Data mining study of hormone biosynthesis gene expression reveals new aspects of somatic embryogenesis regulation

Saptari, Rizka Tamania; Susila, Hendry

doi:10.1007/s11627-018-9947-5

Cited by 9 publications

(7 citation statements)

References 53 publications

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“…Thus, the tryptophan-dependent TAA1-YUC pathway of IAA biosynthesis seems to commonly contribute to the auxin accumulation that is associated with the embryogenic transition in the somatic cells of plants. However, insights into the available RNA-seq data of an O. sativa embryogenic culture [72] indicated only a limited number of auxin biosynthesis-related transcripts and suggested a much less intensive activity of the TAA1-YUC IAA biosynthesis pathway in this plant than the one in Arabidopsis [73]. However, understanding the auxin biosynthesis pathways in O. sativa is still not well developed and further analyses are needed to reach a conclusion about the SE-associated auxin production in the model plants Arabidopsis vs. O. sativa.…”

Section: Biosynthesis and Accumulation Of Auxin During Sementioning

confidence: 97%

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Wójcik

Wójcikowska

Gaj

2020

IJMS

109

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Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.

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Section: Biosynthesis and Accumulation Of Auxin During Sementioning

confidence: 97%

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Wójcik

Wójcikowska

Gaj

2020

IJMS

109

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“…PMN was used to find genes in the biosynthetic pathways of metabolites which showed altered concentration in the mutants and P-deprived plants. Saptari and Susila (2018) examined the expression of hormone biosynthesis genes during somatic embryogenesis in Arabidopsis and rice. The authors used PMN to identify hormone biosynthetic genes and performed expression analysis on the identified gene set.…”

Section: Discussionmentioning

confidence: 99%

Plant Metabolic Network: A multi-species resource of plant metabolic information

Hawkins

Ginzburg

Zhao

et al. 2021

Preprint

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Plant metabolism is a pillar of our ecosystem, food security, and economy. To understand and engineer plant metabolism, we first need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we previously created the Plant Metabolic Network (PMN), an online resource of curated and computationally predicted information about the enzymes, compounds, reactions, and pathways that make up plant metabolism. Here we report PMN 15, which contains genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants, and new tools for analyzing and viewing metabolism information across species and integrating omics data in a metabolic context. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell-type specific metabolic pathways. This work shows the continued growth and refinement of the PMN resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

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“…In addition, antagonistic interaction may also act by via stabilizing the GA repressor DELLA proteins by ethylene signaling via EIN3 and CTR1 (Zheng et al, 2013a ). Finally, Saptari and Susila ( 2019 ) demonstrated that AGL15, FUS3 , and BBM show increased transcript accumulation in response to ethylene via EIN3, whereas Zheng et al ( 2013a ), showed a positive correlation between ethylene and GmAGL15, GmAGL18, GmFUS3, and GmABI3 in soybean. Conversely, these genes showed a general negative correlation with biologically active GA (Zheng et al, 2016 ).…”

Section: Agl15 and Hormone Relations In Somatic Embryogenesismentioning

confidence: 99%

AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism

et al. 2022

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Plants have amazing regenerative properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is somatic embryogenesis, by which an embryonic structure is formed that “converts” into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops to meet agricultural challenges. Regeneration of transformed cells is needed for this applied work as well as basic research to understand gene function. Here we focus on a MADS-domain transcription factor, AGAMOUS-Like15 (AGL15) that shows a positive correlation between accumulation levels and capacity for somatic embryogenesis. We relate AGL15 function to other transcription factors, hormones, and epigenetic modifiers involved in somatic embryo development.

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Data mining study of hormone biosynthesis gene expression reveals new aspects of somatic embryogenesis regulation

Cited by 9 publications

References 53 publications

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Plant Metabolic Network: A multi-species resource of plant metabolic information

AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism

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