11 results on '"Birnbaum, KD"'
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2. Plant regeneration: REF1 calls the fouls.
- Author
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Birnbaum KD
- Subjects
- Signal Transduction, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, Arabidopsis physiology, Plant Development physiology, Regeneration physiology
- Abstract
Regenerative organisms such as plants must have specific signals that respond to damage and instruct remnant tissue to undergo repair. A recent paper identifies a long-sought candidate for the signal that links injury to regenerative programs., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
3. Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration.
- Author
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Lee LR, Guillotin B, Rahni R, Hutchison C, Desvoyes B, Gutierrez C, and Birnbaum KD
- Abstract
The plasticity of plant cells underlies their wide capacity to regenerate, with increasing evidence in plants and animals implicating cell cycle dynamics in cellular reprogramming. To investigate the cell cycle during cellular reprogramming, we developed a comprehensive set of cell cycle phase markers in the Arabidopsis root. Using single-cell RNA-seq profiles and live imaging during regeneration, we found that a subset of cells near an ablation injury dramatically increases division rate by truncating G1. Cells in G1 undergo a transient nuclear peak of glutathione (GSH) prior to coordinated entry into S phase followed by rapid divisions and cellular reprogramming. A symplastic block of the ground tissue impairs regeneration, which is rescued by exogenous GSH. We propose a model in which GSH from the outer tissues is released upon injury licensing an exit from G1 near the wound to induce rapid cell division and reprogramming., Competing Interests: Declaration of Interests The authors declare no competing interests.
- Published
- 2024
- Full Text
- View/download PDF
4. A common regulatory switch controls a suite of C4 traits in multiple cell types.
- Author
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Camo-Escobar D, Alcalá-Gutiérrez C, Palafox-Figueroa E, Guillotin B, Hernández-Coronado M, Coyac-Rodríguez JL, Cerbantez-Bueno VE, Vélez-Ramírez A, de Folter S, Birnbaum KD, and Ortiz-Ramírez C
- Abstract
The C4 photosynthetic pathway provided a major advantage to plants growing in hot, dry environments, including the ancestors of our most productive crops. Two traits were essential for the evolution of this pathway: increased vein density and the functionalization of bundle sheath cells for photosynthesis. Although GRAS transcriptional regulators, including SHORT ROOT (SHR), have been implicated in mediating leaf patterning in both C3 and C4 species, little is known about what controls the specialized features of the cells that mediate C4 metabolism and physiology. We show in the model monocot, Setaria viridis , that SHR regulates components of multiple cell identities, including chloroplast biogenesis and photosynthetic gene expression in bundle sheath cells, a central feature of C4 plants. Furthermore, we found that it also contributes to the two-cell compartmentalization of the characteristic four-carbon shuttle pathway. Disruption of SHR function clearly reduced photosynthetic capacity and seed yield in mutant plants under heat stress. Together, these results show how cell identities are remodeled by SHR to host the suite of traits characteristic of C4 regulation, which are a main engineering target in non-C4 crops to improve climate resilience., Competing Interests: Competing interests The authors declare no competing interests.
- Published
- 2024
- Full Text
- View/download PDF
5. Philip N. Benfey (1953-2023).
- Author
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Coruzzi GM and Birnbaum KD
- Subjects
- Plant Development genetics, Genomics history
- Abstract
A "ring" master of plant development and cellular genomics.
- Published
- 2023
- Full Text
- View/download PDF
6. A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol.
- Author
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Huang T, Guillotin B, Rahni R, Birnbaum KD, and Wagner D
- Abstract
Background: In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported., Results: We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol., Conclusions: The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues., (© 2023. The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
7. A pan-grass transcriptome reveals patterns of cellular divergence in crops.
- Author
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Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, and Birnbaum KD
- Subjects
- Base Sequence, Gene Expression Regulation, Plant genetics, Plant Roots cytology, Single-Cell Gene Expression Analysis, Sequence Analysis, RNA, Evolution, Molecular, Sorghum cytology, Sorghum genetics, Transcriptome genetics, Zea mays cytology, Zea mays genetics, Setaria Plant cytology, Setaria Plant genetics, Crops, Agricultural cytology, Crops, Agricultural genetics
- Abstract
Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits
1 . Key traits that distinguish these species are mediated by specialized cell types2 . Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2023
- Full Text
- View/download PDF
8. Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense.
- Author
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Hernández-Coronado M, Dias Araujo PC, Ip PL, Nunes CO, Rahni R, Wudick MM, Lizzio MA, Feijó JA, and Birnbaum KD
- Subjects
- Arabidopsis metabolism, Arabidopsis Proteins metabolism, Chromatin metabolism, Plants metabolism, Receptors, Glutamate genetics, Signal Transduction physiology, Gene Expression Regulation, Plant genetics, Receptors, Glutamate metabolism, Regeneration physiology
- Abstract
Wounding is a trigger for both regeneration and defense in plants, but it is not clear whether the two responses are linked by common activation or regulated as trade-offs. Although plant glutamate-receptor-like proteins (GLRs) are known to mediate defense responses, here, we implicate GLRs in regeneration through dynamic changes in chromatin and transcription in reprogramming cells near wound sites. We show that genetic and pharmacological inhibition of GLR activity increases regeneration efficiency in multiple organ repair systems in Arabidopsis and maize. We show that the GLRs work through salicylic acid (SA) signaling in their effects on regeneration, and mutants in the SA receptor NPR1 are hyper-regenerative and partially resistant to GLR perturbation. These findings reveal a conserved mechanism that regulates a trade-off between defense and regeneration, and they also offer a strategy to improve regeneration in agriculture and conservation., Competing Interests: Declaration of interests A patent (application #63120640) has been filed related to this work on compositions and methods to enhance plant regeneration., (Copyright © 2022 Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
9. The Plant Cell Atlas: focusing new technologies on the kingdom that nourishes the planet.
- Author
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Birnbaum KD, Otegui MS, Bailey-Serres J, and Rhee SY
- Subjects
- Databases as Topic, Plant Cells
- Published
- 2022
- Full Text
- View/download PDF
10. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization.
- Author
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Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y, De Rybel B, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD, and Helariutta Y
- Subjects
- Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Cell Differentiation, GTP-Binding Proteins genetics, GTP-Binding Proteins metabolism, Meristem cytology, Phloem genetics, Phloem metabolism, Plant Roots genetics, Plant Roots growth & development, Plant Roots metabolism, RNA-Seq, Signal Transduction, Single-Cell Analysis, Transcription Factors genetics, Transcriptome, Arabidopsis cytology, Arabidopsis Proteins metabolism, Phloem cytology, Phloem growth & development, Plant Roots cytology, Transcription Factors metabolism
- Abstract
In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
- Published
- 2021
- Full Text
- View/download PDF
11. Ground tissue circuitry regulates organ complexity in maize and Setaria .
- Author
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Ortiz-Ramírez C, Guillotin B, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D, Gallagher KL, and Birnbaum KD
- Subjects
- Flow Cytometry, Genome, Plant, Plant Proteins genetics, Plant Roots genetics, RNA-Seq, Setaria Plant cytology, Setaria Plant genetics, Single-Cell Analysis, Transcription Factors genetics, Transcription, Genetic, Zea mays cytology, Zea mays genetics, Plant Proteins metabolism, Plant Roots cytology, Plant Roots metabolism, Setaria Plant metabolism, Transcription Factors metabolism, Zea mays metabolism
- Abstract
Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of Arabidopsis . Here, we used single-cell RNA sequencing to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue formative transcription factor SHORT-ROOT (SHR) adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue to elaborate anatomical complexity.
- Published
- 2021
- Full Text
- View/download PDF
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