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Gokulan CG, Bangale U, Balija V, Ballichatla S, Potupureddi G, Rao D, Varma P, Magar N, Jallipalli K, Manthri S, Padmakumari AP, Laha GS, Rao LVS, Barbadikar KM, Raman MS, Patel HK, Maganti SM, Sonti RV. Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer resistance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:122. [PMID: 38713254 DOI: 10.1007/s00122-024-04628-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024]
Abstract
KEY MESSAGE By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties. Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB resistance at the vegetative phase in a resistant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB resistance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and resistant lines revealed several genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB resistance. Taken together, our study provides deeper insights into rice-YSB interaction and enhances the understanding of YSB resistance mechanism. Importantly, a promising breeding line and markers for YSB resistance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars.
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Affiliation(s)
- C G Gokulan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Umakanth Bangale
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Vishalakshi Balija
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Suneel Ballichatla
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Gopi Potupureddi
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Deepti Rao
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Prashanth Varma
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Nakul Magar
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Karteek Jallipalli
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Sravan Manthri
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - A P Padmakumari
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - Gouri S Laha
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | - L V Subba Rao
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India
| | | | | | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
- Academy of Scientific and Innovative Research, Uttar Pradesh, Ghaziabad, 201002, India.
| | - Sheshu Madhav Maganti
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, 500030, India.
- ICAR-Central Tobacco Research Institute, Rajamahendravaram, Andhra Pradesh, 533105, India.
| | - Ramesh V Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Wang J, Li M, Nan N, Ma A, Ao M, Yu J, Wang X, Han K, Yun DJ, Liu B, Li N, Xu ZY. OsGADD45a1: a multifaceted regulator of rice architecture, grain yield, and blast resistance. PLANT CELL REPORTS 2024; 43:88. [PMID: 38461436 DOI: 10.1007/s00299-024-03191-1] [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: 02/03/2024] [Accepted: 02/29/2024] [Indexed: 03/12/2024]
Abstract
KEY MESSAGE The homolog gene of the Growth Arrest and DNA Damage-inducible 45 (GADD45) in rice functions in the regulation of plant architecture, grain yield, and blast resistance. The Growth Arrest and DNA Damage-inducible 45 (GADD45) family proteins, well-established stress sensors and tumor suppressors in mammals, serve as pivotal regulators of genotoxic stress responses and tumorigenesis. In contrast, the homolog and role of GADD45 in plants have remained unclear. Herein, using forward genetics, we identified an activation tagging mutant AC13 exhibited dwarf characteristics resulting from the loss-of-function of the rice GADD45α homolog, denoted as OsGADD45a1. osgadd45a1 mutants displayed reduced plant height, shortened panicle length, and decreased grain yield compared to the wild-type Kitaake. Conversely, no obvious differences in plant height, panicle length, or grain yield were observed between wild-type and OsGADD45a1 overexpression plants. OsGADD45a1 displayed relatively high expression in germinated seeds and panicles, with localization in both the nucleus and cytoplasm. RNA-sequencing analysis suggested a potential role for OsGADD45a1 in the regulation of photosynthesis, and binding partner identification indicates OsGADD45a1 interacts with OsRML1 to regulate rice growth. Intriguingly, our study unveiled a novel role for OsGADD45a1 in rice blast resistance, as osgadd45a1 mutant showed enhanced resistance to Magnaporthe oryzae, and the expression of OsGADD45a1 was diminished upon blast fungus treatment. The involvement of OsGADD45a1 in rice blast fungus resistance presents a groundbreaking finding. In summary, our results shed light on the multifaceted role of OsGADD45a1 in rice, encompassing biotic stress response and the modulation of several agricultural traits, including plant height, panicle length, and grain yield.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Mengting Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Ao Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Min Ao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinlei Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaohang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Kangshun Han
- Rice Institute, Tonghua Academy of Agricultural Science, Tonghua, 135007, China
| | - Dae-Jin Yun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 132-798, South Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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Xu L, Wang J, Zhang T, Xiao H, Wang H. Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications. BMC PLANT BIOLOGY 2024; 24:142. [PMID: 38413922 PMCID: PMC10900605 DOI: 10.1186/s12870-024-04844-9] [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: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution. RESULTS The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes. CONCLUSIONS In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.
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Affiliation(s)
- Luyuan Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jinghan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Li W, Gao G, Pan Y, Wang Z, Ruan J, Fan L, Shen Y, Wang H, Li M, Zhang P, Fang L, Fu J, Liu J. Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers. Front Chem 2023; 11:1269911. [PMID: 38099192 PMCID: PMC10720751 DOI: 10.3389/fchem.2023.1269911] [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: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Objective: Although radiation workers are exposed to much lower doses of neutron-γ rays than those suffered in nuclear explosions and accidents, it does not mean that their health is not affected by radiation. Lower doses of radiation do not always cause morphological aberrations in chromosomes, so more sophisticated tests must be sought to specific alterations in the exposed cells. Our goal was to characterize the specific gene expression in lymphocytes from logging workers who were continuously exposed to low doses of neutron-γ radiation. We hypothesized that the combination of cell type-specific transcriptomes and open chromatin profiles would identify lymphocyte-specific gene alterations induced by long-term radiation with low-dose neutron-γ-rays and discover new regulatory pathways and transcriptional regulatory elements. Methods: Lymphocytes were extracted from workers who have been occupationally exposed to neutron-γ and workers unexposed to radiation in the same company. mRNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) were performed, followed integrative analysis to identify specific gene regulatory regions induced by neutron-γ radiation. A qPCR assay was then performed to verify the downregulation of RNA coding for ribosomal proteins and flow cytometry was used to detect ribosomal protein expression and cell cycle alterations. Results: We identified transcripts that were specifically induced by neutron-γ radiation and discovered differential open chromatin regions that correlated with these gene activation patterns. Notably, we observed a downward trend in the expression of both differentially expressed genes and open chromatin peaks. Our most significant finding was that the differential peak upregulated in ATAC-seq, while the differential gene was downregulated in the ribosome pathway. We confirmed that neutron-γ radiation leads to transcriptional inhibition by analyzing the most enriched promoters, examining RPS18 and RPS27A expression by qPCR, and analyzing protein-protein interactions of the differential genes. Ribosomal protein expression and cell cycle were also affected by neutron-γ as detected by flow cytometry. Conclusion: We have comprehensively analyzed the genetic landscape of human lymphocytes based on chromatin accessibility and transcript levels, enabling the identification of novel neutron-γ induced signature genes not previously known. By comparing fine-mapping of open chromatin and RNA reads, we have determined that neutron-γ specifically leads to downregulation of genes in the ribosome pathway, with pseudogenes potentially playing a crucial role.
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Affiliation(s)
- Weiguo Li
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Gang Gao
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Yan Pan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Ziqiang Wang
- School of Biomedical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Jianlei Ruan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Li Fan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Yingjie Shen
- Safety and Environmental Protection Department, Shengli Logging Company, Sinopec Jingwei Co., LTD., Dongying, Shandong, China
| | - Haiqing Wang
- Dongying Center for Disease Control and Prevention, Dongying, Shandong, China
| | - Mian Li
- School of Biomedical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Pinhua Zhang
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Lianying Fang
- School of Preventive Medicine, Shandong First Medical University Institute of Radiation Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jinghong Fu
- School of Preventive Medicine, Shandong First Medical University Institute of Radiation Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jianxiang Liu
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
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Yao P, Zhang C, Zhang D, Qin T, Xie X, Liu Y, Liu Z, Bai J, Bi Z, Cui J, Liang J, Sun C. Characterization and Identification of Drought-Responsive ABA-Aldehyde Oxidase (AAO) Genes in Potato ( Solanum tuberosum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3809. [PMID: 38005706 PMCID: PMC10674669 DOI: 10.3390/plants12223809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Abscisic acid (ABA) is an important stress hormone that affects plants' tolerance to stress. Changes in the content of abscisic can have an impact on plant responses to abiotic stress. The abscisic acid aldehyde oxidase (AAO) plays a crucial role in the final step in the synthesis of abscisic acid; therefore, understanding the function of the AAO gene family is of great significance for insight into plants' response to abiotic stresses. In this study, Solanum tuberosum AAO (StAAO) members were exhaustively explored using genome databases, and nine StAAOs were identified. Chromosomal location analysis indicated that StAAO genes mapped to 4 of the 14 potato chromosomes. Further analyses of gene structure and motif composition showed that members of the specific StAAO subfamily showed relatively conserved characteristics. Phylogenetic relationship analysis indicated that StAAOs proteins were divided into three major clades. Promoter analysis showed that most StAAO promoters contained cis-elements related to abiotic stress response and plant hormones. The results of tissue-specific expression analysis indicated that StAAO4 was predominantly expressed in the roots. Analysis of transcriptome data revealed that StAAO2/4/6 genes responded significantly to drought treatments. Moreover, further qRT-PCR analysis results indicated that StAAO2/4/6 not only significantly responded to drought stress but also to various phytohormone (ABA, SA, and MeJA) and abiotic stresses (salt and low temperature), albeit with different expression patterns. In summary, our study provides comprehensive insights into the sequence characteristics, structural properties, evolutionary relationships, and expression patterns of the StAAO gene family. These findings lay the foundation for a deeper understanding of the StAAO gene family and offer a potential genetic resource for breeding drought-resistant potato varieties.
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Affiliation(s)
- Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
| | - Chunli Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Dan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
| | - Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaofei Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
| | - Jingwen Liang
- Planning and Finance Department, Gansu Agricultural University, Lanzhou 730070, China;
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (D.Z.); (T.Q.); (X.X.); (Y.L.); (Z.L.); (J.B.); (Z.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Jayaprakash A, Roy A, Thanmalagan RR, Arunachalam A, P T V L. Understanding the mechanism of pathogenicity through interactome studies between Arachis hypogaea L. and Aspergillus flavus. J Proteomics 2023; 287:104975. [PMID: 37482270 DOI: 10.1016/j.jprot.2023.104975] [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: 02/06/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Aspergillus flavus (A. flavus) infects the peanut seeds during pre-and post-harvest stages, causing seed quality destruction for humans and livestock consumption. Even though many resistant varieties were developed, the molecular mechanism of defense interactions of peanut against A. flavus still needs further investigation. Hence, an interologous host-pathogen protein interaction (HPPI) network was constructed to understand the subcellular level interaction mechanism between peanut and A. flavus. Out of the top 10 hub proteins of both organisms, protein phosphatase 2C and cyclic nucleotide-binding/kinase domain-containing protein and different ribosomal proteins were identified as candidate proteins involved in defense. Functional annotation and subcellular localization based characterization of HPPI identified protein SGT1 homolog, calmodulin and Rac-like GTP-binding proteins to be involved in defense response against fungus. The relevance of HPPI in infectious conditions was assessed using two transcriptome data which identified the interplay of host kinase class R proteins, bHLH TFs and cell wall related proteins to impart resistance against pathogen infection. Further, the pathogenicity analysis identified glycogen phosphorylase and molecular chaperone and allergen Mod-E/Hsp90/Hsp1 as potential pathogen targets to enhance the host defense mechanism. Hence, the computationally predicted host-pathogen PPI network could provide valuable support for molecular biology experiments to understand the host-pathogen interaction. SIGNIFICANCE: Protein-protein interactions execute significant cellular interactions in an organism and are influenced majorly by stress conditions. Here we reported the host-pathogen protein-protein interaction between peanut and A. flavus, and a detailed network analysis based on function, subcellular localization, gene co-expression, and pathogenicity was performed. The network analysis identified key proteins such as host kinase class R proteins, calmodulin, SGT1 homolog, Rac-like GTP-binding proteins bHLH TFs and cell wall related to impart resistance against pathogen infection. We observed the interplay of defense related proteins and cell wall related proteins predominantly, which could be subjected to further studies. The network analysis described in this study could be applied to understand other host-pathogen systems generally.
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Affiliation(s)
- Aiswarya Jayaprakash
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Abhijeet Roy
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Raja Rajeswary Thanmalagan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Annamalai Arunachalam
- Department of Food Science & Technology, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Lakshmi P T V
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India.
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Fakih Z, Plourde MB, Germain H. Differential Participation of Plant Ribosomal Proteins from the Small Ribosomal Subunit in Protein Translation under Stress. Biomolecules 2023; 13:1160. [PMID: 37509195 PMCID: PMC10377644 DOI: 10.3390/biom13071160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Upon exposure to biotic and abiotic stress, plants have developed strategies to adapt to the challenges imposed by these unfavorable conditions. The energetically demanding translation process is one of the main elements regulated to reduce energy consumption and to selectively synthesize proteins involved in the establishment of an adequate response. Emerging data have shown that ribosomes remodel to adapt to stresses. In Arabidopsis thaliana, ribosomes consist of approximately eighty-one distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. Recent research has revealed that a mutation in a given single RP in plants can not only affect the functions of the RP itself but can also influence the properties of the ribosome, which could bring about changes in the translation to varying degrees. However, a pending question is whether some RPs enable ribosomes to preferentially translate specific mRNAs. To reveal the role of ribosomal proteins from the small subunit (RPS) in a specific translation, we developed a novel approach to visualize the effect of RPS silencing on the translation of a reporter mRNA (GFP) combined to the 5'UTR of different housekeeping and defense genes. The silencing of genes encoding for NbRPSaA, NbRPS5A, and NbRPS24A in Nicotiana benthamiana decreased the translation of defense genes. The NbRACK1A-silenced plant showed compromised translations of specific antioxidant enzymes. However, the translations of all tested genes were affected in NbRPS27D-silenced plants. These findings suggest that some RPS may be potentially involved in the control of protein translation.
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Affiliation(s)
- Zainab Fakih
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada
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Mamani-Huarcaya BM, Navarro-Gochicoa MT, Herrera-Rodríguez MB, Camacho-Cristóbal JJ, Ceacero CJ, Fernández Cutire Ó, González-Fontes A, Rexach J. Leaf Proteomic Analysis in Seedlings of Two Maize Landraces with Different Tolerance to Boron Toxicity. PLANTS (BASEL, SWITZERLAND) 2023; 12:2322. [PMID: 37375947 DOI: 10.3390/plants12122322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Boron (B) toxicity is an important stressor that negatively affects maize yield and the quality of the produce. The excessive B content in agricultural lands is a growing problem due to the increase in arid and semi-arid areas because of climate change. Recently, two Peruvian maize landraces, Sama and Pachía, were physiologically characterized based on their tolerance to B toxicity, the former being more tolerant to B excess than Pachía. However, many aspects regarding the molecular mechanisms of these two maize landraces against B toxicity are still unknown. In this study, a leaf proteomic analysis of Sama and Pachía was performed. Out of a total of 2793 proteins identified, only 303 proteins were differentially accumulated. Functional analysis indicated that many of these proteins are involved in transcription and translation processes, amino acid metabolism, photosynthesis, carbohydrate metabolism, protein degradation, and protein stabilization and folding. Compared to Sama, Pachía had a higher number of differentially expressed proteins related to protein degradation, and transcription and translation processes under B toxicity conditions, which might reflect the greater protein damage caused by B toxicity in Pachía. Our results suggest that the higher tolerance to B toxicity of Sama can be attributed to more stable photosynthesis, which can prevent damage caused by stromal over-reduction under this stress condition.
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Affiliation(s)
- Betty Maribel Mamani-Huarcaya
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain
- Laboratorio de Biotecnología Vegetal, Escuela de Agronomía, Facultad Ciencias Agropecuarias, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
| | | | | | - Juan José Camacho-Cristóbal
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain
| | - Carlos Juan Ceacero
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain
| | - Óscar Fernández Cutire
- Departamento de Agronomía, Facultad Ciencias Agropecuarias, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
| | - Agustín González-Fontes
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain
| | - Jesús Rexach
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain
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9
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Voronezhskaya V, Volkova P, Bitarishvili S, Shesterikova E, Podlutskii M, Clement G, Meyer C, Duarte GT, Kudin M, Garbaruk D, Turchin L, Kazakova E. Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone. PLANTS (BASEL, SWITZERLAND) 2023; 12:2318. [PMID: 37375943 DOI: 10.3390/plants12122318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl exclusion zone and areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns and conducted coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Plants growing under chronic radiation exposure showed complex and multidirectional biological effects, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants showed signs of DNA damage, redox imbalance, and stress responses. The upregulation of histones, chaperones, peroxidases, and secondary metabolism was noted.
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Affiliation(s)
| | | | | | | | | | - Gilles Clement
- Institute Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Christian Meyer
- Institute Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | | | - Maksim Kudin
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
| | - Dmitrii Garbaruk
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
| | - Larisa Turchin
- Polesye State Radiation-Ecological Reserve, 247618 Khoiniki, Belarus
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10
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Identification of Key Gene Network Modules and Hub Genes Associated with Wheat Response to Biotic Stress Using Combined Microarray Meta-analysis and WGCN Analysis. Mol Biotechnol 2023; 65:453-465. [PMID: 35996047 DOI: 10.1007/s12033-022-00541-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/05/2022] [Indexed: 12/31/2022]
Abstract
Wheat (Triticum aestivum) is one of the major crops worldwide and a primary source of calories for human food. Biotic stresses such as fungi, bacteria, and diseases limit wheat production. Although plant breeding and genetic engineering for biotic stress resistance have been suggested as promising solutions to handle losses caused by biotic stress factors, a comprehensive understanding of molecular mechanisms and identifying key genes is a critical step to obtaining success. Here, a network-based meta-analysis approach based on two main statistical methods was used to identify key genes and molecular mechanisms of the wheat response to biotic stress. A total of 163 samples (21,792 genes) from 10 datasets were analyzed. Fisher Z test based on the p-value and REM method based on effect size resulted in 533 differentially expressed genes (p < 0.001 and FDR < 0.001). WGCNA analysis using a dynamic tree-cutting algorithm was used to construct a co-expression network and three significant modules were detected. The modules were significantly enriched by 16 BP terms and 4 KEGG pathways (Benjamini-Hochberg FDR < 0.001). A total of nine hub genes (a top 1.5% of genes with the highest degree) were identified from the constructed network. The identification of DE genes, gene-gene co-expressing network, and hub genes may contribute to uncovering the molecular mechanisms of the wheat response to biotic stress.
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11
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Fakih Z, Plourde MB, Nkouankou CET, Fourcassié V, Bourassa S, Droit A, Germain H. Specific alterations in riboproteomes composition of isonicotinic acid treated arabidopsis seedlings. PLANT MOLECULAR BIOLOGY 2023; 111:379-392. [PMID: 36790538 PMCID: PMC10090002 DOI: 10.1007/s11103-022-01332-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/25/2022] [Indexed: 06/18/2023]
Abstract
Plants have developed strategies to deal with the great variety of challenges they are exposed to. Among them, common targets are the regulation of transcription and translation to finely modulate protein levels during both biotic and abiotic stresses. Increasing evidence suggests that ribosomes are highly adaptable modular supramolecular structures which remodel to adapt to stresses. Each Arabidopsis thaliana ribosome consists of approximately 81 distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. To investigate the identity of ribosomal proteins of the small subunit (RPS) and of the large subunit (RPL) as well as ribosomes-associated proteins, we analysed by LC/MS/MS immunopurified ribosomes from A. thaliana leaves treated with isonicotinic acid (INA), an inducer of plant innate immunity. We quantified a total of 2084 proteins. 165 ribosome-associated proteins showed increased abundance while 52 were less abundant. Of the 52 identified RPS (from a possibility of 104 encoding genes), 15 were deregulated. Similarly, from the 148 possible RPL, 80 were detected and 9 were deregulated. Our results revealed potential candidates involved in innate immunity that could be interesting targets for functional genomic studies.
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Affiliation(s)
- Zainab Fakih
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, G9A 5H9, Trois-Rivières, Québec, Canada
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, G9A 5H9, Trois-Rivières, Québec, Canada
| | - Charlène Eugénie Tomi Nkouankou
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, G9A 5H9, Trois-Rivières, Québec, Canada
| | - Victor Fourcassié
- Proteomics Platform, Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, G1V 4G2, Québec City, Québec, Canada
| | - Sylvie Bourassa
- Proteomics Platform, Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, G1V 4G2, Québec City, Québec, Canada
| | - Arnaud Droit
- Proteomics Platform, Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, G1V 4G2, Québec City, Québec, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics and Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, G9A 5H9, Trois-Rivières, Québec, Canada.
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12
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Bakshi A, Moin M, Gayatri MB, Reddy ABM, Datla R, Madhav MS, Kirti PB. Involvement of Target of Rapamycin (TOR) Signaling in the Regulation of Crosstalk between Ribosomal Protein Small Subunit 6 Kinase-1 (RPS6K-1) and Ribosomal Proteins. PLANTS (BASEL, SWITZERLAND) 2023; 12:176. [PMID: 36616305 PMCID: PMC9824793 DOI: 10.3390/plants12010176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The target of rapamycin (TOR) protein phosphorylates its downstream effector p70kDa ribosomal protein S6 kinases (S6K1) for ribosome biogenesis and translation initiation in eukaryotes. However, the molecular mechanism of TOR-S6K1-ribosomal protein (RP) signaling is not well understood in plants. In the present study, we report the transcriptional upregulation of ribosomal protein large and small subunit (RPL and RPS) genes in the previously established TOR overexpressing transgenic lines of rice (in Oryza sativa ssp. indica, variety BPT-5204, TR-2.24 and TR-15.1) and of Arabidopsis thaliana (in Col 0 ecotype, ATR-1.4.27 and ATR-3.7.32). The mRNA levels of RP genes from this study were compared with those previously available in transcriptomic datasets on the expression of RPs in relation to TOR inhibitor and in the TOR-RNAi lines of Arabidopsis thaliana. We further analyzed TOR activity, i.e., S6K1 phosphorylation in SALK lines of Arabidopsis with mutation in rpl6, rpl18, rpl23, rpl24 and rps28C, where the rpl18 mutant showed inactivation of S6K1 phosphorylation. We also predicted similar putative Ser/Thr phosphorylation sites for ribosomal S6 kinases (RSKs) in the RPs of Oryza sativa ssp. indica and Arabidopsis thaliana. The findings of this study indicate that the TOR pathway is possibly interlinked in a cyclic manner via the phosphorylation of S6K1 as a modulatory step for the regulation of RP function to switch 'on'/'off' the translational regulation for balanced plant growth.
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Affiliation(s)
- Achala Bakshi
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Global Institute for Food Security, Saskatoon, SK S7N 0W9, Canada
| | - Mazahar Moin
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India
| | - Meher B. Gayatri
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Aramati B. M. Reddy
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Raju Datla
- Global Institute for Food Security, Saskatoon, SK S7N 0W9, Canada
| | - Maganti S. Madhav
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Central Tobacco Research Institute, Rajahmundry 533105, Andhra Pradesh, India
| | - Pulugurtha B. Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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13
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Lafuente MT, González-Candelas L. The Role of ABA in the Interaction between Citrus Fruit and Penicillium digitatum. Int J Mol Sci 2022; 23:ijms232415796. [PMID: 36555436 PMCID: PMC9779756 DOI: 10.3390/ijms232415796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Abscisic acid (ABA) protects citrus fruit against Penicillium digitatum infection. The global mechanisms involved in the role of ABA in the P. digitatum-citrus fruit interaction are unknown. Here, we determine the transcriptome differences between the Navelate (Citrus sinensis (L.) Osbeck) orange and its ABA-deficient mutant Pinalate, which is less resistant to infection. Low ABA levels may affect both the constitutive mechanisms that protect citrus fruit against P. digitatum and early responses to infection. The repression of terpenoid, phenylpropanoid and glutation metabolism; of oxidation-reduction processes; and of processes related to the defense response to fungus and plant hormone signal transduction may be one part of the constitutive defense reduced in the mutant against P. digitatum. Our results also provide potential targets for developing P. digitatum-citrus fruit-resistant varieties. Of those up-regulated by ABA, a thaumatin protein and a bifunctional inhibitor/LTP, which are relevant in plant immunity, were particularly remarkable. It is also worth highlighting chlorophyllase 1 (CLH1), induced by infection in Pinalate, and the OXS3 gene, which was down-regulated by ABA, because the absence of OXS3 activates ABA-responsive genes in plants.
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14
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Barraza A, Cabrera-Ponce JL. Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis. Int J Mol Sci 2022; 23:ijms232213835. [PMID: 36430314 PMCID: PMC9696990 DOI: 10.3390/ijms232213835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein-protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs-MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9-may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC. IPN 195, Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
- Correspondence: ; Tel.: +52-462-6239600 (ext. 9421)
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15
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Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective. PLANTS 2022; 11:plants11162097. [PMID: 36015400 PMCID: PMC9415564 DOI: 10.3390/plants11162097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants’ abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty.
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16
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Hashida Y, Tezuka A, Nomura Y, Kamitani M, Kashima M, Kurita Y, Nagano AJ. Fillable and unfillable gaps in plant transcriptome under field and controlled environments. PLANT, CELL & ENVIRONMENT 2022; 45:2410-2427. [PMID: 35610174 PMCID: PMC9544781 DOI: 10.1111/pce.14367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments. We analysed massive transcriptome data of rice plants grown under field and SmartGC conditions to clarify the differences in plant responses to field and controlled environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening but those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature affects transcriptome dynamics only in the morning. We found upregulation of genes related to biotic and abiotic stress, and their expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results reveal fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments and can accelerate the understanding of plant responses to field environments for both basic biology and agricultural applications.
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Affiliation(s)
- Yoichi Hashida
- Faculty of AgricultureTakasaki University of Health and WelfareTakasakiGunmaJapan
| | - Ayumi Tezuka
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Yasuyuki Nomura
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Mari Kamitani
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Makoto Kashima
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
- College of Science and EngineeringAoyama Gakuin UniversitySagamiharaKanagawaJapan
| | - Yuko Kurita
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Atsushi J. Nagano
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaYamagataJapan
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17
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Wang Y, Wang Y, Liu X, Zhou J, Deng H, Zhang G, Xiao Y, Tang W. WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.). Genes (Basel) 2022; 13:genes13061020. [PMID: 35741784 PMCID: PMC9222641 DOI: 10.3390/genes13061020] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/01/2023] Open
Abstract
Frequent high temperature weather affects the growth and development of rice, resulting in the decline of seed–setting rate, deterioration of rice quality and reduction of yield. Although some high temperature tolerance genes have been cloned, there is still little success in solving the effects of high temperature stress in rice (Oryza sativa L.). Based on the transcriptional data of seven time points, the weighted correlation network analysis (WGCNA) method was used to construct a co–expression network of differentially expressed genes (DEGs) between the rice genotypes IR64 (tolerant to heat stress) and Koshihikari (susceptible to heat stress). There were four modules in both genotypes that were highly correlated with the time points after heat stress in the seedling. We further identified candidate hub genes through clustering and analysis of protein interaction network with known–core genes. The results showed that the ribosome and protein processing in the endoplasmic reticulum were the common pathways in response to heat stress between the two genotypes. The changes of starch and sucrose metabolism and the biosynthesis of secondary metabolites pathways are possible reasons for the sensitivity to heat stress for Koshihikari. Our findings provide an important reference for the understanding of high temperature response mechanisms and the cultivation of high temperature resistant materials.
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Affiliation(s)
- Yubo Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Yingfeng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Jieqiang Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
- Correspondence: (Y.X.); (W.T.)
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (Y.W.); (Y.W.); (X.L.); (J.Z.); (H.D.); (G.Z.)
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
- Correspondence: (Y.X.); (W.T.)
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18
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Feiner N, Radersma R, Vasquez L, Ringnér M, Nystedt B, Raine A, Tobi EW, Heijmans BT, Uller T. Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species. iScience 2022; 25:104303. [PMID: 35573201 PMCID: PMC9097707 DOI: 10.1016/j.isci.2022.104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/02/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities. Naturally induced DNA-methylation persists until generation F4 in Daphnia Drug-induced de-methylation is reset after one generation Methylation is enriched in exons suggesting a gene regulatory function Epigenetic inheritance may influence eco-evolutionary dynamics
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Affiliation(s)
| | - Reinder Radersma
- Department of Biology, Lund University, Lund, Sweden
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Louella Vasquez
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Division of Human Nutrition and Health, Department of Agrotechnology and Food Science, Wageningen University & Research, Wageningen, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Martinez-Seidel F, Hsieh YC, Walther D, Kopka J, Pereira Firmino AA. [Formula: see text]: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 2021; 22:605. [PMID: 34930116 PMCID: PMC8686616 DOI: 10.1186/s12859-021-04510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. RESULTS [Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. CONCLUSIONS [Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- School of BioSciences, University of Melbourne, Parkville, VC 3010 Australia
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Makonya GM, Ogola JBO, Gabier H, Rafudeen MS, Muasya AM, Crespo O, Maseko S, Valentine AJ, Ottosen CO, Rosenqvist E, Chimphango SBM. Proteome changes and associated physiological roles in chickpea (Cicer arietinum) tolerance to heat stress under field conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 49:13-24. [PMID: 34794539 DOI: 10.1071/fp21148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Interrogative proteome analyses are used to identify and quantify the expression of proteins involved in heat tolerance and to identify associated physiological processes in heat-stressed plants. The objectives of the study were to identify and quantify the expression of proteins involved in heat tolerance and to identify associated physiological processes in chickpea (Cicer arietinum L.) heat-tolerant (Acc#7) and sensitive genotype (Acc#8) from a field study. Proteomic and gene ontological analyses showed an upregulation in proteins related to protein synthesis, intracellular traffic, defence and transport in the heat-tolerant genotype compared to the susceptible one at the warmer site. Results from KEGG analyses indicate the involvement of probable sucrose-phosphate synthase (EC 2.4.1.14) and sucrose-phosphate phosphatase (EC 3.1.3.24) proteins, that were upregulated in the heat-tolerant genotype at the warmer site, in the starch and sucrose pathway. The presence of these differentially regulated proteins including HSP70, ribulose bisphosphate carboxylase/oxygenase activase, plastocyanin and protoporphyrinogen oxidase suggests their potential role in heat tolerance, at flowering growth stage, in field-grown chickpea. This observation supports unaltered physiological and biochemical performance of the heat-tolerant genotypes (Acc#7) relative to the susceptible genotype (Acc#8) in related studies (Makonya et al. 2019). Characterisation of the candidate proteins identified in the current study as well as their specific roles in the tolerance to heat stress in chickpea are integral to further crop improvement initiatives.
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Affiliation(s)
- Givemore M Makonya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
| | - John B O Ogola
- Department of Plant Production, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa
| | - Hawwa Gabier
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - Mohammed S Rafudeen
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
| | - Olivier Crespo
- Climate System Analysis Group, Environmental and Geographical Science Department, University of Cape Town, Rondebosch, Private Bag X3, Cape Town 7701, South Africa
| | - Sipho Maseko
- Department of Crop Sciences, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
| | - Alex J Valentine
- Botany and Zoology Department, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Carl-Otto Ottosen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, 5792 Aarslev, Denmark
| | - Eva Rosenqvist
- Department of Plant and Environmental Sciences, Section for Crop Science, University of Copenhagen, Hoejbakkegaard Allé 9, 2630 Taastrup, Denmark
| | - Samson B M Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
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22
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Dutta M, Saha A, Moin M, Kirti PB. Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:777285. [PMID: 34899804 PMCID: PMC8660974 DOI: 10.3389/fpls.2021.777285] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023]
Abstract
Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Mazahar Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - Pulugurtha Bharadwaja Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, India
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Fernández H, Grossmann J, Gagliardini V, Feito I, Rivera A, Rodríguez L, Quintanilla LG, Quesada V, Cañal MJ, Grossniklaus U. Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:718932. [PMID: 34868105 PMCID: PMC8633544 DOI: 10.3389/fpls.2021.718932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA3 and GA4, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA4, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA3 and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.
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Affiliation(s)
- Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomics Center, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Móstoles, Spain
| | - Víctor Quesada
- Department of Biochemistry and Molecular Biology, Institute of Oncology of the Principality of Asturias, Oviedo University, Móstoles, Spain
| | - Mª Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021; 4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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25
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Alafari HA, Abd-Elgawad ME. Differential expression gene/protein contribute to heat stress-responsive in Tetraena propinqua in Saudi Arabia. Saudi J Biol Sci 2021; 28:5017-5027. [PMID: 34466077 PMCID: PMC8380999 DOI: 10.1016/j.sjbs.2021.05.016] [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: 01/08/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022] Open
Abstract
Within their natural habitat, plants are subjected to abiotic stresses that include heat stress. In the current study, the effect of 4 h, 24 h, and 48 h of heat stress on Tetraena propinqua ssp. migahidii seedling's protein profile and proteomic analyses were investigated. Total soluble protein SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) profile showed 18-protein bands, the newly synthesized protein band (with molecular weights 86.5, 30.2 and 31.4 KD) at 24 h of heat stress and 48 of normal conditions. Proteomic analysis showed that 81 and 930 targets are involved in gene and protein expression respectively. At 4 h, 57 genes and 110 proteins in C4 reached 56 genes and 173 proteins in T4. At 24 h, 63 genes and 180 proteins in C24 decreased to 54 genes and 151 protein in T24. After 48 h, 56 genes and 136 proteins in C48 increased to 64 genes and 180 proteins in T48. The genes and proteins involved in transcription, translation, photosynthesis, transport, and other unknown metabolic processes, were differentially expressed under treatments of heat stress. These findings provide insights into the molecular mechanisms related to heat stress, in addition to its influence on the physiological traits of T. propinqua seedlings. Heat stress-mediated differential regulation genes indicate a role in the development and stress response of T. propinqua. The candidate dual-specificity genes and proteins identified in this study paves way for more molecular analysis of up-and-down-regulation.
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Affiliation(s)
- Hayat Ali Alafari
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Magda Elsayed Abd-Elgawad
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Botany Department, Faculty of Science, Fayoum University, Fayoum, Egypt
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26
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Dutta M, Moin M, Saha A, Dutta D, Bakshi A, Kirti PB. Gain-of-function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2253-2272. [PMID: 33821294 DOI: 10.1007/s00122-021-03823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 03/23/2021] [Indexed: 05/13/2023]
Abstract
XPB2 and SEN1 helicases were identified through activation tagging as potential candidate genes in rice for inducing high water-use efficiency (WUE) and maintaining sustainable yield under drought stress. As a follow-up on the high-water-use-efficiency screening and physiological analyses of the activation-tagged gain-of-function mutant lines that were developed in an indica rice variety, BPT-5204 (Moin et al. in Plant Cell Environ 39:2440-2459, 2016a, https://doi.org/10.1111/pce.12796 ), we have identified two gain-of-function mutant lines (XM3 and SM4), which evidenced the activation of two helicases, ATP-dependent DNA helicase (XPB2) and RNA helicase (SEN1), respectively. We performed the transcript profiling of XPB2 and SEN1 upon exposure to various stress conditions and found their significant upregulation, particularly in ABA and PEG treatments. Extensive morpho-physiological and biochemical analyses based on 24 metrics were performed under dehydration stress (PEG) and phytohormone (ABA) treatments for the wild-type and the two mutant lines. Principal component analysis (PCA) performed on the dataset captured 72.73% of the cumulative variance using the parameters influencing the first two principal components. The tagged mutants exhibited reduced leaf wilting, improved revival efficiency, constant amylose:amylopectin ratio, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits with respect to their controls. These observations were further validated under greenhouse conditions by the periodic withdrawal of water at the pot level. Germination of the seeds of these mutant lines indicated their insensitivity to high ABA concentration. The associated upregulation of stress-specific genes further suggests that their drought tolerance might be because of the coordinated expression of several stress-responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Mazahar Moin
- Biotechnology Division, Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Dibyendu Dutta
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, 400076, India
| | - Achala Bakshi
- Biotechnology Division, Indian Institute of Rice Research, Hyderabad, 500030, India
| | - P B Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, 500030, India.
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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28
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Vannini C, Domingo G, Fiorilli V, Seco DG, Novero M, Marsoni M, Wisniewski-Dye F, Bracale M, Moulin L, Bonfante P. Proteomic analysis reveals how pairing of a Mycorrhizal fungus with plant growth-promoting bacteria modulates growth and defense in wheat. PLANT, CELL & ENVIRONMENT 2021; 44:1946-1960. [PMID: 33675052 DOI: 10.1111/pce.14039] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Plants rely on their microbiota for improving the nutritional status and environmental stress tolerance. Previous studies mainly focused on bipartite interactions (a plant challenged by a single microbe), while plant responses to multiple microbes have received limited attention. Here, we investigated local and systemic changes induced in wheat by two plant growth-promoting bacteria (PGPB), Azospirillum brasilense and Paraburkholderia graminis, either alone or together with an arbuscular mycorrhizal fungus (AMF). We conducted phenotypic, proteomic, and biochemical analyses to investigate bipartite (wheat-PGPB) and tripartite (wheat-PGPB-AMF) interactions, also upon a leaf pathogen infection. Results revealed that only AMF and A. brasilense promoted plant growth by activating photosynthesis and N assimilation which led to increased glucose and amino acid content. The bioprotective effect of the PGPB-AMF interactions on infected wheat plants depended on the PGPB-AMF combinations, which caused specific phenotypic and proteomic responses (elicitation of defense related proteins, immune response and jasmonic acid biosynthesis). In the whole, wheat responses strongly depended on the inoculum composition (single vs. multiple microbes) and the investigated organs (roots vs. leaf). Our findings showed that AMF is the best-performing microbe, suggesting its presence as the crucial one for synthetic microbial community development.
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Affiliation(s)
- Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | | | - Mara Novero
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Florence Wisniewski-Dye
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgroSup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Lionel Moulin
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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Moin M, Saha A, Bakshi A, Madhav MS, Kirti PB. Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 2021; 789:145670. [PMID: 33892070 DOI: 10.1016/j.gene.2021.145670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - M S Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India; Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad 500030, India
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Discerning molecular diversity and association mapping for phenological, physiological and yield traits under high temperature stress in chickpea (Cicer arietinum L.). J Genet 2021. [DOI: 10.1007/s12041-020-01254-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wytynck P, Lambin J, Chen S, Demirel Asci S, Verbeke I, De Zaeytijd J, Subramanyam K, Van Damme EJ. Effect of RIP Overexpression on Abiotic Stress Tolerance and Development of Rice. Int J Mol Sci 2021; 22:1434. [PMID: 33535383 PMCID: PMC7867109 DOI: 10.3390/ijms22031434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/31/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can inhibit protein translation by depurinating rRNA. Most plant RIPs are synthesized with a leader sequence that sequesters the proteins to a cell compartment away from the host ribosomes. However, several rice RIPs lack these signal peptides suggesting they reside in the cytosol in close proximity to the plant ribosomes. This paper aims to elucidate the physiological function of two nucleocytoplasmic RIPs from rice, in particular, the type 1 RIP referred to as OsRIP1 and a presumed type 3 RIP called nuRIP. Transgenic rice lines overexpressing these RIPs were constructed and studied for developmental effects resulting from this overexpression under greenhouse conditions. In addition, the performance of transgenic seedlings in response to drought, salt, abscisic acid and methyl jasmonate treatment was investigated. Results suggest that both RIPs can affect methyl jasmonate mediated stress responses.
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Affiliation(s)
- Pieter Wytynck
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Jeroen Lambin
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Simin Chen
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Sinem Demirel Asci
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Isabel Verbeke
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Jeroen De Zaeytijd
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Kondeti Subramanyam
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
| | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (P.W.); (J.L.); (S.C.); (S.D.A.); (I.V.); (J.D.Z.); (K.S.)
- Center for Advanced Light Microscopy, Ghent University, 9000 Ghent, Belgium
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Moin M, Saha A, Bakshi A, D. D, M.S. M, P.B. K. Study on Transcriptional Responses and Identification of Ribosomal Protein Genes for Potential Resistance against Brown Planthopper and Gall Midge Pests in Rice. Curr Genomics 2021; 22:98-110. [PMID: 34220297 PMCID: PMC8188583 DOI: 10.2174/1389202922666210219113220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 01/02/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Our previous studies have revealed the roles of ribosomal protein (RP) genes in the abiotic stress responses of rice. METHODS In the current investigation, we examine the possible involvement of these genes in insect stress responses. We have characterized the RP genes that included both Ribosomal Protein Large (RPL) and Ribosomal Protein Small (RPS) subunit genes in response to infestation by two economically important insect pests, the brown planthopper (BPH) and the Asian rice gall midge (GM) in rice. Differential transcript patterns of seventy selected RP genes were studied in a susceptible and a resistant genotype of indica rice: BPT5204 and RPNF05, respectively. An in silico analyses of the upstream regions of these genes also revealed the presence of cis-elements that are associated with wound signaling. RESULTS We identified the genes that were up or downregulated in either one of the genotypes, or both of them after pest infestation. The transcript patterns of a majority of the genes were found to be temporally-regulated by both the pests. In the resistant RPNF05, BPH infestation activated RPL15, L51 and RPS5a genes while GM infestation induced RPL15, L18a, L22, L36.2, L38, RPS5, S9.2 and S25a at a certain point of time. These genes that were particularly upregulated in the resistant genotype, RPNF05, but not in BPT5204 suggest their potential involvement in plant resistance against either of the two pests studied. CONCLUSION Taken together, RPL15, L51, L18a, RPS5, S5a, S9.2, and S25a appear to be the genes with possible roles in insect resistance in rice.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Divya D.
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
| | - Madhav M.S.
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad-500030, India
| | - Kirti P.B.
- Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
- Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad-500030, India
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Kok ADX, Mohd Yusoff NF, Sekeli R, Wee CY, Lamasudin DU, Ong-Abdullah J, Lai KS. Pluronic F-68 Improves Callus Proliferation of Recalcitrant Rice Cultivar via Enhanced Carbon and Nitrogen Metabolism and Nutrients Uptake. FRONTIERS IN PLANT SCIENCE 2021; 12:667434. [PMID: 34149763 PMCID: PMC8207202 DOI: 10.3389/fpls.2021.667434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/27/2021] [Indexed: 05/12/2023]
Abstract
Pluronic F-68 (PF-68) is a non-ionic surfactant used in plant tissue culture as a growth additive. Despite its usage as a plant growth enhancer, the mechanism underlying the growth-promoting effects of PF-68 remains largely unknown. Hence, this study was undertaken to elucidate the growth-promoting mechanism of PF-68 using recalcitrant MR 219 callus as a model. Supplementation of 0.04% PF-68 (optimum concentration) was shown to enhance callus proliferation. The treated callus recorded enhanced sugar content, protein content, and glutamate synthase activity as exemplified in the comparative proteome analysis, showing protein abundance involved in carbohydrate metabolism (alpha amylase), protein biosynthesis (ribosomal proteins), and nitrogen metabolism (glutamate synthase), which are crucial to plant growth and development. Moreover, an increase in nutrients uptake was also noted with potassium topping the list, suggesting a vital role of K in governing plant growth. In contrast, 0.10% PF-68 (high concentration) induced stress response in the callus, revealing an increment in phenylalanine ammonia lyase activity, malondialdehyde content, and peroxidase activity, which were consistent with high abundance of phenylalanine ammonia lyase, peroxidase, and peroxiredoxin proteins detected and concomitant with a reduced level of esterase activity. The data highlighted that incorporation of PF-68 at optimum concentration improved callus proliferation of recalcitrant MR 219 through enhanced carbohydrate metabolism, nitrogen metabolism, and nutrient uptake. However, growth-promoting effects of PF-68 are concentration dependent.
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Affiliation(s)
- Andrew De-Xian Kok
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Fatihah Mohd Yusoff
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Rogayah Sekeli
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Kuala Lumpur, Malaysia
| | - Chien-Yeong Wee
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Kuala Lumpur, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Janna Ong-Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Janna Ong-Abdullah
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
- Kok-Song Lai
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Liu W, Yin T, Zhao Y, Wang X, Wang K, Shen Y, Ding Y, Tang S. Effects of High Temperature on Rice Grain Development and Quality Formation Based on Proteomics Comparative Analysis Under Field Warming. FRONTIERS IN PLANT SCIENCE 2021; 12:746180. [PMID: 34745178 PMCID: PMC8566943 DOI: 10.3389/fpls.2021.746180] [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: 07/23/2021] [Accepted: 09/23/2021] [Indexed: 05/14/2023]
Abstract
With the intensification of global warming, rice production is facing new challenges. Field evidence indicates that elevated temperature during rice grain-filling leads to the further deterioration of grain quality. In order to clarify the potential regulatory mechanism of elevated temperature on the formation of rice quality, the DIA mass spectrometry method under the background of field warming was conducted to investigate the regulatory effects of high temperature on grain development and material accumulation pathways. The results showed that a total of 840 differentially expressed proteins were identified during the grain-filling process under elevated temperature. These differentially expressed proteins participated in carbon metabolism, amino acid biosynthesis, signal transduction, protein synthesis, and alternately affected the material accumulation of rice grains. The significant up-regulation of PPROL 14E, PSB28, granule-bound starch synthase I, and the significant down-regulation of 26.7 kDa heat shock protein would lead to the component difference in grain starch and storage proteins, and that could be responsible for the degradation of rice quality under elevated temperature. Results suggested that proteins specifically expressed under elevated temperature could be the key candidates for elucidating the potential regulatory mechanism of warming on rice development and quality formation. In-depth study on the metabolism of storage compounds would be contributed in further proposing high-quality cultivation control measures suitable for climate warming.
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Affiliation(s)
- Wenzhe Liu
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Tongyang Yin
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yufei Zhao
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Xueqin Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Kailu Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yingying Shen
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - She Tang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
- *Correspondence: She Tang
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Ramu VS, Dawane A, Lee S, Oh S, Lee H, Sun L, Senthil‐Kumar M, Mysore KS. Ribosomal protein QM/RPL10 positively regulates defence and protein translation mechanisms during nonhost disease resistance. MOLECULAR PLANT PATHOLOGY 2020; 21:1481-1494. [PMID: 32964634 PMCID: PMC7548997 DOI: 10.1111/mpp.12991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Ribosomes play an integral part in plant growth, development, and defence responses. We report here the role of ribosomal protein large (RPL) subunit QM/RPL10 in nonhost disease resistance. The RPL10-silenced Nicotiana benthamiana plants showed compromised disease resistance against nonhost pathogen Pseudomonas syringae pv. tomato T1. The RNA-sequencing analysis revealed that many genes involved in defence and protein translation mechanisms were differentially affected due to silencing of NbRPL10. Arabidopsis AtRPL10 RNAi and rpl10 mutant lines showed compromised nonhost disease resistance to P. syringae pv. tomato T1 and P. syringae pv. tabaci. Overexpression of AtRPL10A in Arabidopsis resulted in reduced susceptibility against host pathogen P. syringae pv. tomato DC3000. RPL10 interacts with the RNA recognition motif protein and ribosomal proteins RPL30, RPL23, and RPS30 in the yeast two-hybrid assay. Silencing or mutants of genes encoding these RPL10-interacting proteins in N. benthamiana or Arabidopsis, respectively, also showed compromised disease resistance to nonhost pathogens. These results suggest that QM/RPL10 positively regulates the defence and translation-associated genes during nonhost pathogen infection.
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Affiliation(s)
- Vemanna S. Ramu
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Labortory of Plant Functional GenomicsRegional Centre for BiotechnologyFaridabadIndia
| | - Akashata Dawane
- Labortory of Plant Functional GenomicsRegional Centre for BiotechnologyFaridabadIndia
| | - Seonghee Lee
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Present address:
Gulf Coast Research and Education CenterInstitute of Food and Agricultural ScienceUniversity of FloridaWimaumaFloridaUSA
| | - Sunhee Oh
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
| | | | - Liang Sun
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
| | - Muthappa Senthil‐Kumar
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Present address:
National Institute of Plant Genome ResearchNew DelhiIndia
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Garcia-Molina A, Kleine T, Schneider K, Mühlhaus T, Lehmann M, Leister D. Translational Components Contribute to Acclimation Responses to High Light, Heat, and Cold in Arabidopsis. iScience 2020; 23:101331. [PMID: 32679545 PMCID: PMC7364123 DOI: 10.1016/j.isci.2020.101331] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/26/2020] [Accepted: 06/28/2020] [Indexed: 12/27/2022] Open
Abstract
Plant metabolism is broadly reprogrammed during acclimation to abiotic changes. Most previous studies have focused on transitions from standard to single stressful conditions. Here, we systematically analyze acclimation processes to levels of light, heat, and cold stress that subtly alter physiological parameters and assess their reversibility during de-acclimation. Metabolome and transcriptome changes were monitored at 11 different time points. Unlike transcriptome changes, most alterations in metabolite levels did not readily return to baseline values, except in the case of cold acclimation. Similar regulatory networks operate during (de-)acclimation to high light and cold, whereas heat and high-light responses exhibit similar dynamics, as determined by surprisal and conditional network analyses. In all acclimation models tested here, super-hubs in conditional transcriptome networks are enriched for components involved in translation, particularly ribosomes. Hence, we suggest that the ribosome serves as a common central hub for the control of three different (de-)acclimation responses.
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Affiliation(s)
- Antoni Garcia-Molina
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Kevin Schneider
- Computational Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663 Kaiserslautern, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, 82152 Planegg-Martinsried, Germany.
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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Generation of High Yielding and Fragrant Rice ( Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PLANTS 2020; 9:plants9060788. [PMID: 32586052 PMCID: PMC7355857 DOI: 10.3390/plants9060788] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.
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Martins AC, Mehta A, Murad AM, Mota AP, Saraiva MA, Araújo AC, Miller RN, Brasileiro AC, Guimarães PM. Proteomics unravels new candidate genes for Meloidogyne resistance in wild Arachis. J Proteomics 2020; 217:103690. [DOI: 10.1016/j.jprot.2020.103690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/29/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
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Najeeb S, Ali J, Mahender A, Pang Y, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z. Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2020; 40:10. [PMID: 31975784 PMCID: PMC6944268 DOI: 10.1007/s11032-019-1090-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
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Affiliation(s)
- S. Najeeb
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Science & Technology (SKAUST), Khudwani, Kashmir 190025 India
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Y.L. Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - J. Zilhas
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - V. Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Plant Nutrition, Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, 53012 Bonn, Germany
| | - Lakshminarayana R. Vemireddy
- Department of Genetics and Plant Breeding, Sri Venkateswara Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, Andhra Pradesh 517502 India
| | - Z. Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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Ramos RS, Casati P, Spampinato CP, Falcone Ferreyra ML. Ribosomal Protein RPL10A Contributes to Early Plant Development and Abscisic Acid-Dependent Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:582353. [PMID: 33250910 PMCID: PMC7674962 DOI: 10.3389/fpls.2020.582353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/01/2020] [Indexed: 05/17/2023]
Abstract
Plant ribosomal proteins play universal roles in translation, although they are also involved in developmental processes and hormone signaling pathways. Among Arabidopsis RPL10 family members, RPL10A exhibits the highest expression during germination and early development, suggesting that RPL10A is the main contributor to these processes. In this work, we first analyzed RPL10A expression pattern in Arabidopsis thaliana using transgenic RPL10Apro:GUS plants. The gene exhibits a ubiquitous expression pattern throughout the plant, but it is most strongly expressed in undifferentiated tissues. Interestingly, gene expression was also detected in stomatal cells. We then examined protein function during seedling establishment and abscisic acid (ABA) response. Heterozygous rpl10A mutant plants show decreased ABA-sensitivity during seed germination, are impaired in early seedling and root development, and exhibit reduced ABA-inhibition of stomatal aperture under light conditions. Overexpression of RPL10A does not affect the germination and seedling growth, but RPL10A-overexpressing lines are more sensitive to ABA during early plant development and exhibit higher stomatal closure under light condition both with and without ABA treatment than wild type plants. Interestingly, RPL10A expression is induced by ABA. Together, we conclude that RPL10A could act as a positive regulator for ABA-dependent responses in Arabidopsis plants.
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He X, Li W, Zhang W, Jin X, Shenkute AG, Aynalem T, Xu S, Wang W. Transcriptome Sequencing Analysis Provides Insights Into the Response to Fusarium oxysporum in Lilium pumilum. Evol Bioinform Online 2019; 15:1176934319838818. [PMID: 31223231 PMCID: PMC6563521 DOI: 10.1177/1176934319838818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Lily basal rot, caused by Fusarium oxysporum f. sp. lilii, is one of the most serious diseases of lily. Although the lily germplasm which is resistant to F. oxysporum has been used in disease-resistant breeding, few studies on its molecular mechanism of disease resistance have been reported. To comprehensively study the mechanism of resistance to F. oxysporum, transcriptome sequencings of root tissues from Lilium pumilum inoculated with F. oxysporum or sterile water for 6, 12, or 24 h were performed. A total of 50 GB of data were obtained from the transcriptome sequencings of the 6 L. pumilum samples, and 217 098 Unigenes were obtained after the de novo assembly, of which 38.36% Unigenes were annotated. The sequencing results showed that the numbers of differentially expressed genes at 6, 12, and 24 h after inoculation compared with the control were 111, 254, and 2500, respectively. The functional enrichment analysis of the differentially expressed genes showed that several pathways were involved in responses of L. pumilum, mainly including starch and sucrose metabolism, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, vitamin B6 (VB6) biosynthesis, acid biosynthesis, proteasome, and ribosome. Transcription factor analysis revealed that the WRKY and ERF families played important roles in responses of L. pumilum to F. oxysporum. The results of this study elucidate the molecular responses to F. oxysporum in lily and lay a theoretical foundation for improving lily breeding and strategies for lily basal rot resistance.
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Affiliation(s)
- Xiangfeng He
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.,Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Wanyue Li
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Wenzhu Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Xiaotong Jin
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Awraris Getachew Shenkute
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tessema Aynalem
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Shufa Xu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenhe Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.,Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
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Structure and Activity of a Cytosolic Ribosome-Inactivating Protein from Rice. Toxins (Basel) 2019; 11:toxins11060325. [PMID: 31174339 PMCID: PMC6628440 DOI: 10.3390/toxins11060325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosome-inactivating proteins (RIPs) are cytotoxic enzymes that inhibit protein translation by depurinating ribosomal RNA. Although most plant RIPs are synthesized with leader sequences that sequester them away from the host ribosomes, several RIPs from cereals lack these signal peptides and therefore probably reside in the cytosol near the plant ribosomes. More than 30 RIP genes have been identified in the rice (Oryza sativa spp. japonica) genome, many of them lacking a signal peptide. This paper focuses on a presumed cytosolic type-1 RIP from rice, referred to as OsRIP1. Using 3D modeling it is shown that OsRIP1 structurally resembles other cereal RIPs and has an active site that meets the requirements for activity. Furthermore, localization studies indicate that OsRIP1-eGFP fusion proteins reside in the nucleocytoplasmic space when expressed in epidermal cells of Nicotiana benthamiana or Arabidopsis thaliana suspension cells. Finally, OsRIP1 was recombinantly produced in Escherichia coli and was demonstrated to possess catalytic activity. Interestingly, this recombinant RIP inactivates wheat ribosomes far less efficiently than rabbit ribosomes in an in vitro system. These findings raise some interesting questions concerning the mode of action and physiological role of OsRIP1. This is the first time a RIP from rice is investigated at protein level and is shown to possess biological activity.
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Bakshi A, Moin M, Madhav MS, Kirti PB. Target of rapamycin, a master regulator of multiple signalling pathways and a potential candidate gene for crop improvement. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:190-205. [PMID: 30411830 DOI: 10.1111/plb.12935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/05/2018] [Indexed: 06/08/2023]
Abstract
The target of rapamycin (TOR) protein regulates growth and development in photosynthetic and non-photosynthetic eukaryotes. Although the TOR regulatory networks are involved in nutrient and energy signalling, and transcriptional and translational control of multiple signalling pathways, the molecular mechanism of TOR regulation of plant abiotic stress responses is still unclear. The TOR-mediated transcriptional regulation of genes encoding ribosomal proteins (RP) is a necessity under stress conditions for balanced growth and productivity in plants. The activation of SnRKs (sucrose non-fermenting-related kinases) and the inactivation of TOR signalling in abiotic stresses is in line with the accumulation of ABA and transcriptional activation of stress responsive genes. Autophagy is induced under abiotic stress conditions, which results in degradation of proteins and the release of amino acids, which might possibly induce phosphorylation of TOR and, hence, its activation. TOR signalling also has a role in regulating ABA biosynthesis for transcriptional regulation of stress-related genes. The switch between activation and inactivation of TOR by its phosphorylation and de-phosphorylation maintains balanced growth in response to stresses. In the present review, we discuss the important signalling pathways that are regulated by TOR and try to assess the relationship between TOR signalling and tolerance to abiotic stresses in plants. The review also discusses possible cross-talk between TOR and RP genes in response to abiotic stresses.
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Affiliation(s)
- A Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Morpho-Physiological and Proteomic Analyses of Eucalyptus camaldulensis as a Bioremediator in Copper-Polluted Soil in Saudi Arabia. PLANTS 2019; 8:plants8020043. [PMID: 30781434 PMCID: PMC6409862 DOI: 10.3390/plants8020043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/24/2022]
Abstract
The present investigation aimed to assess the impact of copper (Cu) stress on the physiological and proteomic behavior of Eucalyptus camaldulensis.E. camaldulensis is likely a potential phytoremediator in areas vulnerable to Cu contamination, such as the industrial areas of Riyadh. To realize this objective, young seedlings of E. camaldulensis were potted in an open area with soil comprised of clay and sand. Different doses of Cu (30, 50, and 100 µM) were applied to the plants as CuSO4·5H2O for 6 weeks. Plant growth was monitored during the Cu exposure period, and morphological and physiological indicators were measured once a week to determine the growth rates. A proteomics study was also conducted to find out the influence of Cu stress on proteins. Our results showed that growth was negatively affected by Cu treatment, particularly at the highest concentrations. Moreover, using a proteomic analysis showed 26 targets involved in protein expression. Elevated levels of Cu increased the expression of 11 proteins and decreased the expression of 15 proteins. Changes were detected in proteins involved in photosynthesis, translation, transcription, metabolism, and antioxidant enzymes. Our findings provided insights into the molecular mechanisms related to Cu stress, in addition to its influence on the morphological and physiological attributes of E. camaldulensis seedlings. This investigation aimed to characterize the mechanism behind the impact of Cu stress on the plant.
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Vemanna RS, Bakade R, Bharti P, Kumar MKP, Sreeman SM, Senthil-Kumar M, Makarla U. Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:193. [PMID: 30894866 PMCID: PMC6415615 DOI: 10.3389/fpls.2019.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.
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Affiliation(s)
- Ramu S. Vemanna
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
- Regional Center for Biotechnology, Faridabad, India
- *Correspondence: Ramu S. Vemanna, ;
| | - Rahul Bakade
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | - Pooja Bharti
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | | | | | - Udayakumar Makarla
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
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Guedes FADF, Rossetto PDB, Guimarães F, Wilwerth MW, Paes JES, Nicolás MF, Reinert F, Peixoto RS, Alves-Ferreira M. Characterization of Laguncularia racemosa transcriptome and molecular response to oil pollution. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 205:36-50. [PMID: 30317019 DOI: 10.1016/j.aquatox.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are ecosystems of economic and ecological importance. Laguncularia racemosa (Combretaceae), popularly known as white mangrove, is a species that greatly contributes to the community structure of neotropical and West African mangrove forests. Despite the significance of these ecosystems, they have been destroyed by oil spills that can cause yellowing of leaves, increased sensitivity to other stresses and death of trees. However, the molecular response of plants to oil stress is poorly known. In this work, Illumina reads were de novo assembled into 46,944 transcripts of L. racemosa roots and leaves, including putative isoform variants. In addition to improving the genomic information available for mangroves, the L. racemosa assembled transcriptome allowed us to identify reference genes to normalize quantitative real-time PCR (qPCR) expression data from oil-stressed mangrove plants, which were used in RNASeq validation. The analysis of expression changes induced by the oil exposure revealed 310 and 286 responsive transcripts of leaves and roots, respectively, mainly up-regulated. Enriched GO categories related to chloroplasts and photosynthesis were found among both leaf and root oil-responsive transcripts, while "response to heat" and "response to hypoxia" were exclusively enriched in leaves and roots, respectively. The comparison of L. racemosa 12-h-oil-stressed leaf expression profile to previous Arabidopsis heat-stress studies and co-expression evidence also pointed to similarities between the heat and oil responses, in which the HSP-coding genes seem to play a key role. A subset of the L. racemosa oil-responsive root genes exhibited similar up-regulation profiles to their Arabidopsis homologs involved in hypoxia responses, including the HRA1 and LBD41 TF-coding genes. Genes linked to the ethylene pathway such as those coding for ERF TFs were also modulated during the L. racemosa root response to oil stress. Taken together, these results show that oil contamination affects photosynthesis, protein metabolism, hypoxia response and the ethylene pathway in L. racemosa 12-h-oil-exposed leaves and roots.
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Affiliation(s)
- Fernanda Alves de Freitas Guedes
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Priscilla de Barros Rossetto
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Fábia Guimarães
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Maurício Wolf Wilwerth
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Jorge Eduardo Santos Paes
- Centro de Pesquisa e Desenvolvimento Leopoldo Américo Miguez de Mello, PETROBRAS/CENPES, Cidade Universitária, Av. Horácio de Macedo, nº 950, 21941-915, Rio de Janeiro, RJ, Brazil.
| | - Marisa Fabiana Nicolás
- Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, n(o)333 - Quitandinha, 25651-075, Petrópolis, RJ, Brazil.
| | - Fernanda Reinert
- Laboratório de Ecofisiologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Raquel Silva Peixoto
- Laboratório de Ecologia Microbiana Molecular, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco K, 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Márcio Alves-Ferreira
- Laboratório de Genética Molecular e Biotecnologia Vegetal, CCS Cidade Universitária, UFRJ - Av. Prof. Rodolpho Paulo Rocco, s/n, Bloco A, 21941-617, Rio de Janeiro, RJ, Brazil.
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Cen W, Liu J, Lu S, Jia P, Yu K, Han Y, Li R, Luo J. Comparative proteomic analysis of QTL CTS-12 derived from wild rice (Oryza rufipogon Griff.), in the regulation of cold acclimation and de-acclimation of rice (Oryza sativa L.) in response to severe chilling stress. BMC PLANT BIOLOGY 2018; 18:163. [PMID: 30097068 PMCID: PMC6086036 DOI: 10.1186/s12870-018-1381-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/30/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is a thermophilic crop vulnerable to chilling stress. However, common wild rice (Oryza rufipogon Griff.) in Guangxi (China) has the ability to tolerate chilling stress. To better understand the molecular mechanisms underlying chilling tolerance in wild rice, iTRAQ-based proteomic analysis was performed to examine CTS-12, a major chilling tolerance QTL derived from common wild rice, mediated chilling and recovery-induced differentially expressed proteins (DEPs) between the chilling-tolerant rice line DC90 and the chilling-sensitive 9311. RESULTS Comparative analysis identified 206 and 155 DEPs in 9311 and DC90, respectively, in response to the whole period of chilling and recovery. These DEPs were clustered into 6 functional groups in 9311 and 4 in DC90. The majority were enriched in the 'structural constituent of ribosome', 'protein-chromophore linkage', and 'photosynthesis and light harvesting' categories. Short Time-series Expression Miner (STEM) analysis revealed distinct dynamic responses of both chloroplast photosynthetic and ribosomal proteins between 9311 and DC90. CONCLUSION CTS-12 might mediate the dynamic response of chloroplast photosynthetic and ribosomal proteins in DC90 under chilling (cold acclimation) and recovery (de-acclimation) and thereby enhancing the chilling stress tolerance of this rice line. The identified DEPs and the involvement of CTS-12 in mediating the dynamic response of DC90 at the proteomic level illuminate and deepen the understanding of the mechanisms that underlie chilling stress tolerance in wild rice.
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Affiliation(s)
- Weijian Cen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Jianbin Liu
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Siyuan Lu
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Peilong Jia
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Kai Yu
- Shanghai MHelix BioTech Co., Ltd, Shanghai, 201900 People’s Republic of China
| | - Yue Han
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Jijing Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
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Kaur P, Singh N, Pal P, Kaur A. Traditional and improved paddy varieties: Composition, protein, pasting, and gluten-free chapati making properties. Cereal Chem 2018. [DOI: 10.1002/cche.10080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Parmeet Kaur
- Department of Food Science and Technology; Guru Nanak Dev University; Amritsar India
| | - Narpinder Singh
- Department of Food Science and Technology; Guru Nanak Dev University; Amritsar India
| | - Priyanka Pal
- Department of Food Science and Technology; Guru Nanak Dev University; Amritsar India
| | - Amritpal Kaur
- Department of Food Science and Technology; Guru Nanak Dev University; Amritsar India
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Keller M, Simm S. The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen. BMC Genomics 2018; 19:447. [PMID: 29884134 PMCID: PMC5994098 DOI: 10.1186/s12864-018-4824-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/24/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and proteome. At the same time, pollen development and viability is largely sensitive to stress, particularly to elevated temperatures. The transcriptomic and proteomic changes during pollen development and of different stages in response to elevated temperature was targeted to define the underlying molecular principles. RESULTS The analysis of the transcriptome and proteome of Solanum lycopersicum pollen at tetrad, post-meiotic and mature stage before and after heat stress yielded a decline of the transcriptome but an increase of the proteome size throughout pollen development. Comparison of the transcriptome and proteome led to the discovery of two modes defined as direct and delayed translation. Here, genes of distinct functional processes are under the control of direct and delayed translation. The response of pollen to elevated temperature occurs rather at proteome, but not as drastic at the transcriptome level. Heat shock proteins, proteasome subunits, ribosomal proteins and eukaryotic initiation factors are most affected. On the example of heat shock proteins we demonstrate a decoupling of transcript and protein levels as well as a distinct regulation between the developmental stages. CONCLUSIONS The transcriptome and proteome of developing pollen undergo drastic changes in composition and quantity. Changes at the proteome level are a result of two modes assigned as direct and delayed translation. The response of pollen to elevated temperature is mainly regulated at the proteome level, whereby proteins related to synthesis and degradation of proteins are most responsive and might play a central role in the heat stress response of pollen.
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Affiliation(s)
- Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, D-60438 Frankfurt am Main, Germany
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