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Biswas R, Chaudhuri S. AtHMGB15 regulates tapetal apoptosis in pollen development and actin dynamics during pollen germination in arabidopsis. PLANT REPRODUCTION 2024:10.1007/s00497-024-00505-x. [PMID: 38904831 DOI: 10.1007/s00497-024-00505-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
KEY MESSAGE ARID-HMG DNA binding protein, AtHMGB15, regulates pollen development and pollen germination in Arabidopsis. Previous studies have shown that ARID-HMG DNA binding protein, AtHMGB15 regulate pollen development and pollen germination in Arabidopsis. Here, we performed transcriptome and cytological studies to understand the role of AtHMGB15 in regulating pollen wall morphology and the pollen tube germination rate. Our result showed abnormal vacuolization in the tapetal cells during anther maturation and prolonged PCD in AtHMGB15 loss-of-function mutant. The tapetum has the ability to perform both secretory and biosynthetic activities critical for pollen maturation and pollen viability. Interestingly, expression of PCD executer genes CEP1, MC9 and RNS3 were significant down-regulation of in athmgb15-4. The growth of pollen tubes is regulated by the actin cytoskeleton dynamics. To address the defect in pollen tube growth of athmgb15, we monitored the actin network in growing pollen tubes of wildtype and athmgb15-4 using Rhodamine-phalloidin fluorescence. Our results indicate a highly fragmented actin distribution in athmgb15-4 pollen tubes with a lesser number of long actin fibers and significantly low f-actin concentration at the apex. q-RTPCR further indicates significant downy-regulation of actin regulatory proteins VLN2 and PRF4. Collectively, our results suggest that AtHMGB15 being a nuclear architectural protein orchestrates high-order chromatin organization to promote the transcription of genes responsible for pollen development and pollen germination.
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Affiliation(s)
- Ruby Biswas
- Department of Biological Sciences, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Shubho Chaudhuri
- Department of Biological Sciences, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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2
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Zheng J, Tang H, Wang J, Liu Y, Ge L, Liu G, Shi Q, Zhang Y. Genome-Wide Identification and Expression Analysis of the High-Mobility Group B ( HMGB) Gene Family in Plant Response to Abiotic Stress in Tomato. Int J Mol Sci 2024; 25:5850. [PMID: 38892039 PMCID: PMC11172549 DOI: 10.3390/ijms25115850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, we identified 11 members of the HMGB family in tomato using BLAST. We employed genome-wide identification, gene structure analysis, domain conservation analysis, cis-acting element analysis, collinearity analysis, and qRT-PCR-based expression analysis to study these 11 genes. These genes were categorized into four groups based on their unique protein domain structures. Despite their structural diversity, all members contain the HMG-box domain, a characteristic feature of the HMG superfamily. Syntenic analysis suggested that tomato SlHMGBs have close evolutionary relationships with their homologs in other dicots. The promoter regions of SlHMGBs are enriched with numerous cis-elements related to plant growth and development, phytohormone responsiveness, and stress responsiveness. Furthermore, SlHMGB members exhibited distinct tissue-specific expression profiles, suggesting their potential roles in regulating various aspects of plant growth and development. Most SlHMGB genes respond to a variety of abiotic stresses, including salt, drought, heat, and cold. For instance, SlHMGB2 and SlHMGB4 showed positive responses to salt, drought, and cold stresses. SlHMGB1, SlHMGB3, and SlHMGB8 were involved in responses to two types of stress: SlHMGB1 responded to drought and heat, while SlHMGB3 and SlHMGB8 responded to salt and heat. SlHMGB6 and SlHMGB11 were solely regulated by drought and heat stress, respectively. Under various treatment conditions, the number of up-regulated genes significantly outnumbered the down-regulated genes, implying that the SlHMGB family may play a crucial role in mitigating abiotic stress in tomato. These findings lay a foundation for further dissecting the precise roles of SlHMGB genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Yan Zhang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, China; (J.Z.); (H.T.); (J.W.); (Y.L.); (L.G.); (G.L.); (Q.S.)
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3
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Zhang ZB, Xiong T, Wang XJ, Chen YR, Wang JL, Guo CL, Ye ZY. Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae. PLoS One 2024; 19:e0302292. [PMID: 38626181 PMCID: PMC11020792 DOI: 10.1371/journal.pone.0302292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.
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Affiliation(s)
- Zai-Bao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiao-Jia Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jing-Lei Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Cong-Li Guo
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zi-Yi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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Zhang C, Zhang C, Xu X, Liao M, Tong N, Zhang Z, Chen Y, Xu Han X, Lin Y, Lai Z. Transcriptome analysis provides insight into the regulatory mechanisms underlying pollen germination recovery at normal high ambient temperature in wild banana ( Musa itinerans). FRONTIERS IN PLANT SCIENCE 2023; 14:1255418. [PMID: 37822335 PMCID: PMC10562711 DOI: 10.3389/fpls.2023.1255418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Introduction Cultivated banana are polyploid, with low pollen fertility, and most cultivars are male sterile, which leads to difficulties in banana breeding research. The selection of male parent with excellent resistance and pollen fertility is therefore essential for banana breeding. Wild banana (Musa itinerans) have developed many good characteristics during natural selection and constitute an excellent gene pool for breeding. Therefore, research on wild banana breeding is very important for banana breeding. Results In the current analysis, we examined the changes in viability of wild banana pollens at different temperatures by in vitro germination, and found that the germination ability of wild banana pollens cultured at 28°C for 2 days was higher than that of pollens cultured at 23°C (pollens that could not germinate normally under low temperature stress), 24°C (cultured at a constant temperature for 2 days) and 32°C (cultured at a constant temperature for 2 days). To elucidate the molecular mechanisms underlying the germination restoration process in wild banana pollens, we selected the wild banana pollens that had lost its germination ability under low temperature stress (23°C) as the control group (CK) and the wild banana pollens that had recovered its germination ability under constant temperature incubation of 28°C for 2 days as the treatment group (T) for transcriptome sequencing. A total of 921 differentially expressed genes (DEGs) were detected in CK vs T, of which 265 were up-regulated and 656 were down-regulated. The combined analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the activation, metabolism of various substances (lipids, sugars, amino acids) play a major role in restoring pollen germination capacity. TCA cycle and the sesquiterpenoid and triterpenoid biosynthetic pathways were also significantly enriched in the KEGG pathway. And we found that some DEGs may be associated with pollen wall formation, DNA methylation and DNA repair. The cysteine content, free fatty acid (FFA) content, H2O2 content, fructose content, and sucrose content of pollen were increased at treatment of 28°C, while D-Golactose content was decreased. Finally, the GO pathway was enriched for a total of 24 DEGs related to pollen germination, of which 16 DEGs received targeted regulation by 14 MYBs. Discussions Our study suggests that the balance between various metabolic processes, pollen wall remodelling, DNA methylation, DNA repairs and regulation of MYBs are essential for germination of wild banana pollens.
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Affiliation(s)
- Chunyu Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengyu Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoqiong Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Minzhang Liao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ning Tong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xu Xu Han
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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Alcantud R, Weiss J, Terry MI, Bernabé N, Verdú-Navarro F, Fernández-Breis JT, Egea-Cortines M. Flower transcriptional response to long term hot and cold environments in Antirrhinum majus. FRONTIERS IN PLANT SCIENCE 2023; 14:1120183. [PMID: 36778675 PMCID: PMC9911551 DOI: 10.3389/fpls.2023.1120183] [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: 12/09/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew Antirrhinum majus plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditions for a period of two years. Flower size, petal anthocyanin content and pollen viability obtained higher values in cold conditions, decreasing in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions and stable in control and hot temperatures, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production. Scent complexity was low in cold temperatures. The transcriptomic analysis of mature flowers, followed by gene enrichment analysis and CNET plot visualization, showed two groups of genes. One group comprised genes controlling the affected traits, and a second group appeared as long-term adaptation to non-optimal temperatures. These included hypoxia, unsaturated fatty acid metabolism, ribosomal proteins, carboxylic acid, sugar and organic ion transport, or protein folding. We found a differential expression of floral organ identity functions, supporting the flower size data. Pollinator-related traits such as scent and color followed opposite trends, indicating an equilibrium for rendering the organs for pollination attractive under changing climate conditions. Prolonged heat or cold cause structural adaptations in protein synthesis and folding, membrane composition, and transport. Thus, adaptations to cope with non-optimal temperatures occur in basic cellular processes.
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Affiliation(s)
- Raquel Alcantud
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Marta I. Terry
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Nuria Bernabé
- Department of Informatics and Systems, Campus de Espinardo, Universidad de Murcia, Instituto Murciano de Investigaciones Biomédicas (IMIB)-Arrixaca, Murcia, Spain
| | - Fuensanta Verdú-Navarro
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
- R&D Department, Bionet Engineering, Av/Azul, Parque Tecnológico Fuente Álamo, Murcia, Spain
| | - Jesualdo Tomás Fernández-Breis
- Department of Informatics and Systems, Campus de Espinardo, Universidad de Murcia, Instituto Murciano de Investigaciones Biomédicas (IMIB)-Arrixaca, Murcia, Spain
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, Cartagena, Spain
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The involvement of an HMG-box gene in germ cell genesis in Pyropia haitanensis. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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7
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Jiang J, Xu P, Zhang J, Li Y, Zhou X, Jiang M, Zhu J, Wang W, Yang L. Global transcriptome analysis reveals potential genes associated with genic male sterility of rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1004781. [PMID: 36340380 PMCID: PMC9635397 DOI: 10.3389/fpls.2022.1004781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Rapeseed is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been widely used successfully for rapeseed hybrid production. The physiological and molecular mechanism of pollen development in GMS lines of rapeseed (Brassica napus L.) need to be determined for the creation of hybrids and cultivation of new varieties. However, limited studies have focused on systematically mining genes that regulate the pollen development of GMS lines in B. napus. In the present study, to determine the stage at which pollen development begins to show abnormality in the GMS lines, we performed semi-thin section analysis of the anthers with five pollen development stages. The results indicated that the abnormal pollen development in DGMS lines might start at the meiotic stage, and abnormal pollen development in RGMS lines probably occurred before the tetrad stage. To investigate the critical genes and pathways involved in pollen development in GMS lines, we constructed and sequenced 24 transcriptome libraries for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines (6251AB and 6284AB) and two dominant GMS (DGMS) lines (4001AB and 4006AB). A total of 23,554 redundant DEGs with over two-fold change between sterile and fertile lines were obtained. A total of 346 DEGs were specifically related to DGMS, while 1,553 DEGs were specifically related to RGMS. A total of 1,545 DEGs were shared between DGMS and RGMS. And 253 transcription factors were found to be differentially expressed between the sterile and fertile lines of GMS. In addition, 6,099 DEGs possibly related to anther, pollen, and microspore development processes were identified. Many of these genes have been reported to be involved in anther and microspore developmental processes. Several DEGs were speculated to be key genes involved in the regulation of fertility. Three differentially expressed genes were randomly selected and their expression levels were verified by quantitative PCR (qRT-PCR). The results of qRT-PCR largely agreed with the transcriptome sequencing results. Our findings provide a global view of genes that are potentially involved in GMS occurrence. The expression profiles and function analysis of these DEGs were provided to expand our understanding of the complex molecular mechanism in pollen and sterility development in B. napus.
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Affiliation(s)
- Jianxia Jiang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Pengfei Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Junying Zhang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yanli Li
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xirong Zhou
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Jiang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jifeng Zhu
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Weirong Wang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liyong Yang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Xu K, Chen S, Li T, Yu S, Zhao H, Liu H, Luo L. Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:711271. [PMID: 34421959 PMCID: PMC8375505 DOI: 10.3389/fpls.2021.711271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 05/05/2023]
Abstract
Drought stress adversely affects crop growth and productivity worldwide. In response, plants have evolved several strategies in which numerous genes are induced to counter stress. High mobility group (HMG) proteins are the second most abundant family of chromosomal proteins. They play a crucial role in gene transcriptional regulation by modulating the chromatin/DNA structure. In this study, we isolated a novel HMG gene, OsHMGB707, one of the candidate genes localized in the quantitative trait loci (QTL) interval of rice drought tolerance, and examined its function on rice stress tolerance. The expression of OsHMGB707 was up-regulated by dehydration and high salt treatment. Its overexpression significantly enhanced drought tolerance in transgenic rice plants, whereas its knockdown through RNA interference (RNAi) did not affect the drought tolerance of the transgenic rice plants. Notably, OsHMGB707-GFP is localized in the cell nucleus, and OsHMGB707 is protein-bound to the synthetic four-way junction DNA. Several genes were up-regulated in OsHMGB707-overexpression (OE) rice lines compared to the wild-type rice varieties. Some of the genes encode stress-related proteins (e.g., DREB transcription factors, heat shock protein 20, and heat shock protein DnaJ). In summary, OsHMGB707 encodes a stress-responsive high mobility group protein and regulates rice drought tolerance by promoting the expression of stress-related genes.
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Affiliation(s)
- Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Shoujun Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Zhao
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai, China
- *Correspondence: Hongyan Liu,
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Lijun Luo,
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10
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Mallik R, Prasad P, Kundu A, Sachdev S, Biswas R, Dutta A, Roy A, Mukhopadhyay J, Bag SK, Chaudhuri S. Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194644. [PMID: 33068782 DOI: 10.1016/j.bbagrm.2020.194644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/12/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022]
Abstract
AtHMGB15 belongs to a group of ARID-HMG proteins which are plant specific. The presence of two known DNA binding domains: AT rich interacting domain (ARID) and High Mobility Group (HMG)-box, in one polypeptide, makes this protein intriguing. Although proteins containing individual HMG and ARID domains have been characterized, not much is known about the role of ARID-HMG proteins. Promoter analysis of AtHMGB15 showed the presence of various stress responsive cis regulatory elements along with MADS-box containing transcription factors. Our result shows that the expression of AtHMGB15 increased significantly upon application of cold stress. Using ChIP-chip approach, we have identified 6128 and 4689 significantly enriched loci having AtHMGB15 occupancy under control and cold stressed condition respectively. GO analysis shows genes belonging to abiotic stress response, cold response and root development were AtHMGB15 targets during cold stress. DNA binding and footprinting assays further identified A(A/C)--ATA---(A/T)(A/T) as AtHMGB15 binding motif. The enriched probe distribution in both control and cold condition shows a bias of AtHMGB15 binding towards the transcribed (gene body) region. Further, the expression of cold stress responsive genes decreased in athmgb15 knockout plants compared to wild-type. Taken together, binding enrichment of AtHMGB15 to the promoter and upstream to stress loci suggest an unexplored role of the protein in stress induced transcription regulation.
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Affiliation(s)
- Rwitie Mallik
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Priti Prasad
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Anindya Kundu
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Sonal Sachdev
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Ruby Biswas
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Jayanta Mukhopadhyay
- Department of Chemistry, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P1/12 C.I.T Scheme VII M, Kolkata 700054, India.
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Li S, Xin M, Luan J, Liu D, Wang C, Liu C, Zhang W, Zhou X, Qin Z. Overexpression of CsHMGB Alleviates Phytotoxicity and Propamocarb Residues in Cucumber. FRONTIERS IN PLANT SCIENCE 2020; 11:738. [PMID: 32595667 PMCID: PMC7304447 DOI: 10.3389/fpls.2020.00738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Cucumber (Cucumis sativus L.) is one of the most economically important fruits of the Cucurbitaceae family, therefore consideration of potential pesticide residues in the fruit in the context of cucumber breeding and production programs is important. Propamocarb (a pesticide commonly used to prevent downy mildew) is widely used in cucumber cultivation, but the molecular mechanism underlying the degradation and metabolism of propamocarb in cucumber is not well understood. We screened a candidate CsHMGB gene (CsaV3-5G28190) for response to propamocarb exposure using transcriptome data. The coding region of CsHMGB was 624 bp in length and encoded the conserved HMB-box region. CsHMGB expression differed significantly between the "D0351" genotype, which accumulated low levels of propamocarb, and the "D9320" genotype, which accumulated high levels of propamocarb. CsHMGB expression was positively correlated with propamocarb levels in the cucumber peel. CsHMGB expression was upregulated in the fruit peels of the "D0351" genotype following exposure to propamocarb stress for 3-120 h, but no difference was observed in expression between propamocarb treatment and control for the "D9320" genotype. For the "D0351" genotype, CsHMGB expression was higher in the fruit peels and leaves than that in female flowers; expression was moderate in the stems and fruit pulps, and weak in male flowers and roots. The CsHMGB protein was targeted to the nucleus in Arabidopsis protoplasts and in the epidermis of Nicotiana benthamiana leaves. We measured MDA, O2 -, and H2O2 levels in cucumber plants and found that they were likely to accumulate reactive oxygen species (ROS) in response to propamocarb stress. Analysis of antioxidant enzyme activity (SOD, POD, CAT, APX, GPX, GST, and GR) and the ascorbate-glutathione (AsA-GSH) system showed that the resistance of the plants was reduced and the levels of propamocarb residue was increased in CsHMGB-silenced plants in response to propamocarb stress. Conversely, overexpression of CsHMGB promoted glutathione-dependent detoxification by AsA-GSH system and improved the antioxidant potential, reduced the accumulation of ROS. Ultimately, the metabolism of propamocarb in cucumber was increased via increase in the wax levels and the stomatal conductance.
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Affiliation(s)
- Shengnan Li
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Ming Xin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Jie Luan
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Dong Liu
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Chunhua Wang
- College of Horticulture, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chunhong Liu
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Wenshuo Zhang
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Xiuyan Zhou
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
| | - Zhiwei Qin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, China
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13
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Ganguly P, Saha S, Behera AP, Roy A, Datta AB, Chaudhuri S. RETRACTED: Interaction of AtHMGB15, an ARID-HMG family protein, with RING-H2 type E3 ubiquitin ligase AtATL79. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:32-43. [PMID: 30348326 DOI: 10.1016/j.plantsci.2018.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/28/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Payel Ganguly
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Sudip Saha
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Aditya Prasad Behera
- Department of Biochemistry, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Ajit Bikram Datta
- Department of Biochemistry, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India.
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14
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Li LX, Liao HZ, Jiang LX, Tan Q, Ye D, Zhang XQ. Arabidopsis thaliana NOP10 is required for gametophyte formation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:723-736. [PMID: 29578643 DOI: 10.1111/jipb.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/22/2018] [Indexed: 05/19/2023]
Abstract
The female gametophyte is crucial for sexual reproduction of higher plants, yet little is known about the molecular mechanisms underlying its development. Here, we report that Arabidopsis thaliana NOP10 (AtNOP10) is required for female gametophyte formation. AtNOP10 was expressed predominantly in the seedling and reproductive tissues, including anthers, pollen grains, and ovules. Mutations in AtNOP10 interrupted mitosis of the functional megaspore during early development and prevented polar nuclear fusion in the embryo sacs. AtNOP10 shares a high level of amino acid sequence similarity with Saccharomyces cerevisiae (yeast) NOP10 (ScNOP10), an important component of the H/ACA small nucleolar ribonucleoprotein particles (H/ACA snoRNPs) implicated in 18S rRNA synthesis and rRNA pseudouridylation. Heterologous expression of ScNOP10 complemented the mutant phenotype of Atnop10. Thus, AtNOP10 influences functional megaspore mitosis and polar nuclear fusion during gametophyte formation in Arabidopsis.
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Affiliation(s)
- Lin-Xiao Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong-Ze Liao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery and Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Li-Xi Jiang
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qing Tan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - De Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xue-Qin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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15
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Zhu L, Chu LC, Liang Y, Zhang XQ, Chen LQ, Ye D. The Arabidopsis CrRLK1L protein kinases BUPS1 and BUPS2 are required for normal growth of pollen tubes in the pistil. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:474-486. [PMID: 29763520 DOI: 10.1111/tpj.13963] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 05/10/2023]
Abstract
In flowering plants, the interaction of pollen tubes with female tissues is important for the accomplishment of double fertilization. Little information is known about the mechanisms that underlie signalling between pollen tubes and female tissues. In this study, two Arabidopsis pollen tube-expressed CrRLK1L protein kinases, Buddha's Paper Seal 1 (BUPS1) and BUPS2, were identified as being required for normal tip growth of pollen tubes in the pistil. They are expressed prolifically in pollen and pollen tubes and are localized on the plasma membrane of the pollen tube tip region. Mutations in BUPS1 drastically reduced seed set. Most of the bups1 mutant pollen tubes growing in the pistil exhibited a swollen pollen tube tip, leading to failure of fertilization. The bups2 pollen tubes had a slightly abnormal morphology but could still accomplish double fertilization. The bups1 bups2 double mutant exhibited a slightly enhanced phenotype compared to the single bups1 mutants. The BUPS1 proteins could form homomers and heteromers with BUPS2, whereas BUPS2 could only form heteromers with BUPS1. The BUPS proteins could interact with the Arabidopsis pollen-expressed RopGEFs in the yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. The results indicated that the BUPSs may mediate normal polar growth of pollen tubes in the pistil.
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Affiliation(s)
- Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang-Cui Chu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xue-Qin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Li-Qun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - De Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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16
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Yang F, Li W, Jiang N, Yu H, Morohashi K, Ouma WZ, Morales-Mantilla DE, Gomez-Cano FA, Mukundi E, Prada-Salcedo LD, Velazquez RA, Valentin J, Mejía-Guerra MK, Gray J, Doseff AI, Grotewold E. A Maize Gene Regulatory Network for Phenolic Metabolism. MOLECULAR PLANT 2017; 10:498-515. [PMID: 27871810 DOI: 10.1016/j.molp.2016.10.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/20/2016] [Accepted: 10/31/2016] [Indexed: 05/23/2023]
Abstract
The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.
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Affiliation(s)
- Fan Yang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Jiang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Haidong Yu
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Kengo Morohashi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wilberforce Zachary Ouma
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel E Morales-Mantilla
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Fabio Andres Gomez-Cano
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Mukundi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Luis Daniel Prada-Salcedo
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Roberto Alers Velazquez
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jasmin Valentin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Maria Katherine Mejía-Guerra
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH 43560, USA
| | - Andrea I Doseff
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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17
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Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2016; 92:371-88. [PMID: 27503561 DOI: 10.1007/s11103-016-0519-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/28/2016] [Indexed: 05/22/2023]
Abstract
ARID-HMG DNA-binding proteins represent a novel group of HMG-box containing protein family where the AT-rich interaction domain (ARID) is fused with the HMG-box domain in a single polypeptide chain. ARID-HMG proteins are highly plant specific with homologs found both in flowering plants as well as in moss such as Physcomitrella. The expression of these proteins is ubiquitous in plant tissues and primarily localises in the cell nucleus. HMGB proteins are involved in several nuclear processes, but the role of ARID-HMG proteins in plants remains poorly explored. Here, we performed DNA-protein interaction studies with Arabidopsis ARID-HMG protein HMGB11 (At1g55650) to understand the functionality of this protein and its individual domains. DNA binding assays revealed that AtHMGB11 can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA. Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys(85) from the ARID domain and Arg(199) & Lys(202) from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. Overall, the study signifies that both the ARID and the HMG-box domain contribute to the optimal functioning of ARID-HMG protein in vivo.
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Affiliation(s)
- Adrita Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Arkajyoti Dutta
- Department of Chemistry, Bose Institute, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, 700054, India
| | | | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Kolkata, 700054, India.
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18
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Cui HH, Liao HZ, Tang Y, Du XY, Chen LQ, Ye D, Zhang XQ. ABORTED GAMETOPHYTE 1 is required for gametogenesis in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:1003-1016. [PMID: 25693728 DOI: 10.1111/jipb.12341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/11/2015] [Indexed: 06/04/2023]
Abstract
In flowering plants, the male and female gametogenesis is a crucial step of sexual reproduction. Although many genes have been identified as being involved in the gametogenesis process, the genetic mechanisms underlying gametogenesis remains poorly understood. We reported here characterization of the gene, ABORTED GAMETOPHYTE 1 (AOG1) that is newly identified as essential for gametogenesis in Arabidopsis thaliana. AOG1 is expressed predominantly in reproductive tissues including the developing pollen grains and ovules. The AOG1 protein shares no significant amino acid sequence similarity with other documented proteins and is located mainly in nuclei of the cells. Mutation in AOG1 caused degeneration of pollen at the uninucleate microspore stage and severe defect in embryo sacs, leading to a significant reduction in male and female fertility. Furthermore, the molecular analyses showed that the aog1 mutant significantly affected the expression of several genes, which are required for gametogenesis. Our results suggest that AOG1 plays important roles in gametogenesis at the stage prior to pollen mitosis I (PMI) in Arabidopsis, possibly through collaboration with other genes.
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Affiliation(s)
- Hong-Hui Cui
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hong-Ze Liao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Tang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin-Yu Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Li-Qun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - De Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xue-Qin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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19
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Antosch M, Schubert V, Holzinger P, Houben A, Grasser KD. Mitotic lifecycle of chromosomal 3xHMG-box proteins and the role of their N-terminal domain in the association with rDNA loci and proteolysis. THE NEW PHYTOLOGIST 2015; 208:1067-1077. [PMID: 26213803 DOI: 10.1111/nph.13575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 05/21/2023]
Abstract
The high mobility group (HMG)-box is a DNA-binding domain characteristic of various eukaryotic DNA-binding proteins. 3xHMG-box proteins (containing three copies of the HMG-box domain and a unique basic N-terminal domain) are specific for plants and the Arabidopsis genome encodes two versions termed 3xHMG-box1 and 3xHMG-box2, whose expression is cell cycle-dependent, peaking during mitosis. Here, we analysed in detail the spatiotemporal expression, subcellular localisation and chromosome association of the Arabidopsis thaliana 3xHMG-box proteins. Live cell imaging and structured illumination microscopy revealed that the expression of the 3xHMG-box proteins is induced in late G2 phase of the cell cycle and upon nuclear envelope breakdown in prophase they rapidly associate with the chromosomes. 3xHMG-box1 associates preferentially with 45S rDNA loci and the basic N-terminal domain is involved in the targeting of rDNA loci. Shortly after mitosis the 3xHMG-box proteins are degraded and an N-terminal destruction-box mediates the proteolysis. Ectopic expression/localisation of 3xHMG-box1 in interphase nuclei results in reduced plant growth and various developmental defects including early bolting and abnormal flower morphology. The remarkable conservation of 3xHMG-box proteins within the plant kingdom, their characteristic expression during mitosis, and their striking association with chromosomes, suggest that they play a role in the organisation of plant mitotic chromosomes.
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Affiliation(s)
- Martin Antosch
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Philipp Holzinger
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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20
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Xu Y, Zong W, Hou X, Yao J, Liu H, Li X, Zhao Y, Xiong L. OsARID3, an AT-rich Interaction Domain-containing protein, is required for shoot meristem development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:806-817. [PMID: 26121094 DOI: 10.1111/tpj.12927] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 06/04/2023]
Abstract
The shoot apical meristem (SAM) produces all of the plant's aerial organs. The SAM is established either during embryogenesis or experimentally in in vitro tissue culture. Although several factors including the Class I KNOTTED1-LIKE HOMEOBOX (KNOXI) proteins, auxin, and cytokinin are known to play essential roles in SAM development, the underlying mechanisms of SAM formation and maintenance are still largely not understood. Herein we demonstrate that OsARID3, a member of the rice (Oryza sativa) AT-rich Interaction Domain (ARID) family, is required for SAM development. Disruption of OsARID3 leads to a defective SAM, early seedling lethality, and impaired capacity of in vitro shoot regeneration. We show that the expression levels of several KNOXI genes and the biosynthetic genes for auxin and cytokinin are significantly altered in the Osarid3 mutant calli. Moreover, we determine that auxin concentrations are increased, whereas cytokinin levels are decreased, in Osarid3 calli. Furthermore, chromatin immunoprecipitation results demonstrate that OsARID3 binds directly to the KNOXI gene OSH71, the auxin biosynthetic genes OsYUC1 and OsYUC6, and the cytokinin biosynthetic genes OsIPT2 and OsIPT7. We also show through electrophoretic mobility shift assays that OsARID3 specifically binds to the AT-rich DNA sequences of the identified target genes. We conclude that OsARID3 is an AT-rich specific DNA-binding protein and that it plays a major role in SAM development in rice.
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Affiliation(s)
- Yan Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Zong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Hou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jialing Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunde Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0116, USA
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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21
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Rutley N, Twell D. A decade of pollen transcriptomics. PLANT REPRODUCTION 2015; 28:73-89. [PMID: 25761645 PMCID: PMC4432081 DOI: 10.1007/s00497-015-0261-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/24/2015] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Overview of pollen transcriptome studies. Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.
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Affiliation(s)
- Nicholas Rutley
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
| | - David Twell
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
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Fritzsch B, Jahan I, Pan N, Elliott KL. Evolving gene regulatory networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system. Cell Tissue Res 2014; 359:295-313. [PMID: 25416504 DOI: 10.1007/s00441-014-2043-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/20/2014] [Indexed: 12/18/2022]
Abstract
Understanding the evolution of the neurosensory system of man, able to reflect on its own origin, is one of the major goals of comparative neurobiology. Details of the origin of neurosensory cells, their aggregation into central nervous systems and associated sensory organs and their localized patterning leading to remarkably different cell types aggregated into variably sized parts of the central nervous system have begun to emerge. Insights at the cellular and molecular level have begun to shed some light on the evolution of neurosensory cells, partially covered in this review. Molecular evidence suggests that high mobility group (HMG) proteins of pre-metazoans evolved into the definitive Sox [SRY (sex determining region Y)-box] genes used for neurosensory precursor specification in metazoans. Likewise, pre-metazoan basic helix-loop-helix (bHLH) genes evolved in metazoans into the group A bHLH genes dedicated to neurosensory differentiation in bilaterians. Available evidence suggests that the Sox and bHLH genes evolved a cross-regulatory network able to synchronize expansion of precursor populations and their subsequent differentiation into novel parts of the brain or sensory organs. Molecular evidence suggests metazoans evolved patterning gene networks early, which were not dedicated to neuronal development. Only later in evolution were these patterning gene networks tied into the increasing complexity of diffusible factors, many of which were already present in pre-metazoans, to drive local patterning events. It appears that the evolving molecular basis of neurosensory cell development may have led, in interaction with differentially expressed patterning genes, to local network modifications guiding unique specializations of neurosensory cells into sensory organs and various areas of the central nervous system.
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Affiliation(s)
- Bernd Fritzsch
- Department of Biology, University of Iowa, CLAS, 143 BB, Iowa City, IA, 52242, USA,
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