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Wang R, Cheng Y, Jiang N, Jiang T, Wei Z. Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar. Plant Sci 2024; 343:112058. [PMID: 38447913 DOI: 10.1016/j.plantsci.2024.112058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Yujia Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Nan Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China.
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China.
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Wu R, Li Y, Wang L, Li Z, Wu R, Xu K, Liu Y. The DBB Family in Populus trichocarpa: Identification, Characterization, Evolution and Expression Profiles. Molecules 2024; 29:1823. [PMID: 38675643 DOI: 10.3390/molecules29081823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1-PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yuxin Li
- Melbourne School of Design, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lin Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zitian Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Runbin Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kehang Xu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yixin Liu
- College of Landscape Architecture and Art, Northwest A & F University, Yangling 712100, China
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Yu J, Gao B, Li D, Li S, Chiang VL, Li W, Zhou C. Ectopic Expression of PtrLBD39 Retarded Primary and Secondary Growth in Populus trichocarpa. Int J Mol Sci 2024; 25:2205. [PMID: 38396881 PMCID: PMC10889148 DOI: 10.3390/ijms25042205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Primary and secondary growth of trees are needed for increments in plant height and stem diameter, respectively, affecting the production of woody biomass for applications in timber, pulp/paper, and related biomaterials. These two types of growth are believed to be both regulated by distinct transcription factor (TF)-mediated regulatory pathways. Notably, we identified PtrLBD39, a highly stem phloem-specific TF in Populus trichocarpa and found that the ectopic expression of PtrLBD39 in P. trichocarpa markedly retarded both primary and secondary growth. In these overexpressing plants, the RNA-seq, ChIP-seq, and weighted gene co-expression network analysis (WGCNA) revealed that PtrLBD39 directly or indirectly regulates TFs governing vascular tissue development, wood formation, hormonal signaling pathways, and enzymes responsible for wood components. This regulation led to growth inhibition, decreased fibrocyte secondary cell wall thickness, and reduced wood production. Therefore, our study indicates that, following ectopic expression in P. trichocarpa, PtrLBD39 functions as a repressor influencing both primary and secondary growth.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
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Okińczyc P, Widelski J, Nowak K, Radwan S, Włodarczyk M, Kuś PM, Susniak K, Korona-Głowniak I. Phytochemical Profiles and Antimicrobial Activity of Selected Populus spp. Bud Extracts. Molecules 2024; 29:437. [PMID: 38257349 PMCID: PMC10819791 DOI: 10.3390/molecules29020437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Buds of poplar trees (Populus species) are often covered with sticky, usually polyphenol-rich, exudates. Moreover, accessible data showed that some Populus bud extracts may be excellent antibacterial agents, especially against Gram-positive bacteria. Due to the fragmentary nature of the data found, we conducted a systematic screening study. The antimicrobial activity of two extract types (semi-polar-ethanolic and polar-ethanolic-water (50/50; V/V)) from 27 bud samples of different poplar taxons were compared. Antimicrobial assays were performed against Gram-positive (five strains) and Gram-negative (six strains) bacteria as well as fungi (three strains) and covered the determination of minimal inhibitory, bactericidal, and fungicidal concentrations. The composition of extracts was later investigated by ultra-high-performance liquid chromatography coupled with ultraviolet detection (UHPLC-DAD) and with electrospray-quadrupole-time-of-flight tandem mass spectrometry (UHPLC-ESI-qTOF-MS). As a result, most of the extracts exhibited good (MIC ≤ 62.5 µg/mL) or moderate (62.5 < MIC ≤ 500 µg/mL) activity against Gram-positives and Helicobacter pylori, as well as fungi. The most active were ethanolic extracts from P. trichocarpa, P. trichocarpa clone 'Robusta', and P. tacamahaca × P. trichocarpa. The strongest activity was observed for P. tacamahaca × P. trichocarpa. Antibacterial activity was supposedly connected with the abundant presence of flavonoids (pinobanksin, pinobanksin 3-acetate, chrysin, pinocembrin, galangin, isosakuranetin dihydrochalcone, pinocembrin dihydrochalcone, and 2',6'-dihydroxy-4'-methoxydihydrochalcone), hydroxycinnamic acids monoesters (p-methoxycinnamic acid cinnamyl ester, caffeic acid phenethylate and different isomers of prenyl esters), and some minor components (balsacones).
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Affiliation(s)
- Piotr Okińczyc
- Department of Pharmacognosy and Herbal Medicines, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, PL-50-556 Wrocław, Poland; (M.W.); (P.M.K.)
| | - Jarosław Widelski
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, Chodźki 1, PL-20-093 Lublin, Poland
| | - Kinga Nowak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, PL-62-035 Kórnik, Poland;
| | - Sylwia Radwan
- Laboratory of Elemental Analysis and Structural Research, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, PL-50-556 Wrocław, Poland;
| | - Maciej Włodarczyk
- Department of Pharmacognosy and Herbal Medicines, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, PL-50-556 Wrocław, Poland; (M.W.); (P.M.K.)
| | - Piotr Marek Kuś
- Department of Pharmacognosy and Herbal Medicines, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, PL-50-556 Wrocław, Poland; (M.W.); (P.M.K.)
| | - Katarzyna Susniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodźki 1, PL-20-093 Lublin, Poland; (K.S.); (I.K.-G.)
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodźki 1, PL-20-093 Lublin, Poland; (K.S.); (I.K.-G.)
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Li S, Devi B, Allam G, Bhullar A, Murmu J, Li E, Hepworth SR. Regulation of secondary growth by poplar BLADE-ON-PETIOLE genes in Arabidopsis. Front Plant Sci 2023; 14:1244583. [PMID: 38034559 PMCID: PMC10682204 DOI: 10.3389/fpls.2023.1244583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
BLADE-ON-PETIOLE (BOP) genes are essential regulators of vegetative and reproductive development in land plants. First characterized in Arabidopsis thaliana (Arabidopsis), members of this clade function as transcriptional co-activators by recruiting TGACG-motif binding (TGA) basic leucine zipper (bZIP) transcription factors. Highly expressed at organ boundaries, these genes are also expressed in vascular tissue and contribute to lignin biosynthesis during secondary growth. How these genes function in trees, which undergo extensive secondary growth to produce wood, remains unclear. Here, we investigate the functional conservation of BOP orthologs in Populus trichocarpa (poplar), a widely-used model for tree development. Within the poplar genome, we identified two BOP-like genes, PtrBPL1 and PtrBPL2, with abundant transcripts in stems. To assess their functions, we used heterologous assays in Arabidopsis plants. The promoters of PtrBPL1 and PtrBPL2, fused with a β-glucuronidase (GUS) reporter gene showed activity at organ boundaries and in secondary xylem and phloem. When introduced into Arabidopsis plants, PtrBPL1 and PtrBPL2 complemented leaf and flower patterning defects in bop1 bop2 mutants. Notably, Arabidopsis plants overexpressing PtrBPL1 and PtrBPL2 showed defects in stem elongation and the lignification of secondary tissues in the hypocotyl and stem. Finally, PtrBPL1 and PtrBPL2 formed complexes with TGA bZIP proteins in yeast. Collectively, our findings suggest that PtrBPL1 and PtrBPL2 are orthologs of Arabidopsis BOP1 and BOP2, potentially contributing to secondary growth regulation in poplar trees. This work provides a foundation for functional studies in trees.
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Yang G, Wang S, Long L, Yu X, Cai H, Chen P, Gu L, Yang M. Genome-wide identification and expression analysis of PtJAZ gene family in poplar ( Populus trichocarpa). BMC Genom Data 2023; 24:55. [PMID: 37735623 PMCID: PMC10515044 DOI: 10.1186/s12863-023-01150-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ gene family in Populus trichocarpa. Through a series of bioinformatic approaches, their expression patterns under various stress conditions have been analyzed to explore and excavate the endogenous resistance genes of poplar and provide a theoretical basis for breeding new varieties of poplar resistance. RESULTS A total of 13 PtJAZ genes have been identified in P. trichocarpa and designated as PtJAZ1-PtJAZ13. Those 13 PtJAZ genes were unevenly distributed on nine chromosomes, and they could be divided into four subfamilies. The gene structures and motif composition of the members derived from the same subfamily were similar. Collinearity analysis demonstrated that, compared with Arabidopsis thaliana and Oryza sativa, the most collinear pairs (13) were found in P. trichocarpa and Eucalyptus robusta. Cis-acting element analysis suggested that the promoter regions of PtJAZs contained a large number of hormones and stress response elements, of which abscisic acid (ABA) and methyl jasmonate (MeJA) hormone response elements were the most abundant. The PtJAZ genes not only had diverse expression patterns in different tissues, but they also responded to various abiotic and biotic stress conditions. The co-expression network and GO and KEGG analyses showed that JAZ genes were closely related to insect resistance. CONCLUSIONS In this study, applying bioinformatic methods, 13 PtJAZ gene family members from P. trichocarpa were identified and comprehensively analyzed. By further studying the function of the poplar JAZ gene family, the aim is to select genes with better insect resistance and stress resistance so as to lay a solid foundation for the subsequent breeding of new poplar varieties.
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Affiliation(s)
- Gaixia Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Lianxiang Long
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Xiaoyue Yu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Hongyu Cai
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China.
| | - Lijiao Gu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China.
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, 071000, China.
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Sun L, Dong X, Song X. PtrABR1 Increases Tolerance to Drought Stress by Enhancing Lateral Root Formation in Populus trichocarpa. Int J Mol Sci 2023; 24:13748. [PMID: 37762051 PMCID: PMC10530772 DOI: 10.3390/ijms241813748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Roots are the main organ for water uptake and the earliest part of a plant's response to drought, making them of great importance to our understanding of the root system's response to drought. However, little is known about the underlying molecular mechanisms that control root responses to drought stress. Here, we identified and functionally characterized the AP2/ERF family transcription factor (TF) PtrABR1 and the upstream target gene zinc-finger protein TF PtrYY1, which respond to drought stress by promoting the growth and development of lateral roots in Populus trichocarpa. A root-specific induction of PtrABR1 under drought stress was explored. The overexpression of PtrABR1 (PtrABR1-OE) promoted root growth and development, thereby increasing tolerance to drought stress. In addition, PtrYY1 is directly bound to the promoter of PtrABR1 under drought stress, and the overexpression of PtrYY1 (PtrYY1-OE) promoted lateral root growth and development and increased tolerance to drought stress. An RNA-seq analysis of PtrABR1-OE with wild-type (WT) poplar identified PtrGH3.6 and PtrPP2C44, which share the same pattern of expression changes as PtrABR1. A qRT-PCR and cis-element analysis further suggested that PtrGH3.6 and PtrPP2C44 may act as potential downstream targets of PtrABR1 genes in the root response pathway to drought stress. In conclusion, these results reveal a novel drought regulatory pathway in which PtrABR1 regulates the network through the upstream target gene PtrYY1 and the potential downstream target genes PtrGH3.6 and PtrPP2C44, thereby promoting root growth and development and improving tolerance to drought stress.
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Affiliation(s)
- Lijiao Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.S.); (X.D.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Dong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.S.); (X.D.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xingshun Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (L.S.); (X.D.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Wu R, Guo L, Guo Y, Ma L, Xu K, Zhang B, Du L. The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles. BMC Genom Data 2023; 24:37. [PMID: 37403017 PMCID: PMC10320924 DOI: 10.1186/s12863-023-01138-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, classification, conserved motifs, cis-elements, chromosomal locations, evolution and expression patterns of the PtGLK genes in the woody model plant Populus trichocarpa were analyzed in detail. In total, 55 putative PtGLKs (PtGLK1-PtGLK55) were identified and divided into 11 distinct subfamilies according to the gene structure, motif composition and phylogenetic analysis. Synteny analysis showed that 22 orthologous pairs and highly conservation between regions of GLK genes across P. trichocarpa and Arabidopsis were identified. Furthermore, analysis of the duplication events and divergence times provided insight into the evolutionary patterns of GLK genes. The previously published transcriptome data indicated that PtGLK genes exhibited distinct expression patterns in various tissues and different stages. Additionally, several PtGLKs were significantly upregulated under the responses of cold stress, osmotic stress, and methyl jasmonate (MeJA) and gibberellic acid (GA) treatments, implying that they might take part in abiotic stress and phytohormone responses. Overall, our results provide comprehensive information on the PtGLK gene family and elucidate the potential functional characterization of PtGLK genes in P. trichocarpa.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lin Guo
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yueyang Guo
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lehang Ma
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kehang Xu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Boyu Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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Wang R, Zhao W, Yao W, Wang Y, Jiang T, Liu H. Genome-Wide Analysis of Strictosidine Synthase-like Gene Family Revealed Their Response to Biotic/Abiotic Stress in Poplar. Int J Mol Sci 2023; 24:10117. [PMID: 37373265 DOI: 10.3390/ijms241210117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The strictosidine synthase-like (SSL) gene family is a small plant immune-regulated gene family that plays a critical role in plant resistance to biotic/abiotic stresses. To date, very little has been reported on the SSL gene in plants. In this study, a total of thirteen SSLs genes were identified from poplar, and these were classified into four subgroups based on multiple sequence alignment and phylogenetic tree analysis, and members of the same subgroup were found to have similar gene structures and motifs. The results of the collinearity analysis showed that poplar SSLs had more collinear genes in the woody plants Salix purpurea and Eucalyptus grandis. The promoter analysis revealed that the promoter region of PtrSSLs contains a large number of biotic/abiotic stress response elements. Subsequently, we examined the expression patterns of PtrSSLs following drought, salt, and leaf blight stress, using RT-qPCR to validate the response of PtrSSLs to biotic/abiotic stresses. In addition, the prediction of transcription factor (TF) regulatory networks identified several TFs, such as ATMYB46, ATMYB15, AGL20, STOP1, ATWRKY65, and so on, that may be induced in the expression of PtrSSLs in response to adversity stress. In conclusion, this study provides a solid basis for a functional analysis of the SSL gene family in response to biotic/abiotic stresses in poplar.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenna Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Huanzhen Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Ma X, Yang H, Bu Y, Zhang Y, Sun N, Wu X, Jing Y. Genome-wide identification of the NRAMP gene family in Populus trichocarpa and their function as heavy metal transporters. Ecotoxicol Environ Saf 2023; 261:115110. [PMID: 37300917 DOI: 10.1016/j.ecoenv.2023.115110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
The natural resistance-associated macrophage protein (NRAMP) gene family plays a key role in essential mineral nutrient homeostasis, as well as toxic metal accumulation, translocation, and detoxification. Although the NRAMP family genes have been widely identified in various species, they still require to be analyzed comprehensively in tree species. In this study, a total of 11 NRAMP members (PtNRAMP1-11) were identified in Populus trichocarpa, a woody model plant, and further subdivided into three groups based on phylogenetic analysis. Chromosomal location analysis indicated that the PtNRAMP genes were unevenly distributed on six of the 19 Populus chromosomes. Gene expression analysis indicated that the PtNRAMP genes were differentially responsive to metal stress, including iron (Fe) and manganese (Mn) deficiency, as well as Fe, Mn, zinc (Zn), and cadmium (Cd) toxicity. Furthermore, the PtNRAMP gene functions were characterized using a heterologous yeast expression system. The results showed that PtNRAMP1, PtNRAMP2, PtNRAMP4, PtNRAMP9, PtNRAMP10, and PtNRAMP11 displayed the ability to transport Cd into yeast cells. In addition, PtNRAMP1, PtNRAMP6, and PtNRAMP7 complemented the Mn uptake mutant, while PtNRAMP1, PtNRAMP6, PtNRAMP7, and PtNRAMP9 complemented the Fe uptake mutant. In conclusion, our findings revealed the respective functions of PtNRAMPs during metal transport as well as their potential role in micronutrient biofortification and phytoremediation.
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Affiliation(s)
- Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China.
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11
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Harman-Ware AE, Martin MZ, Engle NL, Doeppke C, Tschaplinski TJ. Rapid screening of secondary aromatic metabolites in Populus trichocarpa leaves. Biotechnol Biofuels Bioprod 2023; 16:41. [PMID: 36899393 DOI: 10.1186/s13068-023-02287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND High-throughput metabolomics analytical methodology is needed for population-scale studies of bioenergy-relevant feedstocks such as poplar (Populus sp.). Here, the authors report the relative abundance of extractable aromatic metabolites in Populus trichocarpa leaves rapidly estimated using pyrolysis-molecular beam mass spectrometry (py-MBMS). Poplar leaves were analyzed in conjunction with and validated by GC/MS analysis of extracts to determine key spectral features used to build PLS models to predict the relative composition of extractable aromatic metabolites in whole poplar leaves. RESULTS The Pearson correlation coefficient for the relative abundance of extractable aromatic metabolites based on ranking between GC/MS analysis and py-MBMS analysis of the Boardman leaf set was 0.86 with R2 = 0.76 using a simplified prediction approach from select ions in MBMS spectra. Metabolites most influential to py-MBMS spectral features in the Clatskanie set included the following compounds: catechol, salicortin, salicyloyl-coumaroyl-glucoside conjugates, α-salicyloylsalicin, tremulacin, as well as other salicylates, trichocarpin, salicylic acid, and various tremuloidin conjugates. Ions in py-MBMS spectra with the highest correlation to the abundance of extractable aromatic metabolites as determined by GC/MS analysis of extracts, included m/z 68, 71, 77, 91, 94, 105, 107, 108, and 122, and were used to develop the simplified prediction approach without PLS models or a priori measurements. CONCLUSIONS The simplified py-MBMS method is capable of rapidly screening leaf tissue for relative abundance of extractable aromatic secondary metabolites to enable prioritization of samples in large populations requiring comprehensive metabolomics that will ultimately inform plant systems biology models and advance the development of optimized biomass feedstocks for renewable fuels and chemicals.
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12
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Geng L, Ren J, Ji X, Yan S, Song XS. Over-expression of DREB46 enhances drought tolerance in Populus trichocarpa. J Plant Physiol 2023; 281:153923. [PMID: 36657232 DOI: 10.1016/j.jplph.2023.153923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/20/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
The drought responsive element binding (DREB) gene family has a significant role in plant abiotic stress responses. Here, we cloned a drought-inducible DREB gene, DREB46 (Potri.019G075500), and investigated its function in drought tolerance in Populus trichocarpa. Under treatment with exogenous abscisic acid and 6% PEG6000, DREB46 was rapidly and abundantly expressed. We successfully inserted P. trichocarpa DREB46 constructs into P. trichocarpa. After 11 d of drought stress and 3 d of rehydration treatment, the DREB46 over-expression (OE) lines exhibited significantly increased survival rates relative to the wild type (WT). Histochemical staining showed that the accumulation of reactive oxygen species (ROS) in transgenic plants under drought stress was lower than that in WT plants. Furthermore, OE plants displayed higher superoxide dismutase, peroxidase, and catalase activities and proline content, but lower malondialdehyde content than the WT plants under drought stress. In contrast, DREB46-RNA interference (RNAi) lines exhibited the opposite phenotype. Under PEG-6000 stress, OE plants produced significantly more adventitious roots (ARs) than WT plants. In contrast, RNAi-mediated DREB46-inhibited poplar exhibited fewer ARs. Quantitative real-time PCR indicated that WOX11/12a (Potri.013G066900), a gene related to root growth and development regulation, was significantly increased in OE plants. Additionally, yeast two-hybrid (Y2H) assays showed that DREB46 could interact with protein kinase MPK1 (Potri.002G032100) and protein phosphatase PP2C47 (Potri.007G058700), respectively, and this result was also verified by luciferase complementation assay. Transient co-expression results of leaves showed that PP2C47 and DREB46 Agrobacterium-transformed leaves had strong drought tolerance. These results show that DREB46 plays a key role in drought tolerance by inducing the ROS scavenging system and increasing the number of ARs.
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Affiliation(s)
- Liangzhuang Geng
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jing Ren
- College of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaolong Ji
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shaopeng Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xing Shun Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China; Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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13
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Liu Y, Wang R, Yu J, Huang S, Zhang Y, Wei H, Wei Z. Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa. Int J Mol Sci 2023; 24. [PMID: 36614182 DOI: 10.3390/ijms24010740] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
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14
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Zhen C, Hua X, Jiang X, Tong G, Li C, Yang C, Cheng Y. Cas9/gRNA-Mediated Mutations in PtrFLA40 and PtrFLA45 Reveal Redundant Roles in Modulating Wood Cell Size and SCW Synthesis in Poplar. Int J Mol Sci 2022; 24. [PMID: 36613871 DOI: 10.3390/ijms24010427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) play an important role in plant development and adaptation to the environment. However, the roles of FLAs in wood formation remain poorly understood. Here, we identified a total of 50 PtrFLA genes in poplar. They were classified into four groups: A to D, among which group A was the largest group with 28 members clustered into four branches. Most PtrFLAs of group A were dominantly expressed in developing xylem based on microarray and RT-qPCR data. The roles of PtrFLA40 and PtrFLA45 in group A were investigated via the Cas9/gRNA-induced mutation lines. Loss of PtrFLA40 and PtrFLA45 increased stem length and diameter in ptrfla40ptrfla45 double mutants, but not in ptrfla40 or ptrfla45 single mutants. Further, our findings indicated that the ptrfla40ptrfla45 mutants enlarged the cell size of xylem fibers and vessels, suggesting a negative modulation in stem xylem cell size. In addition, wood lignin content in the ptrfla40fla45 mutants was increased by nearly 9%, and the lignin biosynthesis-related genes were significantly up-regulated in the ptrfla40fla45 mutants, in agreement with the increase in wood lignin content. Overall, Cas9/gRNA-mediated mutations in PtrFLA40 and PtrFLA45 reveal redundant roles in modulating wood cell size and secondary cell wall (SCW) synthesis in poplar.
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15
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Zhou M, Peng N, Yang C, Wang C. The Poplar ( Populus trichocarpa) Dehydrin Gene PtrDHN-3 Enhances Tolerance to Salt Stress in Arabidopsis. Plants (Basel) 2022; 11:2700. [PMID: 36297724 PMCID: PMC9611832 DOI: 10.3390/plants11202700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Dehydrin (DHN), a member of the late embryogenesis abundant protein (LEA) family, was recently found to play a role in physiological responses to salt and drought stress. In this study, we identified and cloned the PtrDHN-3 gene from Populus trichocarpa. The PtrDHN-3 protein encoded 226 amino acids, having a molecular weight of 25.78 KDa and an isoelectric point of 5.18. It was identified as a SKn-type DHN and was clustered with other resistance-related DHN proteins. Real-time fluorescent quantitative PCR showed that transcription levels of PtrDHN-3 were induced by mannitol stress, and more significantly by salt stress. Meanwhile, in a yeast transgenic assay, salt tolerance increased in the PtrDHN-3 transgenic yeast, while the germination rate, fresh weight and chlorophyll content increased in PtrDHN-3-overexpressing transgenic Arabidopsis plants (OE) under salt stress. Significant increases in expression levels of six antioxidant enzymes genes, and SOD and POD enzyme activity was also observed in the OE lines, resulting in a decrease in O2- and H2O2 accumulation. The proline content also increased significantly compared with the wild-type, along with expression of proline synthesis-related genes P5CS1 and P5CS2. These findings suggest that PtrDHN-3 plays an important role in salt resistance in plants.
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16
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Zhang Y, Liu Y, Wang X, Wang R, Chen X, Wang S, Wei H, Wei Z. PtrWOX13A Promotes Wood Formation and Bioactive Gibberellins Biosynthesis in Populus trichocarpa. Front Plant Sci 2022; 13:835035. [PMID: 35837467 PMCID: PMC9274204 DOI: 10.3389/fpls.2022.835035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
WUSCHEL-related homeobox (WOX) genes are plant-specific transcription factors (TFs) involved in multiple processes of plant development. However, there have hitherto no studies on the WOX TFs involved in secondary cell wall (SCW) formation been reported. In this study, we identified a Populus trichocarpa WOX gene, PtrWOX13A, which was predominantly expressed in SCW, and then characterized its functions through generating PtrWOX13A overexpression poplar transgenic lines; these lines exhibited not only significantly enhanced growth potential, but also remarkably increased SCW thicknesses, fiber lengths, and lignin and hemicellulose contents. However, no obvious change in cellulose content was observed. We revealed that PtrWOX13A directly activated its target genes through binding to two cis-elements, ATTGATTG and TTAATSS, in their promoter regions. The fact that PtrWOX13A responded to the exogenous GAs implies that it is responsive to GA homeostasis caused by GA inactivation and activation genes (e.g., PtrGA20ox4, PtrGA2ox1, and PtrGA3ox1), which were regulated by PtrWOX13A directly or indirectly. Since the master switch gene of SCW formation, PtrWND6A, and lignin biosynthesis regulator, MYB28, significantly increased in PtrWOX13A transgenic lines, we proposed that PtrWOX13A, as a higher hierarchy TF, participated in SCW formation through controlling the genes that are components of the known hierarchical transcription regulation network of poplar SCW formation, and simultaneously triggering a gibberellin-mediated signaling cascade. The discovery of PtrWOX13A predominantly expressed in SCW and its regulatory functions in the poplar wood formation has important implications for improving the wood quality of trees via genetic engineering.
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Affiliation(s)
- Yang Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xueying Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuebing Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Zhigang Wei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
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17
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Ye X, Wang S, Zhao X, Gao N, Wang Y, Yang Y, Wu E, Jiang C, Cheng Y, Wu W, Liu S. Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. Plant J 2022; 110:978-993. [PMID: 35218100 DOI: 10.1111/tpj.15714if] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 06/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.
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Affiliation(s)
- Xiaoxue Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ni Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yao Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ernest Wu
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
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18
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Ye X, Wang S, Zhao X, Gao N, Wang Y, Yang Y, Wu E, Jiang C, Cheng Y, Wu W, Liu S. Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. Plant J 2022; 110:978-993. [PMID: 35218100 DOI: 10.1111/tpj.15714] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 06/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.
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Affiliation(s)
- Xiaoxue Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ni Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yao Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ernest Wu
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
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19
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Ren M, Zhang Y, Wang R, Liu Y, Li M, Wang X, Chen X, Luan X, Zhang H, Wei H, Yang C, Wei Z. PtrHAT22, as a higher hierarchy regulator, coordinately regulates secondary cell wall component biosynthesis in Populus trichocarpa. Plant Sci 2022; 316:111170. [PMID: 35151454 DOI: 10.1016/j.plantsci.2021.111170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/20/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) II transcription factors (TFs) have been reported to play vital roles in diverse biological processes of plants. However, it remains unclear whether HD-Zip II TFs regulate secondary cell wall (SCW) in woody plants. In this study, we performed the functional characterization of a Populus trichocarpa HD-Zip II TF, PtrHAT22, which encodes a nuclear localized transcription repressor predominantly expressing in secondary developing tissues. Overexpression of PtrHAT22 showed arrested growths, including reduced heights and diameters above the ground, small leaves, and decreased biomass. Meanwhile, the contents of lignin, cellulose, and thickness of SCW significantly decreased, whilst the content of hemicellulose obviously increased in PtrHAT22 transgenic poplar. The expressions of some wood-associated TFs and structural genes significantly changed accordingly with the alternations of SCW characteristics in PtrHAT22 transgenic poplar. Furthermore, PtrHAT22 directly repressed the promoter activities of PtrMYB20, PtrMYB28, and PtrCOMT2, and bind two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggested that PtrHAT22, as a higher hierarchy TF like PtrWNDs, exerted coordination regulation of poplar SCW component biosynthesis through directly and indirectly regulating structural genes and different hierarchy TFs of SCW formation network.
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Affiliation(s)
- Mengxuan Ren
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Yang Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Meiliang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xueying Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xuebing Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xue Luan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China.
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China.
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20
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Wu K, Qu Y, Rong H, Han X, Tian Y, Xu L. Identification and Expression Analysis of the Populus trichocarpa GASA-Gene Family. Int J Mol Sci 2022; 23:ijms23031507. [PMID: 35163431 PMCID: PMC8835824 DOI: 10.3390/ijms23031507] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 02/04/2023] Open
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays an important regulatory role in the growth and development of plants. In this study, we identified 19 GASA genes using bioinformatics-based methods in Populus trichocarpa, and these PtGASA genes could be divided into three categories based on their phylogenetic relationships. Based on an analysis of the structure and motifs of these genes, it was concluded that PtGASA class II members are more conserved than class I and class III members are, and the results of collinearity analysis showed that members of class II are collinearly related in poplar. Expression analysis of Populus trichocarpa roots, stems, and leaves showed that most of the PtGASA genes are expressed at higher levels in the stems or roots than in the leaves; a similar expression pattern was found in Vitis vinifera, indicating that the GASA-family members mainly play a role in the morphogenesis of poplar. Considering the phenomenon of gene amplification, we found that the higher the similarity of homologous genes was, the more similar the expression patterns. This study represents the first whole-genome identification and expression-profile analysis of the GASA-gene family in poplar, a model species, laying a foundation for functional studies of poplar GASA genes and serving as a reference for related research on other woody plant species.
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Affiliation(s)
| | | | | | | | | | - Li’an Xu
- Correspondence: ; Tel.: +86-25-8542-7882
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21
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Baer AB, Fickle JC, Medina J, Robles C, Pratt RB, Jacobsen AL. Xylem biomechanics, water storage, and density within roots and shoots of an angiosperm tree species. J Exp Bot 2021; 72:7984-7997. [PMID: 34410349 DOI: 10.1093/jxb/erab384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Xylem is a complex tissue that forms the bulk of tree bodies and has several functions, including to conduct water, store water and nutrients, and biomechanically support the plant body. We examined how xylem functional traits varied at different positions within 9-year-old Populus balsamifera subsp. trichocarpa. Whole trees were excavated, and xylem samples were collected at 1-m increments along the main root-to-shoot axis of six trees, from root tip to shoot tip. We examined biomechanical and water-storage traits of the xylem, including using a non-invasive imaging technique to examine water content within long, intact branches (high-resolution computed tomography; microCT). Xylem density, strength, and stiffness were greater in shoots than roots. Along the main root-to-shoot axis, xylem strength and stiffness were greatest at shoot tips, and the tissue became linearly weaker and less stiff down the plant and through the root. Roots had greater water storage with lower biomechanical support, and shoots had biomechanically stronger and stiffer xylem with lower water storage. These findings support trade-offs among xylem functions between roots and shoots. Understanding how xylem functions differ throughout tree bodies is important in understanding whole-tree functioning and how terrestrial plants endure numerous environmental challenges over decades of growth.
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Affiliation(s)
- Alex B Baer
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
| | - Jaycie C Fickle
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
| | - Jackeline Medina
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
| | - Catherine Robles
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
| | - R Brandon Pratt
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
| | - Anna L Jacobsen
- Department of Biology, California State University, Bakersfield, CA, 93311, USA
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22
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Dong F, Wang Y, Tang M. Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress. J Fungi (Basel) 2021; 7:jof7121024. [PMID: 34947006 PMCID: PMC8703858 DOI: 10.3390/jof7121024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/20/2022] Open
Abstract
Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor-P. trichocarpa-B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes' expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.
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Affiliation(s)
- Fengxin Dong
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
| | - Yihan Wang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
| | - Ming Tang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: ; Tel.: +86-1370-922-9152
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23
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Zhao X, Tan L, Wang S, Shen Y, Guo L, Ye X, Liu S, Feng Y, Wu W. The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. Int J Mol Sci 2021; 22:ijms222111369. [PMID: 34768799 PMCID: PMC8583155 DOI: 10.3390/ijms222111369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors in plant development and abiotic/hormone-related stresses. However, evidence that SR proteins contribute to the process in woody plants has been lacking. Using phylogenetics, gene synteny, transgenic experiments, and RNA-seq analysis, we identified 24 PtSR genes and explored their evolution, expression, and function in Popolus trichocarpa. The PtSR genes were divided into six subfamilies, generated by at least two events of genome triplication and duplication. Notably, they were constitutively expressed in roots, stems, and leaves, demonstrating their fundamental role in P. trichocarpa. Additionally, most PtSR genes (~83%) responded to at least one stress (cold, drought, salt, SA, MeJA, or ABA), and, especially, cold stress induced a dramatic perturbation in the expression and/or alternative splicing (AS) of 18 PtSR genes (~75%). Evidentially, the overexpression of PtSCL30 in Arabidopsis decreased freezing tolerance, which probably resulted from AS changes of the genes (e.g., ICE2 and COR15A) critical for cold tolerance. Moreover, the transgenic plants were salt-hypersensitive at the germination stage. These indicate that PtSCL30 may act as a negative regulator under cold and salt stress. Altogether, this study sheds light on the evolution, expression, and AS of PtSR genes, and the functional mechanisms of PtSCL30 in woody plants.
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Affiliation(s)
- Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Ying Feng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Correspondence: (Y.F.); (W.W.)
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Correspondence: (Y.F.); (W.W.)
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24
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Yang J, Lv W, Shao L, Fu Y, Liu H, Yang C, Chen A, Xie X, Wang Z, Li C. PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species. Front Plant Sci 2021; 12:737004. [PMID: 34691113 PMCID: PMC8529222 DOI: 10.3389/fpls.2021.737004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/02/2021] [Indexed: 06/04/2023]
Abstract
In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.
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Affiliation(s)
- Jingli Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Wanqiu Lv
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Haimei Liu
- Biology Group, Jiamusi No.1 High School, Jiamusi, China
| | - Chengjun Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Aihua Chen
- Economic Forest Laboratory, Mudanjiang Branch of Heilongjiang Academy of Forestry, Mudanjiang, China
| | - Xieyu Xie
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Zhiwei Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
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25
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Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. Front Plant Sci 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
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Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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26
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Zhao H, Niu Y, Dong H, Jia Y, Wang Y. Characterization of the Function of Two S1Fa-Like Family Genes From Populus trichocarpa. Front Plant Sci 2021; 12:753099. [PMID: 34671378 PMCID: PMC8521066 DOI: 10.3389/fpls.2021.753099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
S1Fa-like transcription factors (TFs) are small molecular weight proteins that contain both nuclear localization and DNA binding domains. However, the functions of S1Fa-like TFs are poorly understood. In the present study, we identified the S1Fa-like TFs from the Populus trichocarpa genome, which revealed two S1Fa-like TF genes, PtS1Fa1 and PtS1Fa2. PtS1Fa1 and PtS1Fa2 expression was suppressed by drought and salt stress, and was also significantly altered by ABA, MeJA, or SA treatment. Both PtS1Fa1 and PtS1Fa2 are nuclear proteins. Transgenic P. trichocarpa plants overexpressing PtS1Fa1 and PtS1Fa2, respectively, were generated. The plants overexpressing PtS1Fa2 showed increased fresh weight, chlorophyll content, and root length and weight compared with those in wild-type (WT) P. trichocarpa under drought conditions. Meanwhile, these phenotype traits of plants overexpressing PtS1Fa1 were similar to those of WT plants. Furthermore, overexpression of PtS1Fa2 reduced the malondialdehyde (MDA) content, electrolyte leakage, H2O2 and O2- contents, and increased superoxide dismutase (SOD) and peroxidase (POD) activities. The expression of SOD and POD was also induced by PtS1Fa2. However, overexpression of PtS1Fa1 failed to affect any of these physiological parameters or SOD and POD gene expression. These results suggested that PtS1Fa2 plays a role in drought tolerance, and confers drought tolerance by increase antioxidant activity to reduce reactive oxygen species (ROS) accumulation.
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27
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Shen CC, Chen MX, Xiao T, Zhang C, Shang J, Zhang KL, Zhu FY. Global proteome response to Pb(II) toxicity in poplar using SWATH-MS-based quantitative proteomics investigation. Ecotoxicol Environ Saf 2021; 220:112410. [PMID: 34126303 DOI: 10.1016/j.ecoenv.2021.112410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 05/07/2023]
Abstract
Lead (Pb) toxicity is a growing serious environmental pollution that threatens human health and crop productivity. Poplar, as an important economic and ecological forest species, has the characteristics of fasting growth and accumulating heavy metals, which is a powerful model plant for phytoremediation. Here, a novel label-free quantitative proteomic platform of SWATH-MS was applied to detect proteome changes in poplar seedling roots following Pb treatment. In total 4388 unique proteins were identified and quantified, among which 542 proteins showed significant abundance changes upon Pb(II) exposure. Functional categorizations revealed that differentially expressed proteins (DEPs) primarily distributed in specialized biological processes. Particularly, lignin and flavonoid biosynthesis pathway were strongly activated upon Pb exposure, implicating their potential roles for Pb detoxification in poplar. Furthermore, hemicellulose and pectin related cell wall proteins exhibited increased abundances, where may function as a sequestration reservoir to reduce Pb toxicity in cytoplasm. Simultaneously, up-regulation of glutathione metabolism may serve as a protective role for Pb-induced oxidative damages in poplar. Further correlation investigation revealed an extra layer of post-transcriptional regulation during Pb response in poplar. Overall, our work represents multiply potential regulators in mediating Pb tolerance in poplar, providing molecular targets and strategies for phytoremediation.
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Affiliation(s)
- Cong-Cong Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tian Xiao
- Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
| | - Cheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China; International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jun Shang
- SpecAlly Life Technology Co., Ltd and Wuhan Institute of Biotechnology, Wuhan, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China; International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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28
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Zuo Z, Sun X, Cao L, Zhang S, Yu J, Xu X, Xu Z, Liu G, Qu C. Genome-wide identification of FRK genes in Populus trichocarpa and their expression under different nitrogen treatments. Physiol Mol Biol Plants 2021; 27:1919-1931. [PMID: 34616114 PMCID: PMC8484491 DOI: 10.1007/s12298-021-01055-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Fructokinase (FRK) is the main fructose phosphorylase and plays an important role in catalyzing the irreversible reaction of free fructose phosphorylation. In order to study the regulatory effect of different forms and concentrations of nitrogen on PtFRK genes in Populus trichocarpa, seven genes encoding the hypothetical FRK proteins were identified in Populus trichocarpa genome by bioinformatics method. Phylogenetic analysis revealed that PtFRK family genes can be divided into two subgroups: SI (PtFRK 1, 3, 4, 6) and SII (PtFRK 2, 5, 7). The tissue-specific expression data obtained from PopGenIE indicate that PtFRK2, 3, 4 and 5 are expressed highly in the stem. Quantitative real-time RT-PCR illustrate that PtFRK1-7 showed different expression patterns in different tissues under different concentrations and morphological nitrogen application. Under high nitrate treatment, the expression levels of PtFRK1, 2, 3 and 6 in stem increased significantly, while under low nitrate treatment, only the expression of PtFRK1, 4 in the upper stem and the expression of PtFRK3, 5 in the lower stem increased significantly. In contrast, ammonium tends to inhibit the expression of PtFRKs in lower stems, the expression levels of PtFRK2, 3, 4 and 5 are significantly reduced under ammonium treatment. However, high ammonium had significant effects on PtFRK6 in the apical bud and upper leaves, which were 6 and 8 times of the control, respectively. These results laid the foundation for the study of the PtFRK gene family of poplar and provided a theoretical basis for the molecular mechanism of nitrogen regulating cell wall development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01055-6.
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Affiliation(s)
- Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- Daxinganling Survey, Planning and Design Institute of State Forestry and Grassland Administration, Jiagedaqi, 165000 People’s Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Shuang Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040 People’s Republic of China
- College of Life Science, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040 People’s Republic of China
- College of Life Science, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040 People’s Republic of China
- College of Forestry, Guizhou University, Guiyang, 550025 People’s Republic of China
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Zhao H, Qu C, Zuo Z, Cao L, Zhang S, Xu X, Xu Z, Liu G. Genome Identification and Expression Profiles in Response to Nitrogen Treatment Analysis of the Class I CCoAOMT Gene Family in Populus. Biochem Genet 2021. [PMID: 34410559 DOI: 10.1007/s10528-021-10112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Lignin is essential for the characteristics and quality of timber. Nitrogen has significant effects on lignin contents in plants. Nitrogen has been found to affect wood quality in plantations and lignin content in plants. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is an important methyltransferase in lignin biosynthesis. However, the classification of woody plant CCoAOMT gene family members and the regulation mechanism of nitrogen are not clear. Bioinformatics methods were used to predict the members, classification, and transcriptional distribution of the CCoAOMT gene family in Populus trichocarpa. The results showed that there were five PtCCoAOMTs identified, and they could be divided into three sub-groups according to their structural and phylogenetic features. The results of tissue expression specificity analysis showed that: PtCCoAOMT1 was highly expressed in roots and internodes; PtCCoAOMT2 was highly expressed in roots, nodes, and internodes, PtCCoAOMT3 was highly expressed in stems; PtCCoAOMT4 was highly expressed in young leaves, and, PtCCoAOMT5 was highly expressed in roots. Different forms and concentrations of nitrogen had varying effects on the expression patterns of genes in different plant tissue types. The results of real-time PCR showed that the expression levels of PtCCoAOMT1 and PtCCoAOMT2 in stems increased significantly under different forms of nitrogen. PtCCoAOMT3 and PtCCoAOMT4 were induced by nitrate nitrogen in upper stems and lower leaves, respectively. PtCCoAOMT4 and PtCCoAOMT5 were induced by different concentrations of nitrate nitrogen in lower stems and roots, respectively. These results could provide valuable information for revealing the differences between functions and expression patterns of the various CCoAOMT gene family members under different forms and concentrations of exogenous nitrogen in poplar.
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Xu C, Zhang S, Suo J, Chang R, Xu X, Xu Z, Yang C, Qu C, Liu G. Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment. 3 Biotech 2021; 11:370. [PMID: 34295610 DOI: 10.1007/s13205-021-02918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022] Open
Abstract
Plant Pectin acetylesterase (PAE) belongs to family CE13 of carbohydrate esterases in the CAZy database. The ability of PAE to regulate the degree of acetylation of pectin, an important polysaccharide in the cell wall, affects the structure of plant cell wall. In this study, ten PtPAE genes were identified and characterized in Populus trichocarpa genome using bioinformatics methods, and the physiochemical properties such as molecular weight, isoelectric points, and hydrophilicity, as well as the secondary and tertiary structure of the protein were predicted. According to phylogenetic analysis, ten PtPAEs can be divided into three evolutionary clades, each of which had similar gene structure and motifs. Tissue-specific expression profiles indicated that the PtPAEs had different expression patterns. Real-time quantitative PCR (RT-qPCR) analysis showed that transcription level of PtPAEs was regulated by different CO2 and nitrogen concentrations. These results provide important information for the study of the phylogenetic relationship and function of PtPAEs in Populus trichocarpa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02918-1.
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Xu W, Cheng H, Zhu S, Cheng J, Ji H, Zhang B, Cao S, Wang C, Tong G, Zhen C, Mu L, Zhou Y, Cheng Y. Functional understanding of secondary cell wall cellulose synthases in Populus trichocarpa via the Cas9/gRNA-induced gene knockouts. New Phytol 2021; 231:1478-1495. [PMID: 33713445 PMCID: PMC8362133 DOI: 10.1111/nph.17338] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/02/2021] [Indexed: 05/12/2023]
Abstract
Plant cellulose is synthesized by a large plasma membrane-localized cellulose synthase (CesA) complex. However, an overall functional determination of secondary cell wall (SCW) CesAs is still lacking in trees, especially one based on gene knockouts. Here, the Cas9/gRNA-induced knockouts of PtrCesA4, 7A, 7B, 8A and 8B genes were produced in Populus trichocarpa. Based on anatomical, immunohistochemical and wood composition evidence, we gained a comprehensive understanding of five SCW PtrCesAs at the genetic level. Complete loss of PtrCesA4, 7A/B or 8A/B led to similar morphological abnormalities, indicating similar and nonredundant genetic functions. The absence of the gelatinous (G) layer, one-layer-walled fibres and a 90% decrease in cellulose in these mutant woods revealed that the three classes of SCW PtrCesAs are essential for multilayered SCW structure and wood G-fibre. In addition, the mutant primary and secondary phloem fibres lost the n(G + L)- and G-layers and retained the thicker S-layers (L, lignified; S, secondary). Together with polysaccharide immunolocalization data, these findings suggest differences in the role of SCW PtrCesAs-synthesized cellulose in wood and phloem fibre wall structures. Overall, this functional understanding of the SCW PtrCesAs provides further insights into the impact of lacking cellulose biosynthesis on growth, SCW, wood G-fibre and phloem fibre wall structures in the tree.
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Affiliation(s)
- Wenjing Xu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
- School of ForestryNortheast Forestry UniversityHarbin150040China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Siran Zhu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Jiyao Cheng
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Huanhuan Ji
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Baocai Zhang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Shenquan Cao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Guimin Tong
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Cheng Zhen
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Liqiang Mu
- School of ForestryNortheast Forestry UniversityHarbin150040China
| | - Yihua Zhou
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
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Apuli RP, Richards T, Rendón-Anaya M, Karacic A, Rönnberg-Wästljung AC, Ingvarsson PK. The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray). BMC Plant Biol 2021; 21:317. [PMID: 34215191 PMCID: PMC8252265 DOI: 10.1186/s12870-021-03103-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment. RESULTS We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions. CONCLUSIONS In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.
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Affiliation(s)
- Rami-Petteri Apuli
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Thomas Richards
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Martha Rendón-Anaya
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Almir Karacic
- Institute for Crop Production Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
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Liu X, Gao Y, Liao J, Miao M, Chen K, Xi F, Wei W, Wang H, Wang Y, Xu X, Reddy ASN, Gu L. Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa. J Integr Plant Biol 2021; 63:1294-1308. [PMID: 33570252 DOI: 10.1111/jipb.13081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Circular RNAs (circRNAs) are a recently discovered type of non-coding RNA derived from pre-mRNAs. R-loops consist of a DNA:RNA hybrid and the associated single-stranded DNA. In Arabidopsis thaliana, circRNA:DNA R-loops regulate alternative splicing (AS) of SEPALLATA3 (SEP3). However, the occurrence and functions of circRNAs and R-loops in Populus trichocarpa are largely unexplored. Here, we performed circRNA-enriched sequencing in the stem-differentiating xylem (SDX) of P. trichocarpa and identified 2,742 distinct circRNAs, including circ-CESA4, circ-IRX7, and circ-GUX1, which are generated from genes involved in cellulose, and hemicellulose biosynthesis, respectively. To investigate the roles of circRNAs in modulating alternative splicing (AS), we detected 7,836 AS events using PacBio Iso-Seq and identified 634 circRNAs that overlapped with 699 AS events. Furthermore, using DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP-seq), we identified 8,932 R-loop peaks that overlapped with 181 circRNAs and 672 AS events. Notably, several SDX-related circRNAs overlapped with R-loop peaks, pointing to their possible roles in modulating AS in SDX. Indeed, overexpressing circ-IRX7 increased the levels of R-loop structures and decreased the frequency of intron retention in linear IRX7 transcripts. This study provides a valuable R-loop atlas resource and uncovers the interplay between circRNAs and AS in SDX of P. trichocarpa.
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Affiliation(s)
- Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiakai Liao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Miao Miao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xi Xu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Bian Z, Wang D, Liu Y, Xi Y, Wang X, Meng S. Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response. Plant Physiol Biochem 2021; 163:178-188. [PMID: 33848930 DOI: 10.1016/j.plaphy.2021.03.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in the model plant species Arabidopsis thaliana, rice and maize but not in woody plant species, which have important economic and ecological value. In this study, we systematically analyzed Populus BGLUs (PtBGLUs) and demonstrated the involvement of several genes under stress conditions. Forty-four PtBGLUs were identified in Populus databases; these genes were located on 11 chromosomes, and the proteins of several PtBGLU genes were highly similar. More than 90% of PtBGLUs contain three conserved motifs. Collinearity results showed that 44 PtBGLU genes resulted from 12 tandem and 5 segmental duplication events. Phylogenetic analysis revealed that 128 BGLU genes from Populus trichocarpa, A. thaliana and Oryza sativa could be classified into 4 subgroups and subgroup Ⅱ and Ⅳ were differently having PtBGLUs and AtBGLUs. We further investigated whether several PtBGLUs responded to drought stress and ABA treatment, and the results showed that most of the selected BGLU genes were expressed in response to stress, which is consistent with previous studies involving rice and Arabidopsis homologous genes. Large numbers of stress-, hormone-, and development-related elements in the PtBGLU promoters suggest that BGLU genes may be involved in complex networks. Taken together, our results provide valuable information for an improved understanding of β-glucosidase function in woody plants.
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Affiliation(s)
- Zhan Bian
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Dongli Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Yunshan Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China; College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing, 404100, China
| | - Yimin Xi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China
| | - Xiaoling Wang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, 330096, China.
| | - Sen Meng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
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He F, Shi YJ, Mi JX, Zhao KJ, Cui XL, Chen LH, Yang HB, Zhang F, Zhao Q, Huang JL, Wan XQ. Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress. Int J Mol Sci 2021; 22:4664. [PMID: 33925110 PMCID: PMC8124260 DOI: 10.3390/ijms22094664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.
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Affiliation(s)
- Fang He
- Correspondence: (F.H.); (X.-Q.W.); Tel.: +86-176-8377-7884 (F.H.); +86-138-8163-4583 (X.-Q.W.)
| | | | | | | | | | | | | | | | | | | | - Xue-Qin Wan
- Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (Y.-J.S.); (J.-X.M.); (K.-J.Z.); (X.-L.C.); (L.-H.C.); (H.-B.Y.); (F.Z.); (Q.Z.); (J.-L.H.)
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Wang H, Chen JG, Chang Y. Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response. Front Plant Sci 2021; 12:650109. [PMID: 33959141 PMCID: PMC8095670 DOI: 10.3389/fpls.2021.650109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis, and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis-acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.
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Affiliation(s)
- Hemeng Wang
- Northeast Agricultural University, Harbin, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ying Chang
- Northeast Agricultural University, Harbin, China
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Zhang S, Cao L, Sun X, Yu J, Xu X, Chang R, Suo J, Liu G, Xu Z, Qu C. Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment. 3 Biotech 2021; 11:149. [PMID: 33732570 DOI: 10.1007/s13205-021-02697-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Plant UDP-glucose 6-dehydrogenase (UGDH) is an important enzyme for the formation of hemicellulose and pectin. Previous studies on UGDH have primarily focused on the biosynthesis of cell wall polysaccharides, while few studies have focused on their regulation by exogenous nitrogen. In the present study, four genes encoding PtUGDH proteins were analyzed by bioinformatics methods. And, the expression profiles of PtUGDH genes under different nitrogen treatments were evaluated with qRT-PCR. The results showed that PtUGDHs have conserved NAD coenzyme binding motif GAGYVGG and the catalytic motif GFGGSCFQKDIL. According to the phylogenetic analysis, PtUGDHs were divided into two subgroups. PtUGDH3 and PtUGDH4 were closely related to AtUGDH1 (important for normal development of Arabidopsis cell wall structure). Chromosomal distribution and genome synteny analysis revealed four segmental-duplicated gene pairs on chr4, 8, 10 and 17. Tissue-specific data from PlantGenIE showed that PtUGDH3 and PtUGDH4 were highly expressed in stems. The qRT-PCR detection showed that the expression of PtUGDH3 in the lower stem and PtUGDH2 of upper leaves were significantly increased induced by low ammonium or nitrate condition. This comprehensive analysis of the UGDH family in poplar provides new insights into their regulation by nitrogen, and would increase our understanding of the roles of UGDHs in hemicellulose and pectin biosynthesis in the cell wall and during poplar development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02697-9.
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Leng X, Wang H, Zhang S, Qu C, Yang C, Xu Z, Liu G. Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa. Genes (Basel) 2021; 12:334. [PMID: 33668872 DOI: 10.3390/genes12030334] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa.
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Lackus ND, Morawetz J, Xu H, Gershenzon J, Dickschat JS, Köllner TG. The Sesquiterpene Synthase PtTPS5 Produces (1 S,5 S,7 R,10 R)-Guaia-4(15)-en-11-ol and (1 S,7 R,10 R)-Guaia-4-en-11-ol in Oomycete-Infected Poplar Roots. Molecules 2021; 26:555. [PMID: 33494506 PMCID: PMC7866031 DOI: 10.3390/molecules26030555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 01/15/2023] Open
Abstract
Pathogen infection often leads to the enhanced formation of specialized plant metabolites that act as defensive barriers against microbial attackers. In this study, we investigated the formation of potential defense compounds in roots of the Western balsam poplar (Populus trichocarpa) upon infection with the generalist root pathogen Phytophthora cactorum (Oomycetes). P. cactorum infection led to an induced accumulation of terpenes, aromatic compounds, and fatty acids in poplar roots. Transcriptome analysis of uninfected and P. cactorum-infected roots revealed a terpene synthase gene PtTPS5 that was significantly induced upon pathogen infection. PtTPS5 had been previously reported as a sesquiterpene synthase producing two unidentified sesquiterpene alcohols as major products and hedycaryol as a minor product. Using heterologous expression in Escherichia coli, enzyme assays with deuterium-labeled substrates, and NMR analysis of reaction products, we could identify the major PtTPS5 products as (1S,5S,7R,10R)-guaia-4(15)-en-11-ol and (1S,7R,10R)-guaia-4-en-11-ol, with the former being a novel compound. The transcript accumulation of PtTPS5 in uninfected and P. cactorum-infected poplar roots matched the accumulation of (1S,5S,7R,10R)-guaia-4(15)-en-11-ol, (1S,7R,10R)-guaia-4-en-11-ol, and hedycaryol in this tissue, suggesting that PtTPS5 likely contributes to the pathogen-induced formation of these compounds in planta.
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Affiliation(s)
- Nathalie D. Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jennifer Morawetz
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
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Gao Y, Liu X, Wu B, Wang H, Xi F, Kohnen MV, Reddy ASN, Gu L. Quantitative profiling of N 6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol 2021; 22:22. [PMID: 33413586 PMCID: PMC7791831 DOI: 10.1186/s13059-020-02241-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A.
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Affiliation(s)
- Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bizhi Wu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. Front Plant Sci 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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Ren M, Zhang Y, Liu C, Liu Y, Tian S, Cheng H, Zhang H, Wei H, Wei Z. Characterization of a High Hierarchical Regulator, PtrGATA12, Functioning in Differentially Regulating Secondary Wall Component Biosynthesis in Populus trichocarpa. Front Plant Sci 2021; 12:657787. [PMID: 33968111 PMCID: PMC8096934 DOI: 10.3389/fpls.2021.657787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/01/2021] [Indexed: 05/16/2023]
Abstract
In plants, GATA transcription factors (TFs) have been reported to play vital roles in to a wide range of biological processes. To date, there is still no report about the involvement and functions of woody plant GATA TFs in wood formation. In this study, we described the functional characterization of a Populus trichocarpa GATA TF, PtrGATA12, which encodes a nuclear-localized transcriptional activator predominantly expressing in developing xylem tissues. Overexpression of PtrGATA12 not only inhibited growths of most phenotypic traits and biomass accumulation, but also altered the expressions of some master TFs and pathway genes involved in secondary cell wall (SCW) and programmed cell death, leading to alternated SCW components and breaking forces of stems of transgenic lines. The significant changes occurred in the contents of hemicellulose and lignin and SCW thicknesses of fiber and vessel that increased by 13.5 and 10.8%, and 20.83 and 11.83%, respectively. Furthermore, PtrGATA12 bound directly to the promoters of a battery of TFs and pathway genes and activated them; the binding sites include two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggest PtrGATA12, as a higher hierarchical TF on the top of PtrWND6A, PtrWND6B, PtrMYB152, and PtrMYB21, exert a coordinated regulation of SCW components biosynthesis pathways through directly and indirectly controlling master TFs, middle-level TFs, and further downstream pathway genes of the currently known hierarchical transcription network that governs SCW formation.
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Affiliation(s)
- Mengxuan Ren
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| | - Yang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Zhigang Wei,
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Sun X, Cao L, Zhang S, Yu J, Xu X, Xu C, Xu Z, Qu C, Liu G. Genome-wide analysis of the RGP gene family in Populus trichocarpa and their expression under nitrogen treatment. Gene Expr Patterns 2020; 38:119142. [PMID: 32898702 DOI: 10.1016/j.gep.2020.119142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 10/23/2022]
Abstract
Reversible glycosylation polypeptide (RGP) is a type of plant-specific protein, primarily involved in the biosynthesis of cell wall polysaccharides, which in turn changes the shape of the cell walls and affects the wood properties of plants. Poplar is a major industrial timber species, and the RGP gene has not been studied. This study uses bioinformatics methods to predict physical and chemical characters such as molecular weight, isoelectric point, and hydrophilicity; and fluorescent quantitative method to determine the effect of different forms of nitrogen on the transcription level of the gene family. The results showed that there are six RGP homologous genes in the Populus trichocarpa genome, which were distributed on the six chromosomes of P. trichocarpa. The family members have a simple gene structure and contain four exons and introns. Phylogenetic tree analysis showed that RGP genes all belong to Class I in P. trichocarpa. Tissue-specific expression analysis showed that PtRGP1 and PtRGP2 were highly expressed in the stems, PtRGP4 and PtRGP5 were highly expressed in the upper leaves, PtRGR3 and PtRGR6 were expressed in stems and internodes, but the relative expression is not high. Quantitative real-time RT-PCR (qRT-PCR) analyses revealed that PtRGP3 and 6 were up-regulated in the upper stem in response to the low ammonium and high nitrate treatments. The influence of nitrogen on the expression of PtRGP3 and 6 genes may affect the formation of the plant secondary cell wall. This study lays a foundation for further study on the function of RGP genes in P. trichocarpa.
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Affiliation(s)
- Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Shuang Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Caifeng Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Zhiru Xu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, PR China; School of Forestry, Northeast Forestry University, Harbin, 150040, China.
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Zhang Y, Liu C, Cheng H, Tian S, Liu Y, Wang S, Zhang H, Saqib M, Wei H, Wei Z. DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems. BMC Genomics 2020; 21:498. [PMID: 32689934 PMCID: PMC7372836 DOI: 10.1186/s12864-020-06902-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022] Open
Abstract
Background As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. Results The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation. Conclusions DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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Leopold DR, Busby PE. Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function. Curr Biol 2020; 30:3260-3266.e5. [PMID: 32679100 DOI: 10.1016/j.cub.2020.06.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 01/08/2023]
Abstract
The composition of host-associated microbiomes can have important consequences for host health and fitness [1-3]. Yet we still lack understanding of many fundamental processes that determine microbiome composition [4, 5]. There is mounting evidence that historical contingency during microbiome assembly may overshadow more deterministic processes, such as the selective filters imposed by host traits [6-8]. More specifically, species arrival order has been frequently shown to affect microbiome composition [9-12], a phenomenon known as priority effects [13-15]. However, it is less clear whether priority effects during microbiome assembly are consequential for the host [16] or whether intraspecific variation in host traits can alter the trajectory of microbiome assembly under priority effects. In a greenhouse inoculation experiment using the black cottonwood (Populus trichocarpa) foliar microbiome, we manipulated host genotype and the colonization order of common foliar fungi. We quantified microbiome assembly outcomes using fungal marker gene sequencing and measured susceptibility of the colonized host to a leaf rust pathogen, Melampsora × columbiana. We found that the effect of species arrival order on microbiome composition, and subsequent disease susceptibility, depended on the host genotype. Additionally, we found that microbiome assembly history can affect host disease susceptibility independent of microbiome composition at the time of pathogen exposure, suggesting that the interactive effects of species arrival order and host genotype can decouple community composition and function. Overall, these results highlight the importance of a key process underlying stochasticity in microbiome assembly while also revealing which hosts are most likely to experience these effects.
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Liu HJ, Wang X, Yang ZL, Ren LL, Qian TT. Identification and biochemical characterization of the glutathione reductase family from Populus trichocarpa. Plant Sci 2020; 294:110459. [PMID: 32234218 DOI: 10.1016/j.plantsci.2020.110459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/14/2020] [Accepted: 02/24/2020] [Indexed: 05/05/2023]
Abstract
Glutathione reductase (GR; EC 1.6.4.2) is a key NADPH-dependent flavo-protein oxidoreductase which can catalyze the oxidized glutathione (GSSG) to reduced glutathione (GSH) to protect plant cells from oxidative damage induced by Reactive oxygen species (ROS) burst. To investigate the biochemical characteristics and functional divergence of Populus GR family, three GR genes (PtGR1.1/1.2/2) were cloned from Populus trichocarpa and their biochemical characteristics were analyzed in this study. All the three genes were expressed in root, stem, leaf and bud, and the expression of PtGR genes were general upregulated under salicylic acid and alamethicin treatment. PtGR1.1 and PtGR1.2 were localized in cytoplasm, while PtGR2 was in chloroplast. The three PtGR proteins showed different enzymatic activities, apparent kinetic characteristic and thermal stability profiles. However, they have similar bivalent metal ions (Cu2+, Cd2+, Zn2+ and Pb2+) sensitivity and optimum pH profiles. Our study sheds light on a comprehensive information of glutathione reductase family in P. trichocarpa, and proved PtGR genes play critical roles when suffering different stresses.
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Affiliation(s)
- Hai-Jing Liu
- Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Ling Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Ling Ren
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ting-Ting Qian
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wei H, Movahedi A, Xu C, Sun W, Wang X, Li D, Zhuge Q. Overexpression of PtDefensin enhances resistance to Septotis populiperda in transgenic poplar. Plant Sci 2020; 292:110379. [PMID: 32005384 DOI: 10.1016/j.plantsci.2019.110379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/04/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Plant defensins have been implicated in the plant defense system, but their role in poplar immunity is still unclear. In the present study, we present evidence that PtDefensin, a putative plant defensin, participates in the defense of poplar plants against Septotis populiperda infection. After the construction of recombinant plasmid PET-32a-PtDefensin, PtDefensin protein was expressed in Escherichia coli strain BL21 (DE3) and purified through Ni-IDA resin affinity chromatography. The Trx-PtDefensin fusion protein displayed no cytotoxic activity against RAW264.7 cells but had cytotoxic activity against E. coli K12D31 cells. Analyses of PtDefensin transcript abundance showed that the expression levels of PtDefensin responded to abiotic and biotic stresses. Overexpression of PtDefensin in 'Nanlin 895' poplars (Populus × euramericana cv 'Nanlin895') increased resistance to Septotis populiperda, coupled with upregulation of MYC2 (basic helix-loop-helix (bHLH) transcription factor) related to jasmonic acid (JA) signal transduction pathways and downregulation of Jasmonate-zim domain (JAZ), an inhibitor in the JA signal transduction pathway. We speculate that systemic acquired resistance (SAR) was activated in non-transgenic poplars after S. populiperda incubation, and that induced systemic resistance (ISR) was activated more obviously in transgenic poplars after S. populiperda incubation. Hence, overexpression of PtDefensin may improve the resistance of poplar plants to pathogens.
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Affiliation(s)
- Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China
| | - Chen Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China; Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, 211171, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China
| | - Xiaoli Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University. Nanjing, 210037, China.
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Gao Y, Yang F, Liu J, Xie W, Zhang L, Chen Z, Peng Z, Ou Y, Yao Y. Genome-Wide Identification of Metal Tolerance Protein Genes in Populus trichocarpa and Their Roles in Response to Various Heavy Metal Stresses. Int J Mol Sci 2020; 21:ijms21051680. [PMID: 32121430 PMCID: PMC7084629 DOI: 10.3390/ijms21051680] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 01/22/2023] Open
Abstract
Metal tolerance proteins (MTPs) are plant divalent cation transporters that play important roles in plant metal tolerance and homeostasis. Poplar is an ideal candidate for the phytoremediation of heavy metals because of its numerous beneficial attributes. However, the definitive phylogeny and heavy metal transport mechanisms of the MTP family in poplar remain unknown. Here, 22 MTP genes in P. trichocarpa were identified and classified into three major clusters and seven groups according to phylogenetic relationships. An evolutionary analysis suggested that PtrMTP genes had undergone gene expansion through tandem or segmental duplication events. Moreover, all PtrMTPs were predicted to localize in the vacuole and/or cell membrane, and contained typical structural features of the MTP family, cation efflux domain. The temporal and spatial expression pattern analysis results indicated the involvement of PtrMTP genes in poplar developmental control. Under heavy metal stress, most of PtrMTP genes were induced by at least two metal ions in roots, stems or leaves. In addition, PtrMTP8.1, PtrMTP9 and PtrMTP10.4 displayed the ability of Mn transport in yeast cells, and PtrMTP6 could transport Co, Fe and Mn. These findings will provide an important foundation to elucidate the biological functions of PtrMTP genes, and especially their role in regulating heavy metal tolerance in poplar.
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Marzec-Schmidt K, Wojciechowska N, Nemeczek K, Ludwików A, Mucha J, Bagniewska-Zadworna A. Allies or Enemies: The Role of Reactive Oxygen Species in Developmental Processes of Black Cottonwood ( Populus trichocarpa). Antioxidants (Basel) 2020; 9:E199. [PMID: 32120843 DOI: 10.3390/antiox9030199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
In contrast to aboveground organs (stems and leaves), developmental events and their regulation in underground organs, such as pioneer and fine roots, are quite poorly understood. The objective of the current study was to achieve a better understanding of the physiological and molecular role of reactive oxygen species (ROS) and ROS-related enzymes in the process of stem and pioneer root development in black cottonwood (Populus trichocarpa), as well as in the senescence of leaves and fine roots. Results of a transcriptomic analysis revealed that primary/secondary growth and senescence are accompanied by substantial changes in the expression of genes related to oxidative stress metabolism. We observed that some mechanisms common for above- and under-ground organs, e.g., the expression of superoxide dismutase (SOD) genes and SOD activity, declined during stems' and pioneer roots' development. Moreover, the localization of hydrogen peroxide (H2O2) and superoxide (O2•-) in the primary and secondary xylem of stems and pioneer roots confirms their involvement in xylem cell wall lignification and the induction of programmed cell death (PCD). H2O2 and O2•- in senescing fine roots were present in the same locations as demonstrated previously for ATG8 (AuTophaGy-related) proteins, implying their participation in cell degradation during senescence, while O2•- in older leaves was also localized similarly to ATG8 in chloroplasts, suggesting their role in chlorophagy. ROS and ROS-related enzymes play an integral role in the lignification of xylem cell walls in Populus trichocarpa, as well as the induction of PCD during xylogenesis and senescence.
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Wei H, Movahedi A, Xu C, Sun W, Wang P, Li D, Yin T, Zhuge Q. Characterization, Expression Profiling, and Functional Analysis of PtDef, a Defensin-Encoding Gene From Populus trichocarpa. Front Microbiol 2020; 11:106. [PMID: 32117134 PMCID: PMC7018670 DOI: 10.3389/fmicb.2020.00106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/17/2020] [Indexed: 01/09/2023] Open
Abstract
PtDef cloned from Populus trichocarpa contained eight cysteine domains specific to defensins. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis showed that PtDef was expressed in all tissues tested, with lower expression in leaves and higher expression in petioles, stems, and roots. Purified fused PtDef inhibited Aspergillus niger, Alternaria Nees, Mucor corymbifer, Marssonina populi, Rhizopus sp., and Neurospora crassa. PtDef also inhibited the growth of Escherichia coli by triggering autolysis. PtDef overexpression in Nanlin895 poplar (Populus × euramericana cv. Nanlin895) enhanced the level of resistance to Septotinia populiperda. qRT-PCR analysis also showed that the expression of 13 genes related to salicylic acid (SA) and jasmonic acid (JA) signal transduction differed between transgenic and wild-type (WT) poplars before and after inoculation, and that PR1-1 (12–72 h), NPR1-2, TGA1, and MYC2-1 expression was higher in transgenic poplars than in WT. During the hypersensitivity response (HR), large amounts of H2O2 were produced by the poplar lines, particularly 12–24 h after inoculation; the rate and magnitude of the H2O2 concentration increase were greater in transgenic lines than in WT. Overall, our findings suggest that PtDef, a defensin-encoding gene of P. trichocarpa, could be used for genetic engineering of woody plants for enhanced disease resistance.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Ali Movahedi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Chen Xu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China.,Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, China
| | - Weibo Sun
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Pu Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Dawei Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Tongming Yin
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Qiang Zhuge
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
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