1
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Wang L, Liu M, Luo Z, Chen Y, Qi Y, Ye M, Chen F, Dai F. Effect of modified atmosphere package on attributes of sweet bamboo shoots after harvest. FRONTIERS IN PLANT SCIENCE 2024; 15:1431097. [PMID: 38947949 PMCID: PMC11212469 DOI: 10.3389/fpls.2024.1431097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024]
Abstract
Tender bamboo shoots undergo rapid senescence that influences their quality and commercial value after harvest. In this study, the tender sweet bamboo shoots ('Wensun') were packed by a passive modified atmosphere packaging (PMAP) to inhibit the senescence process, taking polyethylene package as control. The increase in CO2 and the decrease in O2 gas concentrations in the headspace atmosphere of the packages were remarkably modified by PMAP treatments. The modified gas atmosphere packaging inhibited the changes in firmness, as well as the content of cellulose, total pectin, and lignin in the cell walls of bamboo shoots. The enzymatic activities of cellulase, pectinase, and polygalacturonase that act on cell wall polysaccharides, and phenylalanine ammonia lyase, cinnamyl alcohol dehydrogenase, peroxidase, and laccase regulating the lignin biosynthesis were modified by PMAP treatment different from control during storage. The expression levels of the lignin biosynthesis genes PePAL3/4, PeCAD, Pe4CL5, PeC4H, PeCCOAOMT, PeCOMT, cellulose synthase PeCESA1, and related transcription factors PeSND2, PeKNAT7, PeMYB20, PeMYB63, and PeMYB85 were clearly regulated. These results suggest that PMAP efficiently retards the changes in lignin and cell wall polysaccharides, thus delaying the senescence of tender sweet bamboo shoots during storage.
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Affiliation(s)
- Ling Wang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, China
| | | | | | | | | | | | | | - Fanwei Dai
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, China
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2
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Xu S, Wei X, Yang Q, Hu D, Zhang Y, Yuan X, Kang F, Wu Z, Yan Z, Luo X, Sun Y, Wang S, Feng Y, Xu Q, Zhang M, Yang Y. A KNOX Ⅱ transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in rice. PLANT COMMUNICATIONS 2024:101001. [PMID: 38863209 DOI: 10.1016/j.xplc.2024.101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/21/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Nucleotide-binding site and leucine-rich repeat (NLR) proteins are activated by detecting pathogen effectors, which in turn trigger host defenses and cell death. Although many NLRs have been identified, the mechanisms responsible for NLR-triggered defense responses are still poorly understood. In this study, through a genome-wide association study approach, we identified a novel NLR gene, Blast Resistance Gene 8 (BRG8), which confers resistance to rice blast and bacterial blight diseases. BRG8 overexpression and complementation lines exhibit enhanced resistance to both pathogens. Subcellular localization assays showed that BRG8 is localized in both the cytoplasm and the nucleus. Additional evidence revealed that nuclear-localized BRG8 can enhance rice immunity without a hypersensitive response (HR)-like phenotype. We also demonstrated that the coiled-coil domain of BRG8 not only physically interacts with itself but also interacts with the KNOX Ⅱ protein HOMEOBOX ORYZA SATIVA59 (HOS59). Knockout mutants of HOS59 in the BRG8 background show enhanced resistance to Magnaporthe oryzae strain CH171 and Xoo strain CR4, similar to that of the BRG8 background. By contrast, overexpression of HOS59 in the BRG8 background will compromise the HR-like phenotype and resistance response. Further analysis revealed that HOS59 promotes the degradation of BRG8 via the 26S proteasome pathway. Collectively, our study highlights HOS59 as an NLR immune regulator that fine-tunes BRG8-mediated immune responses against pathogens, providing new insights into NLR associations and functions in plant immunity.
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Affiliation(s)
- Siliang Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Xinghua Wei
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Qinqin Yang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Dongxiu Hu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yuanyuan Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaoping Yuan
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Fengyu Kang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhaozhong Wu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhiqin Yan
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xueqin Luo
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yanfei Sun
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Shan Wang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yue Feng
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qun Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Mengchen Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Yaolong Yang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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3
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Jia LC, Yang ZT, Shang LL, He SZ, Zhang H, Li X, Xin GS. Genome-wide identification and expression analysis of the KNOX family and its diverse roles in response to growth and abiotic tolerance in sweet potato and its two diploid relatives. BMC Genomics 2024; 25:572. [PMID: 38844832 PMCID: PMC11157901 DOI: 10.1186/s12864-024-10470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOXs in sweet potato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis-elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5, and - 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and - 6, and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.
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Affiliation(s)
- Li-Cong Jia
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Zi-Tong Yang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Li-Li Shang
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Shao-Zhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Hainan, 572025, China.
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Hainan, 572025, China.
| | - Guo-Sheng Xin
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China.
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Ezura K, Lu Y, Suzuki Y, Mitsuda N, Ariizumi T. Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2037-2054. [PMID: 38577750 DOI: 10.1111/tpj.16727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.
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Affiliation(s)
- Kentaro Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo, 102-0083, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yu Lu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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5
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Fan C, Lyu M, Zeng B, He Q, Wang X, Lu MZ, Liu B, Liu J, Esteban E, Pasha A, Provart NJ, Wang H, Zhang J. Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis. PLANT, CELL & ENVIRONMENT 2024; 47:1363-1378. [PMID: 38221855 DOI: 10.1111/pce.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
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Affiliation(s)
- Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingjie Lyu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingshan Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qiang He
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bobin Liu
- Jiansu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eddi Esteban
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
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6
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Jia P, Wang Y, Sharif R, Dong QL, Liu Y, Luan HA, Zhang XM, Guo SP, Qi GH. KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review. Int J Biol Macromol 2023; 253:126878. [PMID: 37703987 DOI: 10.1016/j.ijbiomac.2023.126878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
| | - Yuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Qing-Long Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Hao-An Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue-Mei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Sup-Ping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Guo-Hui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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7
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Urbancsok J, Donev EN, Sivan P, van Zalen E, Barbut FR, Derba-Maceluch M, Šimura J, Yassin Z, Gandla ML, Karady M, Ljung K, Winestrand S, Jönsson LJ, Scheepers G, Delhomme N, Street NR, Mellerowicz EJ. Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development. THE NEW PHYTOLOGIST 2023; 240:2312-2334. [PMID: 37857351 DOI: 10.1111/nph.19307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023]
Abstract
Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.
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Affiliation(s)
- János Urbancsok
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Evgeniy N Donev
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Pramod Sivan
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Elena van Zalen
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden
| | - Félix R Barbut
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Marta Derba-Maceluch
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Jan Šimura
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Zakiya Yassin
- RISE Research Institutes of Sweden, Drottning Kristinas väg 61, 11428, Stockholm, Sweden
| | | | - Michal Karady
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, 78371, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | | | - Leif J Jönsson
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Gerhard Scheepers
- RISE Research Institutes of Sweden, Drottning Kristinas väg 61, 11428, Stockholm, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden
- SciLifeLab, Umeå University, 90187, Umeå, Sweden
| | - Ewa J Mellerowicz
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
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8
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Zeng Y, Verstraeten I, Trinh HK, Lardon R, Schotte S, Olatunji D, Heugebaert T, Stevens C, Quareshy M, Napier R, Nastasi SP, Costa A, De Rybel B, Bellini C, Beeckman T, Vanneste S, Geelen D. Chemical induction of hypocotyl rooting reveals extensive conservation of auxin signalling controlling lateral and adventitious root formation. THE NEW PHYTOLOGIST 2023; 240:1883-1899. [PMID: 37787103 DOI: 10.1111/nph.19292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/19/2023] [Indexed: 10/04/2023]
Abstract
Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.
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Affiliation(s)
- Yinwei Zeng
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Inge Verstraeten
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Hoang Khai Trinh
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
- Institute of Food and Biotechnology, Can Tho University, 900000, Can Tho City, Vietnam
| | - Robin Lardon
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Sebastien Schotte
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Damilola Olatunji
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Thomas Heugebaert
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian Stevens
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sara Paola Nastasi
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Alex Costa
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
- Institute of Biophysics, National Research Council of Italy (CNR), 20133, Milan, Italy
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Catherine Bellini
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90736, Umeå, Sweden
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Steffen Vanneste
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Danny Geelen
- Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
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Kang M, Wu H, Liu H, Liu W, Zhu M, Han Y, Liu W, Chen C, Song Y, Tan L, Yin K, Zhao Y, Yan Z, Lou S, Zan Y, Liu J. The pan-genome and local adaptation of Arabidopsis thaliana. Nat Commun 2023; 14:6259. [PMID: 37802986 PMCID: PMC10558531 DOI: 10.1038/s41467-023-42029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.
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Affiliation(s)
- Minghui Kang
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Haolin Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenyu Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yu Han
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chunlin Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Luna Tan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Kangqun Yin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yusen Zhao
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhen Yan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266000, China.
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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10
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Li G, Manzoor MA, Wang G, Chen C, Song C. Comparative analysis of KNOX genes and their expression patterns under various treatments in Dendrobium huoshanense. FRONTIERS IN PLANT SCIENCE 2023; 14:1258533. [PMID: 37860241 PMCID: PMC10582715 DOI: 10.3389/fpls.2023.1258533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
Introduction KNOX plays a pivotal role in governing plant growth, development, and responses to diverse abiotic and biotic stresses. However, information on the relationship between the KNOX gene family and expression levels under different treatments in Dendrobium is still limited. Methods To address this problem, we first used bioinformatics methods and revealed the presence of 19 KNOX genes distributed among 13 chromosomes in the Dendrobium huoshanense genome. Through an analysis of phylogenetic relationships, these genes were classified into three distinct clades: class I, class II, and class M. Our investigation included promoter analysis, revealing various cis-acting elements associated with hormones, growth and development, and abiotic stress responses. Additionally, qRT-PCR experiments were conducted to assess the expression patterns of DhKNOX genes under different treatments, including ABA, MeJA, SA, and drought. Results The results demonstrated differential expression of DhKNOX genes in response to these treatments, thereby highlighting their potential roles in stress adaptation. Discussion Overall, our results contribute important insights for further investigations into the functional characterization of the Dendrobium KNOX gene family, shedding light on their roles in plant development and stress responses.
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Affiliation(s)
- Guohui Li
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Dabieshan Academy of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoyu Wang
- College of pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Cunwu Chen
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Dabieshan Academy of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Cheng Song
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Anhui Dabieshan Academy of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
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11
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Yuan G, Lian Y, Wang J, Yong T, Gao H, Wu H, Yang T, Wang C. AtHSPR functions in gibberellin-mediated primary root growth by interacting with KNAT5 and OFP1 in Arabidopsis. PLANT CELL REPORTS 2023; 42:1629-1649. [PMID: 37597006 DOI: 10.1007/s00299-023-03057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 08/21/2023]
Abstract
KEY MESSAGE AtHSPR forms a complex with KNAT5 and OFP1 to regulate primary root growth through GA-mediated root meristem activity. KNAT5-OFP1 functions as a negative regulator of AtHSPR in response to GA. Plant root growth is modulated by gibberellic acid (GA) signaling and depends on root meristem maintenance. ARABIDOPSIS THALIANA HEAT SHOCK PROTEIN-RELATED (AtHSPR) is a vital regulator of flowering time and salt stress tolerance. However, little is known about the role of AtHSPR in the regulation of primary root growth. Here, we report that athspr mutant exhibits a shorter primary root compared to wild type and that AtHSPR interacts with KNOTTED1-LIKE HOMEOBOX GENE 5 (KNAT5) and OVATE FAMILY PROTEIN 1 (OFP1). Genetic analysis showed that overexpression of KNAT5 or OFP1 caused a defect in primary root growth similar to that of the athspr mutant, but knockout of KNAT5 or OFP1 rescued the short root phenotype in the athspr mutant by altering root meristem activity. Further investigation revealed that KNAT5 interacts with OFP1 and that AtHSPR weakens the inhibition of GIBBERELLIN 20-OXIDASE 1 (GA20ox1) expression by the KNAT5-OFP1 complex. Moreover, root meristem cell proliferation and root elongation in 35S::KNAT5athspr and 35S::OFP1athspr seedlings were hypersensitive to GA3 treatment compared to the athspr mutant. Together, our results demonstrate that the AtHSPR-KNAT5-OFP1 module regulates root growth and development by impacting the expression of GA biosynthetic gene GA20ox1, which could be a way for plants to achieve plasticity in response to the environment.
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Affiliation(s)
- Guoqiang Yuan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuke Lian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Junmei Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Taibi Yong
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huanhuan Gao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Haijun Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Chongying Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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12
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Wang X, Zhang J, Chai M, Han L, Cao X, Zhang J, Kong Y, Fu C, Wang ZY, Mysore KS, Wen J, Zhou C. The role of Class Ⅱ KNOX family in controlling compound leaf patterning in Medicago truncatula. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2279-2291. [PMID: 37526388 DOI: 10.1111/jipb.13549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023]
Abstract
Compound leaf development requires the coordination of genetic factors, hormones, and other signals. In this study, we explored the functions of Class Ⅱ KNOTTED-like homeobox (KNOXII) genes in the model leguminous plant Medicago truncatula. Phenotypic and genetic analyses suggest that MtKNOX4, 5 are able to repress leaflet formation, while MtKNOX3, 9, 10 are not involved in this developmental process. Further investigations have shown that MtKNOX4 represses the CK signal transduction, which is downstream of MtKNOXⅠ-mediated CK biosynthesis. Additionally, two boundary genes, FUSED COMPOUND LEAF1 (orthologue of Arabidopsis Class M KNOX) and NO APICAL MERISTEM (orthologue of Arabidopsis CUP-SHAPED COTYLEDON), are necessary for MtKNOX4-mediated compound leaf formation. These findings suggest, that among the members of MtKNOXⅡ, MtKNOX4 plays a crucial role in integrating the CK pathway and boundary regulators, providing new insights into the roles of MtKNOXⅡ in regulating the elaboration of compound leaves in M. truncatula.
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Affiliation(s)
- Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Maofeng Chai
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Xiaohua Cao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Jing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Yiming Kong
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Zeng-Yu Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kirankumar S Mysore
- Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, 73401, Oklahoma, USA
| | - Jiangqi Wen
- Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, 73401, Oklahoma, USA
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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13
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Edrisi Maryan K, Farrokhi N, Samizadeh Lahiji H. Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network. PLoS One 2023; 18:e0286324. [PMID: 37289769 PMCID: PMC10249815 DOI: 10.1371/journal.pone.0286324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.
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Affiliation(s)
- Khazar Edrisi Maryan
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
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14
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Tian Z, Wang X, Dun X, Tian Z, Zhang X, Li J, Ren L, Tu J, Wang H. Integrating biochemical and anatomical characterizations with transcriptome analysis to dissect superior stem strength of ZS11 ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2023; 14:1144892. [PMID: 37229131 PMCID: PMC10203542 DOI: 10.3389/fpls.2023.1144892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Stem lodging resistance is a serious problem impairing crop yield and quality. ZS11 is an adaptable and stable yielding rapeseed variety with excellent resistance to lodging. However, the mechanism regulating lodging resistance in ZS11 remains unclear. Here, we observed that high stem mechanical strength is the main factor determining the superior lodging resistance of ZS11 through a comparative biology study. Compared with 4D122, ZS11 has higher rind penetrometer resistance (RPR) and stem breaking strength (SBS) at flowering and silique stages. Anatomical analysis shows that ZS11 exhibits thicker xylem layers and denser interfascicular fibrocytes. Analysis of cell wall components suggests that ZS11 possessed more lignin and cellulose during stem secondary development. By comparative transcriptome analysis, we reveal a relatively higher expression of genes required for S-adenosylmethionine (SAM) synthesis, and several key genes (4-COUMATATE-CoA LIGASE, CINNAMOYL-CoA REDUCTASE, CAFFEATE O-METHYLTRANSFERASE, PEROXIDASE) involved in lignin synthesis pathway in ZS11, which support an enhanced lignin biosynthesis ability in the ZS11 stem. Moreover, the difference in cellulose may relate to the significant enrichment of DEGs associated with microtubule-related process and cytoskeleton organization at the flowering stage. Protein interaction network analysis indicate that the preferential expression of several genes, such as LONESOME HIGHWAY (LHW), DNA BINDING WITH ONE FINGERS (DOFs), WUSCHEL HOMEOBOX RELATED 4 (WOX4), are related to vascular development and contribute to denser and thicker lignified cell layers in ZS11. Taken together, our results provide insights into the physiological and molecular regulatory basis for the formation of stem lodging resistance in ZS11, which will greatly promote the application of this superior trait in rapeseed breeding.
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Affiliation(s)
- Zhengshu Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Xiaoxue Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Jinfeng Li
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Lijun Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Jinxing Tu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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15
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Ma Y, Shafee T, Mudiyanselage AM, Ratcliffe J, MacMillan CP, Mansfield SD, Bacic A, Johnson KL. Distinct functions of FASCILIN-LIKE ARABINOGALACTAN PROTEINS relate to domain structure. PLANT PHYSIOLOGY 2023; 192:119-132. [PMID: 36797772 PMCID: PMC10152678 DOI: 10.1093/plphys/kiad097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 05/03/2023]
Abstract
The role of glycoproteins as key cell surface molecules during development and stress is well established; yet, the relationship between their structural features and functional mechanisms is poorly defined. FASCICLIN-LIKE ARABINOGALACTAN PROTEINs (FLAs), which impact plant growth and development, are an excellent example of a glycoprotein family with a complex multidomain structure. FLAs combine globular fasciclin-like (FAS1) domains with regions that are intrinsically disordered and contain glycomotifs for directing the addition of O-linked arabinogalactan (AG) glycans. Additional posttranslational modifications on FLAs include N-linked glycans in the FAS1 domains, a cleaved signal peptide at the N terminus, and often a glycosylphosphatidylinositol (GPI) anchor signal sequence at the C terminus. The roles of glycosylation, the GPI anchor, and FAS1 domain functions in the polysaccharide-rich extracellular matrix of plants remain unclear, as do the relationships between them. In this study, we examined sequence-structure-function relationships of Arabidopsis (Arabidopsis thaliana) FLA11, demonstrated to have roles in secondary cell wall (SCW) development, by introducing domain mutations and functional specialization through domain swaps with FLA3 and FLA12. We identified FAS1 domains as essential for FLA function, differentiating FLA11/FLA12, with roles in SCW development, from FLA3, specific to flowers and involved in pollen development. The GPI anchor and AG glycosylation co-regulate the cell surface location and release of FLAs into cell walls. The AG glycomotif sequence closest to the GPI anchor (AG2) is a major feature differentiating FLA11 from FLA12. The results of our study show that the multidomain structure of different FLAs influences their subcellular location and biological functions during plant development.
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Affiliation(s)
- Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC 3052, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Thomas Shafee
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Asha M Mudiyanselage
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Colleen P MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Antony Bacic
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou 311300, China
| | - Kim L Johnson
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou 311300, China
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16
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Du J, Wang Y, Chen W, Xu M, Zhou R, Shou H, Chen J. High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem. MOLECULAR PLANT 2023; 16:809-828. [PMID: 36895162 DOI: 10.1016/j.molp.2023.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/12/2023] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
The secondary vascular tissue emanating from meristems is central to understanding how vascular plants such as forest trees evolve, grow, and regulate secondary radial growth. However, the overall molecular characterization of meristem origins and developmental trajectories from primary to secondary vascular tissues in woody tree stems is technically challenging. In this study, we combined high-resolution anatomic analysis with a spatial transcriptome (ST) technique to define features of meristematic cells in a developmental gradient from primary to secondary vascular tissues in poplar stems. The tissue-specific gene expression of meristems and derived vascular tissue types were accordingly mapped to specific anatomical domains. Pseudotime analyses were used to track the origins and changes of meristems throughout the development from primary to secondary vascular tissues. Surprisingly, two types of meristematic-like cell pools within secondary vascular tissues were inferred based on high-resolution microscopy combined with ST, and the results were confirmed by in situ hybridization of, transgenic trees, and single-cell sequencing. The rectangle shape procambium-like (PCL) cells develop from procambium meristematic cells and are located within the phloem domain to produce phloem cells, whereas fusiform shape cambium zone (CZ) meristematic cells develop from fusiform metacambium meristematic cells and are located inside the CZ to produce xylem cells. The gene expression atlas and transcriptional networks spanning the primary transition to secondary vascular tissues generated in this work provide new resources for studying the regulation of meristem activities and the evolution of vascular plants. A web server (https://pgx.zju.edu.cn/stRNAPal/) was also established to facilitate the use of ST RNA-seq data.
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Affiliation(s)
- Juan Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yu Hangtang Road, Hangzhou, Zhejiang 310058, China.
| | - Yichen Wang
- Hangzhou Botanical Garden, Taoyuanling Road, Hangzhou, Zhejiang 310013, China
| | - Wenfan Chen
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingling Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yu Hangtang Road, Hangzhou, Zhejiang 310058, China
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, 866 Yu Hangtang Road, Hangzhou, Zhejiang 310058, China; Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yu Hangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, 866 Yu Hangtang Road, Hangzhou, Zhejiang 310058, China.
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17
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Kolkman JM, Moreta DE, Repka A, Bradbury P, Nelson RJ. Brown midrib mutant and genome-wide association analysis uncover lignin genes for disease resistance in maize. THE PLANT GENOME 2023; 16:e20278. [PMID: 36533711 DOI: 10.1002/tpg2.20278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/19/2022] [Indexed: 05/10/2023]
Abstract
Brown midrib (BMR) maize (Zea mays L.) harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate New York highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3, and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot [GLS], and anthracnose leaf blight [ALB]) and bacterial (Stewart's wilt) diseases. The bm1, bm2, and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot (ASR), and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot (GER). Colocalization of quantitative trait loci (QTL) and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered single-nucleotide polymorphism (SNP) associations for resistance to NLB but did not implicate natural functional variation at bm1-bm5. Strong associations implicated a suite of diverse candidate genes including lignin-related genes such as a β-glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP-like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and nonsilage purposes.
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Affiliation(s)
- Judith M Kolkman
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell Univ., Ithaca, NY, 14853, USA
| | - Danilo E Moreta
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell Univ., Ithaca, NY, 14853, USA
| | - Ace Repka
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Rebecca J Nelson
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell Univ., Ithaca, NY, 14853, USA
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell Univ., Ithaca, NY, 14853, USA
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18
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Hung FY, Feng YR, Hsin KT, Shih YH, Chang CH, Zhong W, Lai YC, Xu Y, Yang S, Sugimoto K, Cheng YS, Wu K. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun Biol 2023; 6:219. [PMID: 36828846 PMCID: PMC9958104 DOI: 10.1038/s42003-023-04607-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
The Arabidopsis H3K9 methyltransferases KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are redundantly involved in silencing of transposable elements (TEs). Our recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The transcriptional factors ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target the promoters of KNAT1 and KNAT2, and the binding of KYP depends on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Kuan-Ting Hsin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chung-Han Chang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Wenjian Zhong
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Cheng Lai
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Keiko Sugimoto
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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19
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Prunus Knotted-like Genes: Genome-Wide Analysis, Transcriptional Response to Cytokinin in Micropropagation, and Rootstock Transformation. Int J Mol Sci 2023; 24:ijms24033046. [PMID: 36769369 PMCID: PMC9918302 DOI: 10.3390/ijms24033046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Knotted1-like homeobox (KNOX) transcription factors are involved in plant development, playing complex roles in aerial organs. As Prunus species include important fruit tree crops of Italy, an exhaustive investigation of KNOX genes was performed using genomic and RNA-seq meta-analyses. Micropropagation is an essential technology for rootstock multiplication; hence, we investigated KNOX transcriptional behavior upon increasing 6-benzylaminopurine (BA) doses and the effects on GF677 propagules. Moreover, gene function in Prunus spp. was assessed by Gisela 6 rootstock transformation using fluorescence and peach KNOX transgenes. Based on ten Prunus spp., KNOX proteins fit into I-II-M classes named after Arabidopsis. Gene number, class member distribution, and chromosome positions were maintained, and exceptions supported the diversification of Prunus from Cerasus subgenera, and that of Armeniaca from the other sections within Prunus. Cytokinin (CK) cis-elements occurred in peach and almond KNOX promoters, suggesting a BA regulatory role in GF677 shoot multiplication as confirmed by KNOX expression variation dependent on dose, time, and interaction. The tripled BA concentration exacerbated stress, altered CK perception genes, and modified KNOX transcriptions, which are proposed to concur in in vitro anomalies. Finally, Gisela 6 transformation efficiency varied (2.6-0.6%) with the genetic construct, with 35S:GFP being more stable than 35S:KNOPE1 lines, which showed leaf modification typical of KNOX overexpression.
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20
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Ongoings in the apple watercore: First evidence from proteomic and metabolomic analysis. Food Chem 2023; 402:134226. [DOI: 10.1016/j.foodchem.2022.134226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 09/10/2022] [Indexed: 11/18/2022]
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21
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Chen JJ, Wang W, Qin WQ, Men SZ, Li HL, Mitsuda N, Ohme-Takagi M, Wu AM. Transcription factors KNAT3 and KNAT4 are essential for integument and ovule formation in Arabidopsis. PLANT PHYSIOLOGY 2023; 191:463-478. [PMID: 36342216 PMCID: PMC9806662 DOI: 10.1093/plphys/kiac513] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Integuments form important protective cell layers surrounding the developing ovules in gymno- and angiosperms. Although several genes have been shown to influence the development of integuments, the transcriptional regulatory mechanism is still poorly understood. In this work, we report that the Class II KNOTTED1-LIKE HOMEOBOX (KNOX II) transcription factors KNOTTED1-LIKE HOMEBOX GENE 3 (KNAT3) and KNAT4 regulate integument development in Arabidopsis (Arabidopsis thaliana). KNAT3 and KNAT4 were co-expressed in inflorescences and especially in young developing ovules. The loss-of-function double mutant knat3 knat4 showed an infertility phenotype, in which both inner and outer integuments of the ovule are arrested at an early stage and form an amorphous structure as in the bell1 (bel1) mutant. The expression of chimeric KNAT3- and KNAT4-EAR motif repression domain (SRDX repressors) resulted in severe seed abortion. Protein-protein interaction assays demonstrated that KNAT3 and KNAT4 interact with each other and also with INNER NO OUTER (INO), a key transcription factor required for the outer integument formation. Transcriptome analysis showed that the expression of genes related with integument development is influenced in the knat3 knat4 mutant. The knat3 knat4 mutant also had a lower indole-3-acetic acid (IAA) content, and some auxin signaling pathway genes were downregulated. Moreover, transactivation analysis indicated that KNAT3/4 and INO activate the auxin signaling gene IAA INDUCIBLE 14 (IAA14). Taken together, our study identified KNAT3 and KNAT4 as key factors in integument development in Arabidopsis.
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Affiliation(s)
- Jia-Jun Chen
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wang
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90183, Sweden
| | - Wen-Qi Qin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Shu-Zhen Men
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hui-Ling Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ai-Min Wu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
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22
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Genome-Wide Identification of Wheat KNOX Gene Family and Functional Characterization of TaKNOX14-D in Plants. Int J Mol Sci 2022; 23:ijms232415918. [PMID: 36555558 PMCID: PMC9784718 DOI: 10.3390/ijms232415918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were identified, and we demonstrated the function of the TaKNOX14-D gene under mechanical injury and cold stress. Thirty-six TaKNOX genes were divided into two groups, and thirty-four TaKNOX genes were predicted to be located in the nucleus by Cell-PLoc. These genes contained five tandem duplications. Fifteen collinear gene pairs were exhibited in wheat and rice, one collinear gene pair was exhibited in wheat and Arabidopsis. The phylogenetic tree and motif analysis suggested that the TaKNOX gene appeared before C3 and C4 diverged. Gene structure showed that the numbers of exons and introns in TaKNOX gene are different. Wheat TaKNOX genes showed different expression patterns during the wheat growth phase, with seven TaKNOX genes being highly expressed in the whole growth period. These seven genes were also highly expressed in most tissues, and also responded to most abiotic stress. Eleven TaKNOX genes were up-regulated in the tillering node during the leaf regeneration period after mechanical damage. When treating the wheat with different hormones, the expression patterns of TaKNOX were changed, and results showed that ABA promoted TaKNOX expression and seven TaKNOX genes were up-regulated under cytokinin and auxin treatment. Overexpression of the TaKNOX14-D gene in Arabidopsis could increase the leaf size, plant height and seed size. This gene overexpression in Arabidopsis also increased the compensatory growth capacity after mechanical damage. Overexpression lines also showed high resistance to cold stress. This study provides a better understanding of the TaKNOX genes.
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23
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Bowman JL. The origin of a land flora. NATURE PLANTS 2022; 8:1352-1369. [PMID: 36550365 DOI: 10.1038/s41477-022-01283-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Victoria, Australia.
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24
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Zhou J, Qi Y, Nie J, Guo L, Luo M, McLellan H, Boevink PC, Birch PRJ, Tian Z. A Phytophthora effector promotes homodimerization of host transcription factor StKNOX3 to enhance susceptibility. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6902-6915. [PMID: 35816329 DOI: 10.1093/jxb/erac308] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Oomycete pathogens secrete hundreds of cytoplasmic RxLR effectors to modulate host immunity by targeting diverse plant proteins. Revealing how effectors manipulate host proteins is pivotal to understanding infection processes and to developing new strategies to control plant disease. Here we show that the Phytophthora infestans RxLR effector Pi22798 interacts in the nucleus with a potato class II knotted-like homeobox (KNOX) transcription factor, StKNOX3. Silencing the ortholog NbKNOX3 in Nicotiana benthamiana reduces host colonization by P. infestans, whereas transient and stable overexpression of StKNOX3 enhances infection. StKNOX3 forms a homodimer which is dependent on its KNOX II domain. The KNOX II domain is also essential for Pi22798 interaction and for StKNOX3 to enhance P. infestans colonization, indicating that StKNOX3 homodimerization contributes to susceptibility. However, critically, the effector Pi22798 promotes StKNOX3 homodimerization, rather than heterodimerization to another KNOX transcription factor StKNOX7. These results demonstrate that the oomycete effector Pi22798 increases pathogenicity by promoting homodimerization specifically of StKNOX3 to enhance susceptibility.
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Affiliation(s)
- Jing Zhou
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University (HZAU), Wuhan, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, China
- Hubei Hongshan Laboratory (HZAU), Hubei Province, Wuhan, China
| | - Yetong Qi
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University (HZAU), Wuhan, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, China
| | - Jiahui Nie
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University (HZAU), Wuhan, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, China
| | - Lei Guo
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Ming Luo
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University (HZAU), Wuhan, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, China
| | - Hazel McLellan
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Invergowrie, Dundee, UK
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
| | - Paul R J Birch
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Invergowrie, Dundee, UK
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University (HZAU), Wuhan, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, China
- Hubei Hongshan Laboratory (HZAU), Hubei Province, Wuhan, China
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25
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Ferreira SS, Goeminne G, Simões MS, Pina AVDA, Lima LGAD, Pezard J, Gutiérrez A, Rencoret J, Mortimer JC, Del Río JC, Boerjan W, Cesarino I. Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6307-6333. [PMID: 35788296 DOI: 10.1093/jxb/erac300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
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Affiliation(s)
- Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | - Geert Goeminne
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | | | | | - Jade Pezard
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Wout Boerjan
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, São Paulo, Brazil
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26
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Chen M, Guo L, Ramakrishnan M, Fei Z, Vinod KK, Ding Y, Jiao C, Gao Z, Zha R, Wang C, Gao Z, Yu F, Ren G, Wei Q. Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors. THE PLANT CELL 2022; 34:3577-3610. [PMID: 35766883 PMCID: PMC9516176 DOI: 10.1093/plcell/koac193] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 05/09/2023]
Abstract
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited ∼28 mg g-1 dry weight (DW) lignin and ∼44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | | | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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Ezura K, Nakamura A, Mitsuda N. Genome-wide characterization of the TALE homeodomain family and the KNOX-BLH interaction network in tomato. PLANT MOLECULAR BIOLOGY 2022; 109:799-821. [PMID: 35543849 DOI: 10.1007/s11103-022-01277-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/23/2022] [Indexed: 05/05/2023]
Abstract
Comprehensive yeast and protoplast two-hybrid analyses illustrated the protein-protein interaction network of the TALE homeodomain protein family, KNOX and BLH proteins, in tomato leaf and fruit development. KNOTTED-like (KNOX, KN) proteins and BELL1-like (BLH) proteins, which belong to the same TALE homeodomain family, act together by forming KNOX-BLH heterodimer modules. These modules play crucial roles in regulating multiple developmental processes in plants, like organ differentiation. However, despite the increasing knowledge about individual KNOX and BLH functions, a comprehensive view of their functional protein-protein interaction (PPI) network remains elusive in most plants, including tomato (Solanum lycopersicum), an important model plant to study fruit and leaf development. Here, we characterized eight tomato KNOX genes (SlKN1 to SlKN8) and fourteen tomato BLH genes (SlBLH1 to SlBLH14) by expression profiling, co-expression analysis, and PPI network analysis using two-hybrid techniques in yeasts (Y2H) and protoplasts (P2H). We identified 75 pairwise KNOX-BLH interactions, including ten novel interactors of SlKN2/TKN2, a primary class I KNOX protein, and nine novel interactors of SlKN5, a primary class II KNOX protein. Based on these data, we classified KNOX-BLH modules into several categories, which made us infer the order and combination of the KNOX-BLH modules involved in differentiation processes in leaf and fruit. Notably, the co-expression and interaction of SlKN5 and fruit preferentially expressing BLH1-clade paralogs (SlBLH5/SlBEL11 and SlBLH7) suggest their important roles in regulating fruit differentiation. Furthermore, in silico modeling of the KNOX-BLH modules, sequence analysis, and P2H assay identified several residues and a linker region potentially influencing the affinity of BLHs to KNOXs within their conserved dimerization domains. Together, these findings provide insights into the regulatory mechanism of KNOX-BLH modules underlying tomato organ differentiation.
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Affiliation(s)
- Kentaro Ezura
- Japan Society for the Promotion of Science, Tokyo, Japan.
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan.
| | - Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
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Zhang Y, Yin Q, Qin W, Gao H, Du J, Chen J, Li H, Zhou G, Wu H, Wu AM. The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3477-3495. [PMID: 35188965 DOI: 10.1093/jxb/erac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The production of Arabidopsis seed mucilage involves complex polysaccharide biosynthetic pathways and developmental processes in seed epidermal cells. Although the polysaccharide components of Arabidopsis seed mucilage have been identified, their regulatory mechanism requires further investigation. Here, we show that Class II KNOX gene family members KNAT3 and KNAT7 play an essential role in regulating mucilage production in the early developmental stages of Arabidopsis seeds. Double mutant knat3knat7 resulted in defective seed mucilage production and columellae formation, whereas knat3 showed a normal phenotype compared with wild type, and the mucilage thickness in knat7 was slightly disturbed. Rhamnogalacturonan I (RG-I) and its biosynthetic substrates galacturonic acid and rhamnose were reduced in both the adherent and soluble mucilage of knat3knat7. Comparative transcriptome analysis on whole seeds suggested that polysaccharide, glucosinolate and anthocyanin biosynthetic pathways were specifically repressed in knat3knat7. Transient co-expression of KNAT3 and KNAT7 with promoter regions of candidate genes in Arabidopsis protoplasts revealed that both KNAT3 and KNAT7 act as positive regulators of the RG-I biosynthetic gene MUCILAGE-MODIFIED 4 (MUM4, AT1G53500). Collectively, our results demonstrate that KNAT3 and KNAT7 are multifunctional transcription factors in secondary cell wall development and redundantly modulate mucilage biosynthesis in Arabidopsis seeds.
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Affiliation(s)
- Yuanyuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Qi Yin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Wenqi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Han Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- College of life sciences, South China Agricultural University. Guangzhou, 510642, China
| | - Jinge Du
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Jiajun Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Gongke Zhou
- College of Resource and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
- College of life sciences, South China Agricultural University. Guangzhou, 510642, China
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
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Liang C, Wei C, Wang L, Guan Z, Shi T, Huang J, Li B, Lu Y, Liu H, Wang Y. Characterization of a Novel Creeping Tartary Buckwheat ( Fagopyrum tataricum) Mutant lazy1. FRONTIERS IN PLANT SCIENCE 2022; 13:815131. [PMID: 35574111 PMCID: PMC9094088 DOI: 10.3389/fpls.2022.815131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/02/2022] [Indexed: 06/15/2023]
Abstract
Gravity is known as an important environmental factor involved in the regulation of plant architecture. To identify genes related to the gravitropism of Tartary buckwheat, a creeping line was obtained and designated as lazy1 from the mutant bank by 60Co-γ ray radiation. Genetic analysis indicated that the creeping phenotype of lazy1 was attributed to a single recessive locus. As revealed by the horizontal and inverted suspension tests, lazy1 was completely lacking in shoot negative gravitropism. The creeping growth of lazy1 occurred at the early seedling stage, which could not be recovered by exogenous heteroauxin, hormodin, α-rhodofix, or gibberellin. Different from the well-organized and equivalent cell elongation of wild type (WT), lazy1 exhibited dilated, distorted, and abnormally arranged cells in the bending stem. However, no statistical difference of indole-3-acetic acid (IAA) levels was found between the far- and near-ground bending sides in lazy1, which suggests that the asymmetric cell elongation of lazy1 was not induced by auxin gradient. Whereas, lazy1 showed up-expressed gibberellin-regulated genes by quantitative real-time PCR (qRT-PCR) as well as significantly higher levels of gibberellin, suggesting that gibberellin might be partly involved in the regulation of creeping growth in lazy1. RNA sequencing (RNA-seq) identified a number of differentially expressed genes (DEGs) related to gravitropism at stages I (before bending), II (bending), and III (after bending) between WT and lazy1. Venn diagram indicated that only Pectate lyase 5 was down-expressed at stages I [Log2 fold change (Log2FC): -3.20], II (Log2FC: -4.97), and III (Log2FC: -1.23) in lazy1, compared with WT. Gene sequencing revealed that a fragment deletion occurred in the coding region of Pectate lyase 5, which induced the destruction of a pbH domain in Pectate lyase 5 of lazy1. qRT-PCR indicated that Pectate lyase 5 was extremely down-expressed in lazy1 at stage II (0.02-fold of WT). Meanwhile, lazy1 showed the affected expression of lignin- and cellulose-related genes and cumulatively abnormal levels of pectin, lignin, and cellulose. These results demonstrate the possibility that Pectate lyase 5 functions as the key gene that could mediate primary cell wall metabolism and get involved in the asymmetric cell elongation regulation of lazy1.
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Affiliation(s)
- Chenggang Liang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chunyu Wei
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Li Wang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zhixiu Guan
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Bin Li
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yang Lu
- Guizhou Biotechnology Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Hui Liu
- Guizhou Biotechnology Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Yan Wang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
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Zhao W, Ding L, Liu J, Zhang X, Li S, Zhao K, Guan Y, Song A, Wang H, Chen S, Jiang J, Chen F. Regulation of lignin biosynthesis by an atypical bHLH protein CmHLB in Chrysanthemum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2403-2419. [PMID: 35090011 DOI: 10.1093/jxb/erac015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Stem mechanical strength is one of the most important agronomic traits that affects the resistance of plants against insects and lodging, and plays an essential role in the quality and yield of plants. Several transcription factors regulate mechanical strength in crops. However, mechanisms of stem strength formation and regulation remain largely unexplored, especially in ornamental plants. In this study, we identified an atypical bHLH transcription factor CmHLB (HLH PROTEIN INVOLVED IN LIGNIN BIOSYNTHESIS) in chrysanthemum, belonging to a small bHLH sub-family - the PACLOBUTRAZOL RESISTANCE (PRE) family. Overexpression of CmHLB in chrysanthemum significantly increased mechanical strength of the stem, cell wall thickness, and lignin content, compared with the wild type. In contrast, CmHLB RNA interference lines exhibited the opposite phenotypes. RNA-seq analysis indicated that CmHLB promoted the expression of genes involved in lignin biosynthesis. Furthermore, we demonstrated that CmHLB interacted with Chrysanthemum KNOTTED ARABIDOPSIS THALIANA7 (CmKNAT7) through the KNOX2 domain, which has a conserved function, i.e. it negatively regulates secondary cell wall formation of fibres and lignin biosynthesis. Collectively, our results reveal a novel role for CmHLB in regulating lignin biosynthesis by interacting with CmKNAT7 and affecting stem mechanical strength in Chrysanthemum.
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Affiliation(s)
- Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiayou Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Song Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Que F, Liu Q, Zha R, Xiong A, Wei Q. Genome-Wide Identification, Expansion, and Evolution Analysis of Homeobox Gene Family Reveals TALE Genes Important for Secondary Cell Wall Biosynthesis in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2022; 23:ijms23084112. [PMID: 35456930 PMCID: PMC9032839 DOI: 10.3390/ijms23084112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 02/06/2023] Open
Abstract
The TALE gene family is a subfamily of the homeobox gene family and has been implicated in regulating plant secondary growth. However, reports about the evolutionary history and function of the TALE gene family in bamboo are limited. Here, the homeobox gene families of moso bamboo Olyra latifolia and Bonia amplexicaulis were identified and compared. Many duplication events and obvious expansions were found in the TALE family of woody bamboo. PhTALEs were found to have high syntenies with TALE genes in rice. Through gene co-expression analysis and quantitative real-time PCR analysis, the candidate PhTALEs were thought to be involved in regulating secondary cell wall development of moso bamboo during the fast-growing stage. Among these candidate PhTALEs, orthologs of OsKNAT7, OSH15, and SH5 in moso bamboo may regulate xylan synthesis by regulating the expression of IRX-like genes. These results suggested that PhTALEs may participate in the secondary cell wall deposition in internodes during the fast-growing stage of moso bamboo. The expansion of the TALE gene family may be implicated in the increased lignification of woody bamboo when divergent from herbaceous bamboos.
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Affiliation(s)
- Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China; (F.Q.); (Q.L.); (R.Z.)
| | - Qingnan Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China; (F.Q.); (Q.L.); (R.Z.)
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China; (F.Q.); (Q.L.); (R.Z.)
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (A.X.); (Q.W.)
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China; (F.Q.); (Q.L.); (R.Z.)
- Correspondence: (A.X.); (Q.W.)
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Zhuang Y, Lian W, Tang X, Qi G, Wang D, Chai G, Zhou G. MYB42 inhibits hypocotyl cell elongation by coordinating brassinosteroid homeostasis and signalling in Arabidopsis thaliana. ANNALS OF BOTANY 2022; 129:403-413. [PMID: 34922335 PMCID: PMC8944714 DOI: 10.1093/aob/mcab152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The precise control of brassinosteroid (BR) homeostasis and signalling is a prerequisite for hypocotyl cell elongation in plants. Arabidopsis MYB42 and its paralogue MYB85 were previously identified to be positive regulators of secondary cell wall formation during mature stages. Here, we aim to reveal the role of MYB42 and MYB85 in hypocotyl elongation during the seedling stage and clarify how MYB42 coordinates BR homeostasis and signalling to regulate this process. METHODS Histochemical analysis of proMYB42-GUS transgenic plants was used for determination of the MYB42 expression pattern. The MYB42, 85 overexpression, double mutant and some crossing lines were generated for phenotypic observation and transcriptome analysis. Transcription activation assays, quantitative PCR (qPCR), chromatin immunoprecipitation (ChIP)-qPCR and electrophoretic mobility shift assays (EMSAs) were conducted to determine the relationship of MYB42 and BRASSINAZOLE-RESISTANT 1 (BZR1), a master switch activating BR signalling. KEY RESULTS MYB42 and MYB85 redundantly and negatively regulate hypocotyl cell elongation. They function in hypocotyl elongation by mediating BR signalling. MYB42 transcription was suppressed by BR treatment or in bzr1-1D (a gain-of-function mutant of BZR1), and mutation of both MYB42 and MYB85 enhanced the dwarf phenotype of the BR receptor mutant bri1-5. BZR1 directly repressed MYB42 expression in response to BR. Consistently, hypocotyl length of bzr1-1D was increased by simultaneous mutation of MYB42 and MYB85, but was reduced by overexpression of MYB42. Expression of a number of BR-regulated BZR1 (non-)targets associated with hypocotyl elongation was suppressed by MYB42, 85. Furthermore, MYB42 enlarged its action in BR signalling through feedback repression of BR accumulation and activation of DOGT1/UGT73C5, a BR-inactivating enzyme. CONCLUSIONS MYB42 inhibits hypocotyl elongation by coordinating BR homeostasis and signalling during primary growth. The present study shows an MYB42, 85-mediated multilevel system that contributes to fine regulation of BR-induced hypocotyl elongation.
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Affiliation(s)
- Yamei Zhuang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wenjun Lian
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Xianfeng Tang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Qi
- State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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Nookaraju A, Pandey SK, Ahlawat YK, Joshi CP. Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:493. [PMID: 35214825 PMCID: PMC8880547 DOI: 10.3390/plants11040493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.
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Affiliation(s)
- Akula Nookaraju
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Kaveri Seed Company Limited, Secunderabad 500003, Telangana, India
| | - Shashank K. Pandey
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Yogesh K. Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Chandrashekhar P. Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
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Liu J, Zhang C, Han J, Fang X, Xu H, Liang C, Li D, Yang Y, Cui Z, Wang R, Song J. Genome-Wide Analysis of KNOX Transcription Factors and Expression Pattern of Dwarf-Related KNOX Genes in Pear. FRONTIERS IN PLANT SCIENCE 2022; 13:806765. [PMID: 35154223 PMCID: PMC8831332 DOI: 10.3389/fpls.2022.806765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
KNOTTED1-like homeobox (KNOX) transcription factors (TFs) belonging to the homeobox TF family play important roles in plant growth, development, and responses to abiotic and biotic stress. However, little information is available on KNOX TF in pear (Pyrus). In this study, 19 PbKNOXs TFs were re-identified in pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis revealed that the TFs were clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the KNOX in these clades. PbKNM1 and PbKNM2 are KNM (encodes a MEINOX domain but not a homeodomain) genes identified in pear for the first time. KNOX genes in Pyrus and Malus were closely related, and a collinear relationship among PbKNOX genes in Pyrus and Malus was observed. Analysis of the expression patterns of PbKNOX genes in different tissues, at various growth stages, and in response to abiotic and biotic stress revealed that PbKNOXs are involved in plant growth and development. Our comparative transcriptional analysis of dwarf mutant varieties revealed that genes belonging to class I are highly expressed compared with genes in other classes. Analysis of the expression of PbKNOX genes in the hybrid offspring of vigorous and dwarf varieties revealed that PbKNOX genes were highly expressed in the vigorous offspring and weakly expressed in the dwarf offspring. These findings provide new insight into the function of KNOX TFs in pear and will aid future studies of dwarf fruit trees.
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Affiliation(s)
- Jianlong Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Chenxiao Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jingyue Han
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Xiaoyun Fang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Hongpeng Xu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Chenglin Liang
- Haidu College, Qingdao Agricultural University, Laiyang, China
| | - Dingli Li
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yingjie Yang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Zhenhua Cui
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Ran Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jiankun Song
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Hirai R, Wang S, Demura T, Ohtani M. Histone Deacetylation Controls Xylem Vessel Cell Differentiation via Transcriptional Regulation of a Transcription Repressor Complex OFP1/4-MYB75-KNAT7-BLH6. FRONTIERS IN PLANT SCIENCE 2022; 12:825810. [PMID: 35154217 PMCID: PMC8829346 DOI: 10.3389/fpls.2021.825810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Xylem vessels are indispensable tissues in vascular plants that transport water and minerals. The differentiation of xylem vessel cells is characterized by secondary cell wall deposition and programmed cell death. These processes are initiated by a specific set of transcription factors, called VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, through the direct and/or indirectly induction of genes required for secondary cell wall deposition and programmed cell death. In this study, we explored novel regulatory factors for xylem vessel cell differentiation in Arabidopsis thaliana. We tested the effects of cellular stress inducers on VND7-induced differentiation of xylem vessel cells with the VND7-VP16-GR system, in which VND7 activity is post-translationally induced by dexamethasone application. We established that the histone deacetylase (HDAC) inhibitors trichostatin A (TSA) and sirtinol inhibited VND7-induced xylem vessel cell differentiation. The inhibitory effects of TSA and sirtinol treatment were detected only when they were added at the same time as the dexamethasone application, suggesting that TSA and sirtinol mainly influence the early stages of xylem vessel cell differentiation. Expression analysis revealed that these HDAC inhibitors downregulated VND7-downstream genes, including both direct and indirect targets of transcriptional activation. Notably, the HDAC inhibitors upregulated the transcript levels of negative regulators of xylem vessel cells, OVATE FAMILY PROTEIN1 (OFP1), OFP4, and MYB75, which are known to form a protein complex with BEL1-LIKE HOMEODOMAIN6 (BLH6) to repress gene transcription. The KDB system, another in vitro induction system of ectopic xylem vessel cells, demonstrated that TSA and sirtinol also inhibited ectopic formation of xylem vessel cells, and this inhibition was partially suppressed in knat7-1, bhl6-1, knat7-1 bhl6-1, and quintuple ofp1 ofp2 ofp3 ofp4 ofp5 mutants. Thus, the negative effects of HDAC inhibitors on xylem vessel cell differentiation are mediated, at least partly, by the abnormal upregulation of the transcriptional repressor complex OFP1/4-MYB75-KNAT7-BLH6. Collectively, our findings suggest that active regulation of histone deacetylation by HDACs is involved in xylem vessel cell differentiation via the OFP1/4-MYB75-KNAT7-BLH6 complex.
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Affiliation(s)
- Risaku Hirai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shumin Wang
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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Zhang D, Lan S, Yin WL, Liu ZJ. Genome-Wide Identification and Expression Pattern Analysis of KNOX Gene Family in Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:901089. [PMID: 35712569 PMCID: PMC9197187 DOI: 10.3389/fpls.2022.901089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/19/2022] [Indexed: 05/13/2023]
Abstract
The establishment of lateral organs and subsequent plant architecture involves factors intrinsic to the stem apical meristem (SAM) from which they are derived. KNOTTED1-LIKE HOMEOBOX (KNOX) genes are a family of plant-specific homeobox transcription factors that especially act in determining stem cell fate in SAM. Although KNOXs have been studied in many land plants for decades, there is a dearth of knowledge on KNOX's role in Orchidaceae, the largest and most diverse lineage of flowering plants. In this study, a total of 32 putative KNOX genes were identified in the genomes of five orchid species and further designated into two classes (Class I and Class II) based on phylogenetic relationships. Sequence analysis showed that most orchid KNOX proteins retain four conserved domains (KNOX1, KNOX2, ELK, and Homeobox_KN). Comparative analysis of gene structure showed that the exon-intron structure is conserved in the same clade but most orchids exhibited longer intron, which may be a unique feature of Orchidaceae. Cis-elements identified in the promoter region of orchid KNOXs were found mostly enriched in a function of light responsiveness, followed by MeJA and ABA responsiveness, indicative of their roles in modulating light and phytohormones. Collinear analysis unraveled a one-to-one correspondence among KNOXs in orchids, and all KNOX genes experienced strong purifying selection, indicating the conservation of this gene family has been reinforced across the Orchidaceae lineage. Expression profiles based on transcriptomic data and real-time reverse transcription-quantitative PCR (RT-qPCR) revealed a stem-specific expression of KNOX Class I genes and a broader expression pattern of Class II genes. Taken together, our results provided a comprehensive analysis to uncover the underlying function of KNOX genes in Orchidaceae.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Lun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Wei-Lun Yin,
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Zhong-Jian Liu,
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Ailizati A, Nagahage ISP, Miyagi A, Ishikawa T, Kawai-Yamada M, Demura T, Yamaguchi M. An Arabidopsis NAC domain transcriptional activator VND7 negatively regulates VNI2 expression. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:415-420. [PMID: 35087306 PMCID: PMC8761584 DOI: 10.5511/plantbiotechnology.21.1013a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/13/2021] [Indexed: 05/12/2023]
Abstract
A NAC domain transcription factor, VND-INTERACTING2 (VNI2) is originally isolated as an interacting protein with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel element differentiation. VND7 directly or indirectly induces expression of a number of genes associated with xylem vessel element differentiation, while VNI2 inhibits the transcriptional activation activities of VND7 by forming a protein complex. VNI2 is expressed at an earlier stage of xylem vessel element differentiation than VND7. Here, to investigate whether VND7 also affects VNI2, a transient expression assay was performed. We demonstrated that VND7 downregulated VNI2 expression. Other transcription factors involved in xylem vessel formation did not show the negative regulation of VNI2 expression. Rather, MYB83, a downstream target of VND7, upregulated VNI2 expression. By using the deletion series of the VNI2 promoter, a 400 bp region was identified as being responsible for downregulation by VND7. These data suggested that VND7 and VNI2 mutually regulate each other, and VNI2 expression is both positively and negatively regulated in the transcriptional cascade.
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Affiliation(s)
- Aili Ailizati
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | | | - Atsuko Miyagi
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara 630-0192, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- E-mail: Tel: +81-48-858-3109 Fax: +81-48-858-3107
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Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis. BMC Genomics 2021; 22:865. [PMID: 34856929 PMCID: PMC8638140 DOI: 10.1186/s12864-021-08195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie. Results Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, where fiber growth is at different stages. We identified 6971 non-redundant proteins from bast bark. Proteomic comparison revealed 983 proteins with differential expression between the two bark types. Of these 983 proteins, 46 were identified as the homolog of known secondary wall biosynthetic proteins of Arabidopsis, indicating that they were potentially associated with fiber growth. Then, we proposed a molecular model for the secondary wall biosynthesis of ramie fiber. Furthermore, interaction analysis of 46 candidate proteins revealed two interacting networks that consisted of eight cellulose biosynthetic enzymes and seven lignin biosynthetic proteins, respectively. Conclusion This study sheds light on the proteomic basis underlying bast fiber growth in ramie, and the identification of many candidates associated with fiber growth provides important basis for understanding the fiber growth in this crop. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08195-9.
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Ahlawat YK, Nookaraju A, Harman-Ware AE, Doeppke C, Biswal AK, Joshi CP. Genetic Modification of KNAT7 Transcription Factor Expression Enhances Saccharification and Reduces Recalcitrance of Woody Biomass in Poplars. FRONTIERS IN PLANT SCIENCE 2021; 12:762067. [PMID: 34795688 PMCID: PMC8594486 DOI: 10.3389/fpls.2021.762067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
The precise role of KNAT7 transcription factors (TFs) in regulating secondary cell wall (SCW) biosynthesis in poplars has remained unknown, while our understanding of KNAT7 functions in other plants is continuously evolving. To study the impact of genetic modifications of homologous and heterologous KNAT7 gene expression on SCW formation in transgenic poplars, we prepared poplar KNAT7 (PtKNAT7) overexpression (PtKNAT7-OE) and antisense suppression (PtKNAT7-AS) vector constructs for the generation of transgenic poplar lines via Agrobacterium-mediated transformation. Since the overexpression of homologous genes can sometimes result in co-suppression, we also overexpressed Arabidopsis KNAT7 (AtKNAT7-OE) in transgenic poplars. In all these constructs, the expression of KNAT7 transgenes was driven by developing xylem (DX)-specific promoter, DX15. Compared to wild-type (WT) controls, many SCW biosynthesis genes downstream of KNAT7 were highly expressed in poplar PtKNAT7-OE and AtKNAT7-OE lines. Yet, no significant increase in lignin content of woody biomass of these transgenic lines was observed. PtKNAT7-AS lines, however, showed reduced expression of many SCW biosynthesis genes downstream of KNAT7 accompanied by a reduction in lignin content of wood compared to WT controls. Syringyl to Guaiacyl lignin (S/G) ratios were significantly increased in all three KNAT7 knockdown and overexpression transgenic lines than WT controls. These transgenic lines were essentially indistinguishable from WT controls in terms of their growth phenotype. Saccharification efficiency of woody biomass was significantly increased in all transgenic lines than WT controls. Overall, our results demonstrated that developing xylem-specific alteration of KNAT7 expression affects the expression of SCW biosynthesis genes, impacting at least the lignification process and improving saccharification efficiency, hence providing one of the powerful tools for improving bioethanol production from woody biomass of bioenergy crops and trees.
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Affiliation(s)
- Yogesh Kumar Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, United States
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | | | - Anne E. Harman-Ware
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Crissa Doeppke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Ajaya K. Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Chandrashekhar P. Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, United States
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Zeng Z, Li F, Huang R, Wang Y, Liu T. Phosphoproteome analysis reveals an extensive phosphorylation of proteins associated with bast fiber growth in ramie. BMC PLANT BIOLOGY 2021; 21:473. [PMID: 34656094 PMCID: PMC8520194 DOI: 10.1186/s12870-021-03252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Phosphorylation modification, one of the most common post-translational modifications of proteins, widely participates in the regulation of plant growth and development. Fibers extracted from the stem bark of ramie are important natural textile fibers; however, the role of phosphorylation modification in the growth of ramie fibers is largely unknown. RESULTS Here, we report a phosphoproteome analysis for the barks from the top and middle section of ramie stems, in which the fiber grows at different stages. A total of 10,320 phosphorylation sites from 9,170 unique phosphopeptides that were assigned to 3,506 proteins was identified, and 458 differentially phosphorylated sites from 323 proteins were detected in the fiber developmental barks. Twelve differentially phosphorylated proteins were the homologs of Arabidopsis fiber growth-related proteins. We further focused on the function of the differentially phosphorylated KNOX protein whole_GLEAN_10029667, and found that this protein dramatically repressed the fiber formation in Arabidopsis. Additionally, using a yeast two-hybridization assay, we identified a kinase and a phosphatase that interact with whole_GLEAN_10029667, indicating that they potentially target this KNOX protein to regulate its phosphorylation level. CONCLUSION The finding of this study provided insights into the involvement of phosphorylation modification in ramie fiber growth, and our functional characterization of whole_GLEAN_10029667 provide the first evidence to indicate the involvement of phosphorylation modification in the regulation of KNOX protein function in plants.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant protection, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Yang K, Li L, Lou Y, Zhu C, Li X, Gao Z. A regulatory network driving shoot lignification in rapidly growing bamboo. PLANT PHYSIOLOGY 2021; 187:900-916. [PMID: 34608957 PMCID: PMC8491019 DOI: 10.1093/plphys/kiab289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 05/24/2023]
Abstract
Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.
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Affiliation(s)
- Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lichao Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
- Jiangxi Academy of Forestry, Jiangxi Provincial Key Laboratory of Plant Biotechnology, Nanchang 330013, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xueping Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
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Genome wide identification of StKNOX gene family and characterization of their expression in Solanum tuberosum. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Genome-Wide Identification and Characterization of KNOTTED-Like Homeobox (KNOX) Homologs in Garlic ( Allium sativum L.) and Their Expression Profilings Responding to Exogenous Cytokinin and Gibberellin. Int J Mol Sci 2021; 22:ijms22179237. [PMID: 34502163 PMCID: PMC8430937 DOI: 10.3390/ijms22179237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Garlic (Allium sativum L.) is an important vegetable and is cultivated and consumed worldwide for its economic and medicinal values. Garlic cloves, the major reproductive and edible organs, are derived from the axillary meristems. KNOTTED-like homeobox (KNOX) proteins, such as SHOOT MERISTEM-LESS (STM), play important roles in axillary meristem formation and development. However, the KNOX proteins in garlic are still poorly known. Here, 10 AsKNOX genes, scattered on 5 of the 8 chromosomes, were genome-wide identified and characterized based on the newly released garlic genome. The typical conserved domains of KNOX proteins were owned by all these 10 AsKNOX homologs, which were divided into two Classes (Class I and Class II) based on the phylogenetic analysis. Prediction and verification of the subcellular localizations revealed the diverse subcellular localization of these 10 AsKNOX proteins. Cis-element prediction, tissue expression analysis, and expression profilings in responding to exogenous GA3 and 6-BA showed the potential involvement of AsKNOX genes in the gibberellin and cytokinin signaling pathways. Overall, the results of this work provided a better understanding of AsKNOX genes in garlic and laid an important foundation for their further functional studies.
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Yao T, Feng K, Xie M, Barros J, Tschaplinski TJ, Tuskan GA, Muchero W, Chen JG. Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704697. [PMID: 34484267 PMCID: PMC8416159 DOI: 10.3389/fpls.2021.704697] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jaime Barros
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Zhang X, Zhao J, Wu X, Hu G, Fan S, Ma Q. Evolutionary Relationships and Divergence of KNOTTED1-Like Family Genes Involved in Salt Tolerance and Development in Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:774161. [PMID: 34970288 PMCID: PMC8712452 DOI: 10.3389/fpls.2021.774161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/25/2021] [Indexed: 05/16/2023]
Abstract
The KNOX (KNOTTED1-like homeobox) transcription factors play an important role in leaf, shoot apical meristem and seed development and respond to biotic and abiotic stresses. In this study, we analyzed the diversity and evolutionary history of the KNOX gene family in the genome of tetraploid cotton (Gossypium hirsutum). Forty-four putative KNOX genes were identified. All KNOX genes from seven higher plant species were classified into KNOXI, KNOXII, and KNATM clades based on a phylogenetic analysis. Chromosomal localization and collinearity analysis suggested that whole-genome duplication and a polyploidization event contributed to the expansion of the cotton KNOX gene family. Analyses of expression profiles revealed that the GhKNOX genes likely responded to diverse stresses and were involved in cotton growth developmental processes. Silencing of GhKNOX2 enhanced the salt tolerance of cotton seedlings, whereas silencing of GhKNOX10 and GhKNOX14 reduced seedling tolerance to salt stress. Silencing of GhSTM3 influenced the cotton flowering time and plant development. These findings clarify the evolution of the cotton KNOX gene family and provide a foundation for future functional studies of KNOX proteins in cotton growth and development and response to abiotic stresses.
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Affiliation(s)
- Xiaohong Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Xiangyuan Wu
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Genhai Hu
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
- *Correspondence: Shuli Fan,
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
- Qifeng Ma,
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Seo M, Kim H, Lee JY. Information on the move: vascular tissue development in space and time during postembryonic root growth. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:110-117. [PMID: 32905917 DOI: 10.1016/j.pbi.2020.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 05/27/2023]
Abstract
Cascades of temporal and spatial regulation of gene expression play crucial roles in the vascular development in plant roots. Once vascular cell fates are determined, the timing of their differentiation is tightly controlled in a cell-autonomous manner. In contrast, extensive cell-to-cell communication contributes to the positioning and specifying of vascular cell types in the root meristem. Diverse factors moving short distances in a radial direction were found to be key contributors to these processes. Furthermore, signals from differentiated phloem were found to influence the phloem precursor and determine how the corresponding asymmetric cell division proceeded. These findings highlight the potential importance of underexplored types of intercellular communication in relation to vascular tissue development during postembryonic root growth.
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Affiliation(s)
- Minji Seo
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoujin Kim
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea.
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Qin W, Yin Q, Chen J, Zhao X, Yue F, He J, Yang L, Liu L, Zeng Q, Lu F, Mitsuda N, Ohme-Takagi M, Wu AM. The class II KNOX transcription factors KNAT3 and KNAT7 synergistically regulate monolignol biosynthesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5469-5483. [PMID: 32474603 DOI: 10.1093/jxb/eraa266] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/22/2020] [Indexed: 05/21/2023]
Abstract
The function of the transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is still unclear since it appears to be either a negative or a positive regulator for secondary cell wall deposition with its loss-of-function mutant displaying thicker interfascicular and xylary fiber cell walls but thinner vessel cell walls in inflorescence stems. To explore the exact function of KNAT7, class II KNOTTED1-LIKE HOMEOBOX (KNOX II) genes in Arabidopsis including KNAT3, KNAT4, and KNAT5 were studied together. By chimeric repressor technology, we found that both KNAT3 and KNAT7 repressors exhibited a similar dwarf phenotype. Both KNAT3 and KNAT7 genes were expressed in the inflorescence stems and the knat3 knat7 double mutant exhibited a dwarf phenotype similar to the repressor lines. A stem cross-section of knat3 knat7 displayed an enhanced irregular xylem phenotype as compared with the single mutants, and its cell wall thickness in xylem vessels and interfascicular fibers was significantly reduced. Analysis of cell wall chemical composition revealed that syringyl lignin was significantly decreased while guaiacyl lignin was increased in the knat3 knat7 double mutant. Coincidently, the knat3 knat7 transcriptome showed that most lignin pathway genes were activated, whereas the syringyl lignin-related gene Ferulate 5-Hydroxylase (F5H) was down-regulated. Protein interaction analysis revealed that KNAT3 and KNAT7 can form a heterodimer, and KNAT3, but not KNAT7, can interact with the key secondary cell wall formation transcription factors NST1/2, which suggests that the KNAT3-NST1/2 heterodimer complex regulates F5H to promote syringyl lignin synthesis. These results indicate that KNAT3 and KNAT7 synergistically work together to promote secondary cell wall biosynthesis.
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Affiliation(s)
- Wenqi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Qi Yin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jiajun Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xianhai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Fengxia Yue
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Junbo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Linjie Yang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Lijun Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, Shandong, China
| | - Qingyin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Fachuang Lu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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Meng L, Liu X, He C, Xu B, Li Y, Hu Y. Functional divergence and adaptive selection of KNOX gene family in plants. Open Life Sci 2020; 15:346-363. [PMID: 33817223 PMCID: PMC7874613 DOI: 10.1515/biol-2020-0036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
KNOTTED-like homeodomain (KNOX) genes are transcriptional regulators that play an important role in morphogenesis. In the present study, a comparative analysis was performed to investigate the molecular evolution of the characteristics of the KNOX gene family in 10 different plant species. We identified 129 KNOX gene family members, which were categorized into two subfamilies based on multiple sequence alignment and phylogenetic tree reconstruction. Several segmental duplication pairs were found, indicating that different species share a common expansion model. Functional divergence analysis identified the 15 and 52 amino acid sites with significant changes in evolutionary rates and amino acid physicochemical properties as functional divergence sites. Additional selection analysis showed that 14 amino acid sites underwent positive selection during evolution, and two groups of co-evolutionary amino acid sites were identified by Coevolution Analysis using Protein Sequences software. These sites could play critical roles in the molecular evolution of the KNOX gene family in these species. In addition, the expression profiles of KNOX duplicated genes demonstrated functional divergence. Taken together, these results provide novel insights into the structural and functional evolution of the KNOX gene family.
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Affiliation(s)
- Lingyan Meng
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiaomei Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Congfen He
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, 100048, China
| | - Biyao Xu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
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Jia P, Zhang C, Xing L, Li Y, Shah K, Zuo X, Zhang D, An N, Han M, Ren X. Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica. FRONTIERS IN PLANT SCIENCE 2020; 11:128. [PMID: 32153621 PMCID: PMC7047289 DOI: 10.3389/fpls.2020.00128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/28/2020] [Indexed: 05/11/2023]
Abstract
Knotted1-like Homeobox (KNOX) proteins play important roles in regulating plant growth, development, and other biological processes. However, little information is available on the KNOX gene family in apple (Malus domestica Borkh.). In this study, 22 KNOX genes were identified in the apple genome. The gene structure, protein characteristics, and promoter region were characterized. The MdKNOX family members were divided into three classes based on their phylogenetic relationships. Quantitative real-time PCR analysis revealed that the majority of MdKNOX genes exhibited strongly preferential expression in buds and were significantly up-regulated during the flower induction period. The transcript levels of MdKNOX genes were responsive to treatments with flowering- and stress-related hormones. The putative upstream regulation factor MdGRF could directly bind to the promoter of MdKNOX15 and MdKNOX19, and inhibit their transcriptional activities, which were confirmed by yeast one-hybrid and dual-luciferase assays. The results provide an important foundation for future analysis of the regulation and functions of the MdKNOX gene family.
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Affiliation(s)
- Peng Jia
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Chenguang Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Libo Xing
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Youmei Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Kamran Shah
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Xiya Zuo
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Dong Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Na An
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Mingyu Han
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- *Correspondence: Mingyu Han, ; Xiaolin Ren,
| | - Xiaolin Ren
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- *Correspondence: Mingyu Han, ; Xiaolin Ren,
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