartment just like other animal UGTs and was mainly expressed in the silkworm midgut. We first reported that UGT33D1 was important to BmNPV infection, as silencing UGT33D1 inhibited the BmNPV infection in silkworm BmN cells, while overexpressing the gene promoted viral infection. The molecular pathways regulated by UGT33D1 were analysed via transcriptome sequencing upon UGT33D1 knockdown, highlighting the important role of the gene in maintaining a balanced oxidoreductive state of the organism. In addition, proteins that physically interact with UGT33D1 were identified through immunoprecipitation and mass spectrometry analysis, which includes tubulin, elongation factor, certain ribosomal proteins, histone proteins and zinc finger proteins that had been previously reported for human UGT-interacting proteins. This study provided preliminary but important functional information on UGT33D1 and is hoped to trigger deeper investigations into silkworm UGTs and their functional mechanisms.
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Affiliation(s)
- Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jinying Han
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jingdie Hong
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Fuchuan Cai
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qi Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qian Yu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoyong Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shuhao Huo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Zhou Y, Li A, Du T, Qin Z, Zhang L, Wang Q, Li Z, Hou F. A Small Auxin-Up RNA Gene, IbSAUR36, Regulates Adventitious Root Development in Transgenic Sweet Potato. Genes (Basel) 2024; 15:760. [PMID: 38927696 PMCID: PMC11203243 DOI: 10.3390/genes15060760] [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: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Small auxin-upregulated RNAs (SAURs), as the largest family of early auxin-responsive genes, play important roles in plant growth and development processes, such as auxin signaling and transport, hypocotyl development, and tolerance to environmental stresses. However, the functions of few SAUR genes are known in the root development of sweet potatoes. In this study, an IbSAUR36 gene was cloned and functionally analyzed. The IbSAUR36 protein was localized to the nucleus and plasma membrane. The transcriptional level of this gene was significantly higher in the pencil root and leaf.This gene was strongly induced by indole-3-acetic acid (IAA), but it was downregulated under methyl-jasmonate(MeJA) treatment. The promoter of IbSAUR36 contained the core cis-elements for phytohormone responsiveness. Promoter β-glucuronidase (GUS) analysis in Arabidopsis showed that IbSAUR36 is highly expressed in the young tissues of plants, such as young leaves, roots, and buds. IbSAUR36-overexpressing sweet potato roots were obtained by an efficient Agrobacterium rhizogenes-mediated root transgenic system. We demonstrated that overexpression of IbSAUR36 promoted the accumulation of IAA, upregulated the genes encoding IAA synthesis and its signaling pathways, and downregulated the genes encoding lignin synthesis and JA signaling pathways. Taken together, these results show that IbSAUR36 plays an important role in adventitious root (AR) development by regulating IAA signaling, lignin synthesis, and JA signaling pathways in transgenic sweet potatoes.
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Affiliation(s)
- Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Taifeng Du
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zongyun Li
- Key Laboratory of Phylogeny and Comparative Genomics of the Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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3
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Prakash NR, Kumar K, Muthusamy V, Zunjare RU, Hossain F. Unique genetic architecture of prolificacy in 'Sikkim Primitive' maize unraveled through whole-genome resequencing-based DNA polymorphism. PLANT CELL REPORTS 2024; 43:134. [PMID: 38702564 DOI: 10.1007/s00299-024-03176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/13/2024] [Indexed: 05/06/2024]
Abstract
KEY MESSAGE 'Sikkim Primitive' maize landrace, unique for prolificacy (7-9 ears per plant) possesses unique genomic architecture in branching and inflorescence-related gene(s), and locus Zm00001eb365210 encoding glycosyltransferases was identified as the putative candidate gene underlying QTL (qProl-SP-8.05) for prolificacy. The genotype possesses immense usage in breeding high-yielding baby-corn genotypes. 'Sikkim Primitive' is a native landrace of North Eastern Himalayas, and is characterized by having 7-9 ears per plant compared to 1-2 ears in normal maize. Though 'Sikkim Primitive' was identified in the 1960s, it has not been characterized at a whole-genome scale. Here, we sequenced the entire genome of an inbred (MGUSP101) derived from 'Sikkim Primitive' along with three non-prolific (HKI1128, UMI1200, and HKI1105) and three prolific (CM150Q, CM151Q and HKI323) inbreds. A total of 942,417 SNPs, 24,160 insertions, and 27,600 deletions were identified in 'Sikkim Primitive'. The gene-specific functional mutations in 'Sikkim Primitive' were classified as 10,847 missense (54.36%), 402 non-sense (2.015%), and 8,705 silent (43.625%) mutations. The number of transitions and transversions specific to 'Sikkim Primitive' were 666,021 and 279,950, respectively. Among all base changes, (G to A) was the most frequent (215,772), while (C to G) was the rarest (22,520). Polygalacturonate 4-α-galacturonosyltransferase enzyme involved in pectin biosynthesis, cell-wall organization, nucleotide sugar, and amino-sugar metabolism was found to have unique alleles in 'Sikkim Primitive'. The analysis further revealed the Zm00001eb365210 gene encoding glycosyltransferases as the putative candidate underlying QTL (qProl-SP-8.05) for prolificacy in 'Sikkim Primitive'. High-impact nucleotide variations were found in ramosa3 (Zm00001eb327910) and zeaxanthin epoxidase1 (Zm00001eb081460) genes having a role in branching and inflorescence development in 'Sikkim Primitive'. The information generated unraveled the genetic architecture and identified key genes/alleles unique to the 'Sikkim Primitive' genome. This is the first report of whole-genome characterization of the 'Sikkim Primitive' landrace unique for its high prolificacy.
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Affiliation(s)
- Nitish Ranjan Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, Delhi, 110012, India
| | - Vignesh Muthusamy
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India.
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Cohen JD, Strader LC. An auxin research odyssey: 1989-2023. THE PLANT CELL 2024; 36:1410-1428. [PMID: 38382088 PMCID: PMC11062468 DOI: 10.1093/plcell/koae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The phytohormone auxin is at times called the master regulator of plant processes and has been shown to be a central player in embryo development, the establishment of the polar axis, early aspects of seedling growth, as well as growth and organ formation during later stages of plant development. The Plant Cell has been key, since the inception of the journal, to developing an understanding of auxin biology. Auxin-regulated plant growth control is accomplished by both changes in the levels of active hormones and the sensitivity of plant tissues to these concentration changes. In this historical review, we chart auxin research as it has progressed in key areas and highlight the role The Plant Cell played in these scientific developments. We focus on understanding auxin-responsive genes, transcription factors, reporter constructs, perception, and signal transduction processes. Auxin metabolism is discussed from the development of tryptophan auxotrophic mutants, the molecular biology of conjugate formation and hydrolysis, indole-3-butyric acid metabolism and transport, and key steps in indole-3-acetic acid biosynthesis, catabolism, and transport. This progress leads to an expectation of a more comprehensive understanding of the systems biology of auxin and the spatial and temporal regulation of cellular growth and development.
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Affiliation(s)
- Jerry D Cohen
- Department of Horticultural Science and the Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27008, USA
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5
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Cao Y, Han Z, Zhang Z, He L, Huang C, Chen J, Dai F, Xuan L, Yan S, Si Z, Hu Y, Zhang T. UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development. PLANT COMMUNICATIONS 2024:100938. [PMID: 38689494 DOI: 10.1016/j.xplc.2024.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.
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Affiliation(s)
- Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China.
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6
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Akabane T, Suzuki N, Ikeda K, Yonezawa T, Nagatoishi S, Matsumura H, Yoshizawa T, Tsuchiya W, Kamino S, Tsumoto K, Ishimaru K, Katoh E, Hirotsu N. THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring. Sci Rep 2024; 14:6778. [PMID: 38514802 PMCID: PMC10958001 DOI: 10.1038/s41598-024-57506-z] [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: 01/19/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance (19F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.
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Affiliation(s)
- Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuyoshi Ikeda
- Medicinal Chemistry Data Intelligence Unit, Drug Development Data Intelligence Platform Group, Medical Sciences Innovation Hub Program (MIH), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Satoru Nagatoishi
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Wataru Tsuchiya
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Satoshi Kamino
- CRYO SHIP Incorporated, 1-266-3, Sakuragi-cho, Omiya-ku, Saitama, Saitama, 330-0854, Japan
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Etsuko Katoh
- Department of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
| | - Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
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7
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Gate T, Hill L, Miller AJ, Sanders D. AtIAR1 is a Zn transporter that regulates auxin metabolism in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1437-1450. [PMID: 37988591 PMCID: PMC10901206 DOI: 10.1093/jxb/erad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Root growth in Arabidopsis is inhibited by exogenous auxin-amino acid conjugates, and mutants resistant to one such conjugate [indole-3-acetic acid (IAA)-Ala] map to a gene (AtIAR1) that is a member of a metal transporter family. Here, we test the hypothesis that AtIAR1 controls the hydrolysis of stored conjugated auxin to free auxin through zinc transport. AtIAR1 complements a yeast mutant sensitive to zinc, but not manganese- or iron-sensitive mutants, and the transporter is predicted to be localized to the endoplasmic reticulum/Golgi in plants. A previously identified Atiar1 mutant and a non-expressed T-DNA mutant both exhibit altered auxin metabolism, including decreased IAA-glucose conjugate levels in zinc-deficient conditions and insensitivity to the growth effect of exogenous IAA-Ala conjugates. At a high concentration of zinc, wild-type plants show a novel enhanced response to root growth inhibition by exogenous IAA-Ala which is disrupted in both Atiar1 mutants. Furthermore, both Atiar1 mutants show changes in auxin-related phenotypes, including lateral root density and hypocotyl length. The findings therefore suggest a role for AtIAR1 in controlling zinc release from the secretory system, where zinc homeostasis plays a key role in regulation of auxin metabolism and plant growth regulation.
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Affiliation(s)
- Thomas Gate
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Lionel Hill
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Anthony J Miller
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
| | - Dale Sanders
- Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK
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8
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Gan Y, Yu B, Liu R, Shu B, Liang Y, Zhao Y, Qiu Z, Yan S, Cao B. Systematic analysis of the UDP-glucosyltransferase family: discovery of a member involved in rutin biosynthesis in Solanum melongena. FRONTIERS IN PLANT SCIENCE 2023; 14:1310080. [PMID: 38197083 PMCID: PMC10774229 DOI: 10.3389/fpls.2023.1310080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Eggplant (Solanum melongena) is an economically important crop and rich in various nutrients, among which rutin that has positive effects on human health is found in eggplant. Glycosylation mediated by UDP-glycosyltransferases (UGTs) is a key step in rutin biosynthesis. However, the UGT gene has not been reported in eggplant to date. Herein, 195 putative UGT genes were identified in eggplant by genome-wide analysis, and they were divided into 17 subgroups (Group A-P and Group R) according to the phylogenetic evolutionary tree. The members of Groups A, B, D, E and L were related to flavonol biosynthesis, and rutin was the typical flavonol. The expression profile showed that the transcriptional levels of SmUGT genes in Clusters 7-10 were closely related to those of rutin biosynthetic pathway genes. Notably, SmUGT89B2 was classified into Cluster 7 and Group B; its expression was consistent with rutin accumulation in different tissues and different leaf stages of eggplant. SmUGT89B2 was located in the nucleus and cell membrane. Virus-induced gene silencing (VIGS) and transient overexpression assays showed that SmUGT89B2 can promote rutin accumulation in eggplant. These findings provide new insights into the UGT genes in eggplant, indicating that SmUGT89B2 is likely to encode the final enzyme in rutin biosynthesis.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuangshuang Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetable Engineering and Technology Research Center/College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetable Engineering and Technology Research Center/College of Horticulture, South China Agricultural University, Guangzhou, China
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9
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Zhang X, Shen Z, Sun X, Chen M, Zhang N. Integrated analysis of transcriptomic and proteomic data reveals novel regulators of soybean ( Glycine max) hypocotyl development. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:1086-1098. [PMID: 37866377 DOI: 10.1071/fp23013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
Hypocotyl elongation directly affects the seedling establishment and soil-breaking after germination. In soybean (Glycine max ), the molecular mechanisms regulating hypocotyl development remain largely elusive. To decipher the regulatory landscape, we conducted proteome and transcriptome analysis of soybean hypocotyl samples at different development stages. Our results showed that during hypocotyl development, many proteins were with extreme high translation efficiency (TE) and may act as regulators. These potential regulators include multiple peroxidases and cell wall reorganisation related enzymes. Peroxidases may produce ROS including H2 O2 . Interestingly, exogenous H2 O2 application promoted hypocotyl elongation, supporting peroxidases as regulators of hypocotyl development. However, a vast variety of proteins were shown to be with dramatically changed TE during hypocotyl development, including multiple phytochromes, plasma membrane intrinsic proteins (PIPs) and aspartic proteases. Their potential roles in hypocotyl development were confirmed by that ectopic expression of GmPHYA1 and GmPIP1-6 in Arabidopsis thaliana affected hypocotyl elongation. In addition, the promoters of these potential regulatory genes contain multiple light/gibberellin/auxin responsive elements, while the expression of some members in hypocotyls was significantly regulated by light and exogenous auxin/gibberellin. Overall, our results revealed multiple novel regulatory factors of soybean hypocotyl elongation. Further research on these regulators may lead to new approvals to improve soybean hypocotyl traits.
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Affiliation(s)
- Xueliang Zhang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Zhikang Shen
- Sanya Institute, Henan University, Sanya, China; and State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Xiaohu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Min Chen
- Sanya Institute, Henan University, Sanya, China; and State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Naichao Zhang
- School of Life Sciences, Henan University, Kaifeng, China
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10
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Dash L, Swaminathan S, Šimura J, Gonzales CLP, Montes C, Solanki N, Mejia L, Ljung K, Zabotina OA, Kelley DR. Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth. PLANT PHYSIOLOGY 2023; 193:2480-2497. [PMID: 37606259 PMCID: PMC10663140 DOI: 10.1093/plphys/kiad465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/23/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.
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Affiliation(s)
- Linkan Dash
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Sivakumar Swaminathan
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Jan Šimura
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Caitlin Leigh P Gonzales
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Iowa City, IA 50011, USA
| | - Neel Solanki
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Ludvin Mejia
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Olga A Zabotina
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Dior R Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
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11
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Solanki M, Shukla LI. Recent advances in auxin biosynthesis and homeostasis. 3 Biotech 2023; 13:290. [PMID: 37547917 PMCID: PMC10400529 DOI: 10.1007/s13205-023-03709-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03709-6.
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Affiliation(s)
- Manish Solanki
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
- Puducherry, India
| | - Lata Israni Shukla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
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12
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Ding K, Jia Z, Rui P, Fang X, Zheng H, Chen J, Yan F, Wu G. Proteomics Identified UDP-Glycosyltransferase Family Members as Pro-Viral Factors for Turnip Mosaic Virus Infection in Nicotiana benthamiana. Viruses 2023; 15:1401. [PMID: 37376700 DOI: 10.3390/v15061401] [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: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one of the most prevalent viral pathogens in many regions of the world. Here, we employed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach to characterize cellular protein changes in the early stages of infection of Nicotiana benthamiana by wild type and replication-defective TuMV. A total of 225 differentially accumulated proteins (DAPs) were identified (182 increased and 43 decreased). Bioinformatics analysis showed that a few biological pathways were associated with TuMV infection. Four upregulated DAPs belonging to uridine diphosphate-glycosyltransferase (UGT) family members were validated by their mRNA expression profiles and their effects on TuMV infection. NbUGT91C1 or NbUGT74F1 knockdown impaired TuMV replication and increased reactive oxygen species production, whereas overexpression of either promoted TuMV replication. Overall, this comparative proteomics analysis delineates the cellular protein changes during early TuMV infection and provides new insights into the role of UGTs in the context of plant viral infection.
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Affiliation(s)
- Kaida Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhaoxing Jia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Penghuan Rui
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xinxin Fang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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13
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Jiang X, Lai S, Kong D, Hou X, Shi Y, Fu Z, Liu Y, Gao L, Xia T. Al-induced CsUGT84J2 enhances flavonol and auxin accumulation to promote root growth in tea plants. HORTICULTURE RESEARCH 2023; 10:uhad095. [PMID: 37350798 PMCID: PMC10282599 DOI: 10.1093/hr/uhad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023]
Abstract
Although Al is not necessary or even toxic to most plants, it is beneficial for the growth of tea plants. However, the mechanism through which Al promotes root growth in tea plants remains unclear. In the present study, we found that flavonol glycoside levels in tea roots increased following Al treatment, and the Al-induced UDP glycosyltransferase CsUGT84J2 was involved in this mechanism. Enzyme activity assays revealed that rCsUGT84J2 exhibited catalytic activity on multiple types of substrates, including phenolic acids, flavonols, and auxins in vitro. Furthermore, metabolic analysis with UPLC-QqQ-MS/MS revealed significantly increased flavonol and auxin glycoside accumulation in CsUGT84J2-overexpressing Arabidopsis thaliana. In addition, the expression of genes involved in the flavonol pathway as well as in the auxin metabolism, transport, and signaling pathways was remarkably enhanced. Additionally, lateral root growth and exogenous Al stress tolerance were significantly improved in transgenic A. thaliana. Moreover, gene expression and metabolic accumulation related to phenolic acids, flavonols, and auxin were upregulated in CsUGT84J2-overexpressing tea plants but downregulated in CsUGT84J2-silenced tea plants. In conclusion, Al treatment induced CsUGT84J2 expression, mediated flavonol and auxin glycosylation, and regulated endogenous auxin homeostasis in tea roots, thereby promoting the growth of tea plants. Our findings lay the foundation for studying the precise mechanisms through which Al promotes the growth of tea plants.
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Affiliation(s)
| | | | - Dexu Kong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaohan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Yufeng Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhouping Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Yajun Liu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, China
| | | | - Tao Xia
- Corresponding author: E-mail:
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14
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Yang Q, Zhang Y, Qu X, Wu F, Li X, Ren M, Tong Y, Wu X, Yang A, Chen Y, Chen S. Genome-wide analysis of UDP-glycosyltransferases family and identification of UGT genes involved in abiotic stress and flavonol biosynthesis in Nicotiana tabacum. BMC PLANT BIOLOGY 2023; 23:204. [PMID: 37076827 PMCID: PMC10114341 DOI: 10.1186/s12870-023-04208-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Uridine disphosphate (UDP) glycosyltransferases (UGTs) act upon a huge variety of highly diverse and complex substrates, such as phytohormones and specialized metabolites, to regulate plant growth, development, disease resistance, and environmental interactions. However, a comprehensive investigation of UGT genes in tobacco has not been conducted. RESULTS In this study, we carried out a genome-wide analysis of family-1 UDP glycosyltransferases in Nicotiana tabacum. We predicted 276 NtUGT genes, which were classified into 18 major phylogenetic subgroups. The NtUGT genes were invariably distributed among all the 24 chromosomes with structural diversity in exon/intron structure, conserved motifs, and cis-acting elements of promoters. Three groups of proteins which involved in flavonoid biosynthesis, plant growth and development, transportation and modification were identified that interact with NtUGT proteins using the PPI analysis. Expression analysis of NtUGT genes in cold stress, drought stress and different flower color using both online RNA-Seq data and the realtime PCR analysis, suggested the distinct role of NtUGT genes in resistance of cold, drought and in flavonoid biosynthesis. The enzymatic activities of seven NtUGT proteins that potentially involved in flavonoid glycosylation were analyzed, and found that all seven exhibited activity on myricetin; six (NtUGT108, NtUGT123, NtUGT141, NtUGT155, NtUGT179, and NtUGT195) showed activity on cyanidin; and three (NtUGT108, NtUGT195, and NtUGT217) were active on the flavonol aglycones kaempferol and quercetin, which catalyzing the substrates (myricetin, cyanidin or flavonol) to form new products. We further investigated the enzymatic products and enzymatic properties of NtUGT108, NtUGT195, and NtUGT217, suggested their diverse enzymatic activity toward flavonol, and NtUGT217 showed the highest catalyzed efficient toward quercetin. Overexpression of NtUGT217 significantly increase the content levels of the quercetin-3-O-glucoside, quercetin-3-O-rutinoside and kaempferol-3-O-rutinoside in transgenic tobacco leaves. CONCLUSION We identified 276 UGT genes in Nicotiana tabacum. Our study uncovered valuable information about the phylogenetic structure, distribution, genomic characters, expression patterns and enzymatic activity of NtUGT genes in tobacco. We further identified three NtUGT genes involved in flavonoid biosynthesis, and overexpressed NtUGT217 to validate its function in catalyze quercetin. The results provide key candidate NtUGT genes for future breeding of cold and drought resistance and for potential metabolic engineering of flavonoid compounds.
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Affiliation(s)
- Qing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Qujing Tobacco Company of Yunnan Province, Qujing, 655000, China
| | - Yinchao Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiaoling Qu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Fengyan Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiuchun Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Min Ren
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ying Tong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Yong Chen
- China National Tobacco Corporation, Beijing, 100045, China.
| | - Shuai Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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15
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El Houari I, Klíma P, Baekelandt A, Staswick PE, Uzunova V, Del Genio CI, Steenackers W, Dobrev PI, Filepová R, Novák O, Napier R, Petrášek J, Inzé D, Boerjan W, Vanholme B. Non-specific effects of the CINNAMATE-4-HYDROXYLASE inhibitor piperonylic acid. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37036146 DOI: 10.1111/tpj.16237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Chemical inhibitors are often implemented for the functional characterization of genes to overcome the limitations associated with genetic approaches. Although it is well established that the specificity of the compound is key to success of a pharmacological approach, off-target effects are often overlooked or simply neglected in a complex biological setting. Here we illustrate the cause and implications of such secondary effects by focusing on piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H) that is frequently used to investigate the involvement of lignin during plant growth and development. When supplied to plants, we found that PA is recognized as a substrate by GRETCHEN HAGEN 3.6 (GH3.6), an amido synthetase involved in the formation of the indole-3-acetic acid (IAA) conjugate IAA-Asp. By competing for the same enzyme, PA interferes with IAA conjugation, resulting in an increase in IAA concentrations in the plant. In line with the broad substrate specificity of the GH3 family of enzymes, treatment with PA increased not only IAA levels but also those of other GH3-conjugated phytohormones, namely jasmonic acid and salicylic acid. Finally, we found that interference with the endogenous function of GH3s potentially contributes to phenotypes previously observed upon PA treatment. We conclude that deregulation of phytohormone homeostasis by surrogate occupation of the conjugation machinery in the plant is likely a general phenomenon when using chemical inhibitors. Our results hereby provide a novel and important basis for future reference in studies using chemical inhibitors.
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Affiliation(s)
- Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petr Klíma
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Paul E Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Veselina Uzunova
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, Coventry University, Prior Street, Coventry, CV1 5FB, UK
| | - Ward Steenackers
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petre I Dobrev
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Roberta Filepová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jan Petrášek
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 43, Prague 2, Czech Republic
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
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16
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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17
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Navarro-Quiles C, Mateo-Bonmatí E, Candela H, Robles P, Martínez-Laborda A, Fernández Y, Šimura J, Ljung K, Rubio V, Ponce MR, Micol JL. The Arabidopsis ATP-Binding Cassette E protein ABCE2 is a conserved component of the translation machinery. FRONTIERS IN PLANT SCIENCE 2022; 13:1009895. [PMID: 36325553 PMCID: PMC9618717 DOI: 10.3389/fpls.2022.1009895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.
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Affiliation(s)
| | | | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Pedro Robles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | | | | | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
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18
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Antoniadi I, Mateo-Bonmatí E, Pernisová M, Brunoni F, Antoniadi M, Villalonga MGA, Ament A, Karády M, Turnbull C, Doležal K, Pěnčík A, Ljung K, Novák O. IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth. FRONTIERS IN PLANT SCIENCE 2022; 13:932008. [PMID: 36311087 PMCID: PMC9616112 DOI: 10.3389/fpls.2022.932008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/16/2022] [Indexed: 06/12/2023]
Abstract
Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.
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Affiliation(s)
- Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Eduardo Mateo-Bonmatí
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Markéta Pernisová
- Plant Sciences Core Facility, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), and NCBR, Faculty of Science, Masaryk University, Brno, Czechia
| | - Federica Brunoni
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Mariana Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Anita Ament
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michal Karády
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Colin Turnbull
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Karel Doležal
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
- Department of Chemical Biology, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
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Sun L, Zhao L, Huang H, Zhang Y, Wang J, Lu X, Wang S, Wang D, Chen X, Chen C, Guo L, Xu N, Zhang H, Wang J, Rui C, Han M, Fan Y, Nie T, Ye W. Genome-wide identification, evolution and function analysis of UGTs superfamily in cotton. Front Mol Biosci 2022; 9:965403. [PMID: 36177349 PMCID: PMC9513525 DOI: 10.3389/fmolb.2022.965403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Glycosyltransferases mainly catalyse the glycosylation reaction in living organisms and widely exists in plants. UGTs have been identified from G. raimondii, G. arboreum and G. hirsutum. However, Genome-wide systematic analysis of UGTs superfamily have not been studied in G. barbadense. 752 UGTs were identified from four cotton species and grouped into 18 clades, of which R was newly discovered clades. Most UGTs were clustered at both ends of the chromosome and showed a heterogeneous distribution. UGT proteins were widely distributed in cells, with the highest distribution in chloroplasts. UGTs of the same clade shared similar intron/exon structural features. During evolution, the gene family has undergone strong selection for purification. UGTs were significantly enriched in “transcriptional activity (GO:0016758)” and “metabolic processes (GO:0008152)”. Genes from the same clade differed in function under various abiotic stresses. The analysis of cis-acting element and qRT–PCR may indicate that GHUGTs play important roles in plant growth, development and abiotic stress. We further found that GHUGT74-2 plays an important role under submergence. The study broadens the understanding of UGTs in terms of gene characteristics, evolutionary processes, and gene function in cotton and provides a new way to systematically and globally understand the structure–function relationship of multigene families in the evolutionary process.
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Affiliation(s)
- Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Hong Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Taili Nie
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
- *Correspondence: Wuwei Ye, ; Taili Nie,
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
- *Correspondence: Wuwei Ye, ; Taili Nie,
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The Application of Auxin-like Compounds Promotes Cold Acclimation in the Oilseed Rape Plant. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081283. [PMID: 36013462 PMCID: PMC9409786 DOI: 10.3390/life12081283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022]
Abstract
Cold is a major environmental key factor influencing plant growth, development, and productivity. Responses and adaption processes depend on plant physiological and biochemical modifications, first of all via the hormonal system. Indole-3-acetic acid (IAA) plays a critical role in the processes of plant functioning. To assess the influence of the auxin-like compounds 1-[2-chloroethoxycarbonylmethyl]-4-naphthalenesulfonic acid calcium salt (TA-12) and 1-[2-dimethylaminoethoxycarbonylmethyl]naphthalene chloromethylate (TA-14) in the process of cold acclimation, long-term field trials over four years were performed with two rapeseed (Brassica napus L.) plant cultivars with different wintering resistance in temperate-zone countries. In these two rapeseed cultivars, namely ‘Casino’ (less resistant) and ‘Valesca’ (more resistant), investigations were conducted in the terminal buds and root collars. The application of auxin-like compounds revealed a close interlinkage between the composition of dehydrins and the participation of the phytohormone IAA in the adaptation processes. By applying TA-12 and TA-14, the importance of the proteins, especially the composition of the dehydrins, the IAA amount, and the status of the oilseed rape cultivars at the end of the cold acclimation period were confirmed. Following on from this, when introducing oilseed rape cultivars from foreign countries, it may also be of value to assess their suitability for cultivation in temperate-zone countries.
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Casanova‐Sáez R, Mateo‐Bonmatí E, Šimura J, Pěnčík A, Novák O, Staswick P, Ljung K. Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit. THE NEW PHYTOLOGIST 2022; 235:263-275. [PMID: 35322877 PMCID: PMC9322293 DOI: 10.1111/nph.18114] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/05/2022] [Indexed: 05/25/2023]
Abstract
Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.
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Affiliation(s)
- Rubén Casanova‐Sáez
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre (UPSC)Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Eduardo Mateo‐Bonmatí
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre (UPSC)Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Jan Šimura
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre (UPSC)Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Aleš Pěnčík
- Laboratory of Growth RegulatorsFaculty of SciencePalacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27OlomoucCzech Republic
| | - Ondřej Novák
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre (UPSC)Swedish University of Agricultural Sciences901 83UmeåSweden
- Laboratory of Growth RegulatorsFaculty of SciencePalacký University and Institute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 27OlomoucCzech Republic
| | - Paul Staswick
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | - Karin Ljung
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre (UPSC)Swedish University of Agricultural Sciences901 83UmeåSweden
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Nemati I, Sedghi M, Hosseini Salekdeh G, Tavakkol Afshari R, Naghavi MR, Gholizadeh S. DELAY OF GERMINATION 1 ( DOG1) regulates dormancy in dimorphic seeds of Xanthium strumarium. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:742-758. [PMID: 35569923 DOI: 10.1071/fp21315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1 , the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME /EMB1649 , UBP26 , EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7 /SDG25, ELF6 , and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI , and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3 , PEPC3 , and D2HGDH ) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.
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Affiliation(s)
- Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mohammad Sedghi
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; and Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Reza Tavakkol Afshari
- Department of Agronomy, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Somayeh Gholizadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Ankit A, Singh A, Kumar S, Singh A. Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K +) deficiency response in two contrasting chickpea cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:1054821. [PMID: 36714783 PMCID: PMC9875034 DOI: 10.3389/fpls.2022.1054821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 05/10/2023]
Abstract
Potassium (K+) is an essential macronutrient for plant growth and development. K+ deficiency hampers important plant processes, such as enzyme activation, protein synthesis, photosynthesis and stomata movement. Molecular mechanism of K+ deficiency tolerance has been partly understood in model plants Arabidopsis, but its knowledge in legume crop chickpea is missing. Here, morphophysiological analysis revealed that among five high yielding desi chickpea cultivars, PUSA362 shows stunted plant growth, reduced primary root growth and low K+ content under K+ deficiency. In contrast, PUSA372 had negligible effect on these parameters suggesting that PUSA362 is K+ deficiency sensitive and PUSA372 is a K+ deficiency tolerant chickpea cultivar. RNA-seq based transcriptome analysis under K+ deficiency revealed a total of 820 differential expressed genes (DEG's) in PUSA362 and 682 DEGs in PUSA372. These DEGs belongs to different functional categories, such as plant metabolism, signal transduction components, transcription factors, ion/nutrient transporters, phytohormone biosynthesis and signalling, and root growth and development. RNA-seq expression of randomly selected 16 DEGs was validated by RT-qPCR. Out of 16 genes, 13 showed expression pattern similar to RNA-seq expression, that verified the RNA-seq expression data. Total 258 and 159 genes were exclusively up-regulated, and 386 and 347 genes were down-regulated, respectively in PUSA362 and PUSA372. 14 DEGs showed contrasting expression pattern as they were up-regulated in PUSA362 and down-regulated in PUSA372. These include somatic embryogenesis receptor-like kinase 1, thaumatin-like protein, ferric reduction oxidase 2 and transcription factor bHLH93. Nine genes which were down-regulated in PUSA362 found to be up-regulated in PUSA372, including glutathione S-transferase like, putative calmodulin-like 19, high affinity nitrate transporter 2.4 and ERF17-like protein. Some important carbohydrate metabolism related genes, like fructose-1,6-bisphosphatase and sucrose synthase, and root growth related Expansin gene were exclusively down-regulated, while an ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1) was up-regulated in PUSA362. Interplay of these and several other genes related to hormones (auxin, cytokinin, GA etc.), signal transduction components (like CBLs and CIPKs), ion transporters and transcription factors might underlie the contrasting response of two chickpea cultivars to K+ deficiency. In future, some of these key genes will be utilized in genetic engineering and breeding programs for developing chickpea cultivars with improved K+ use efficiency (KUE) and K+ deficiency tolerance traits.
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Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica. PLANTS 2021; 10:plants10122607. [PMID: 34961078 PMCID: PMC8708889 DOI: 10.3390/plants10122607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/04/2023]
Abstract
Coffea arabica is one of the most important crops worldwide. In vitro culture is an alternative for achieving Coffea regeneration, propagation, conservation, genetic improvement, and genome editing. The aim of this work was to identify proteins involved in auxin homeostasis by isobaric tandem mass tag (TMT) and the synchronous precursor selection (SPS)-based MS3 technology on the Orbitrap Fusion™ Tribrid mass spectrometer™ in three types of biological materials corresponding to C. arabica: plantlet leaves, calli, and suspension cultures. Proteins included in the β-oxidation of indole butyric acid and in the signaling, transport, and conjugation of indole-3-acetic acid were identified, such as the indole butyric response (IBR), the auxin binding protein (ABP), the ATP-binding cassette transporters (ABC), the Gretchen-Hagen 3 proteins (GH3), and the indole-3-acetic-leucine-resistant proteins (ILR). A more significant accumulation of proteins involved in auxin homeostasis was found in the suspension cultures vs. the plantlet, followed by callus vs. plantlet and suspension culture vs. callus, suggesting important roles of these proteins in the cell differentiation process.
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