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Publications (10 of 73) Show all publications
Benstein, R. M., Schmid, M. & You, Y. (2023). Isolation of nuclei tagged in specific cell types (INTACT) in Arabidopsis (2ed.). In: José Luis Riechmann; Cristina Ferrándiz (Ed.), Flower development: methods and protocols (pp. 313-328). New york: Humana Press, 2686
Open this publication in new window or tab >>Isolation of nuclei tagged in specific cell types (INTACT) in Arabidopsis
2023 (English)In: Flower development: methods and protocols / [ed] José Luis Riechmann; Cristina Ferrándiz, New york: Humana Press, 2023, 2, Vol. 2686, p. 313-328Chapter in book (Refereed)
Abstract [en]

Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.

Place, publisher, year, edition, pages
New york: Humana Press, 2023 Edition: 2
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029 ; 2686
Keywords
Arabidopsis, Biotinylation, Cell-type-specific promoter, in situ streptavidin histochemistry, INTACT, low-input RT-qPCR, Shoot apical meristem
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-212822 (URN)10.1007/978-1-0716-3299-4_16 (DOI)37540367 (PubMedID)2-s2.0-85166555325 (Scopus ID)978-1-0716-3298-7 (ISBN)978-1-0716-3299-4 (ISBN)
Available from: 2023-08-16 Created: 2023-08-16 Last updated: 2023-08-16Bibliographically approved
Mateos, J. L., Sanchez, S. E., Legris, M., Esteve-Bruna, D., Torchio, J. C., Petrillo, E., . . . Yanovsky, M. J. (2023). PICLN modulates alternative splicing and light/temperature responses in plants. Plant Physiology, 191(2), 1036-1051
Open this publication in new window or tab >>PICLN modulates alternative splicing and light/temperature responses in plants
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2023 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 191, no 2, p. 1036-1051Article in journal (Refereed) Published
Abstract [en]

Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

Place, publisher, year, edition, pages
Oxford University Press, 2023
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-205183 (URN)10.1093/plphys/kiac527 (DOI)000911677600001 ()36423226 (PubMedID)2-s2.0-85148076794 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 2018.0202EU, Horizon 2020, SIGNAT-644435
Available from: 2023-02-28 Created: 2023-02-28 Last updated: 2023-02-28Bibliographically approved
André, D., Marcon, A., Lee, K. C., Goretti, D., Zhang, B., Delhomme, N., . . . Nilsson, O. (2022). FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees. Current Biology, 32(13), 2988-2996.e4
Open this publication in new window or tab >>FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees
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2022 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 32, no 13, p. 2988-2996.e4Article in journal (Refereed) Published
Abstract [en]

In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1–4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.

Place, publisher, year, edition, pages
Cell Press, 2022
Keywords
annual growth cycle, bud flush, dormancy, FLOWERING LOCUS T, paralogs, Populus
National Category
Botany Forest Science
Identifiers
urn:nbn:se:umu:diva-198221 (URN)10.1016/j.cub.2022.05.023 (DOI)000830839000010 ()2-s2.0-85133969064 (Scopus ID)
Funder
VinnovaKnut and Alice Wallenberg FoundationSwedish Research CouncilThe Kempe Foundations
Available from: 2022-07-21 Created: 2022-07-21 Last updated: 2023-09-05Bibliographically approved
Zacharaki, V., Ponnu, J., Crepin, N., Langenecker, T., Hagmann, J., Skorzinski, N., . . . Schmid, M. (2022). Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant. New Phytologist, 235(1), 220-233
Open this publication in new window or tab >>Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant
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2022 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 235, no 1, p. 220-233Article in journal (Refereed) Published
Abstract [en]

Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1).

Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches.

We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10.

Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
Arabidopsis thaliana, embryogenesis, flowering time, SnRK1 complex, T6P pathway, TPS1
National Category
Botany Genetics
Identifiers
urn:nbn:se:umu:diva-193809 (URN)10.1111/nph.18104 (DOI)000779406900001 ()35306666 (PubMedID)2-s2.0-85127600820 (Scopus ID)
Available from: 2022-05-06 Created: 2022-05-06 Last updated: 2022-07-12Bibliographically approved
Pandey, S. P., Benstein, R. M., Wang, Y. & Schmid, M. (2021). Epigenetic regulation of temperature responses: past successes and future challenges. Journal of Experimental Botany, 72(21), 7482-7497
Open this publication in new window or tab >>Epigenetic regulation of temperature responses: past successes and future challenges
2021 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 72, no 21, p. 7482-7497Article, review/survey (Refereed) Published
Abstract [en]

In contrast to animals, plants cannot avoid unfavorable temperature conditions. Instead, plants have evolved intricate signaling pathways that enable them to perceive and respond to temperature. General acclimation processes that prepare the plant to respond to stressful heat and cold usually occur throughout the whole plant. More specific temperature responses, however, are limited to certain tissues or cell types. While global responses are amenable to epigenomic analyses, responses that are highly localized are more problematic as the chromatin in question is not easily accessible. Here we review current knowledge of the epigenetic regulation of FLOWERING LOCUS C and FLOWERING LOCUS T as examples of temperature-responsive flowering time regulator genes that are expressed broadly throughout the plants and in specific cell types, respectively. While this work has undoubtedly been extremely successful, we reason that future analyses would benefit from higher spatiotemporal resolution. We conclude by reviewing methods and successful applications of tissue-and cell type-specific epigenomic analyses and provide a brief outlook on future single-cell epigenomics.

Place, publisher, year, edition, pages
Oxford University Press, 2021
Keywords
Cell-specific, chromatin, epigenomics, flowering, FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), temperature, tissue-specific, vernalization
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-217884 (URN)10.1093/jxb/erab248 (DOI)000744583700012 ()34051078 (PubMedID)2-s2.0-85121481769 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2016.0025
Available from: 2023-12-12 Created: 2023-12-12 Last updated: 2023-12-19Bibliographically approved
Dikaya, V., El Arbi, N., Rojas-Murcia, N., Muniz Nardeli, S., Goretti, D. & Schmid, M. (2021). Insights into the role of alternative splicing in plant temperature response. Journal of Experimental Botany, 72(21), 7384-7403
Open this publication in new window or tab >>Insights into the role of alternative splicing in plant temperature response
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2021 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 72, no 21, p. 7384-7403Article, review/survey (Refereed) Published
Abstract [en]

Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.

Place, publisher, year, edition, pages
Oxford University Press, 2021
Keywords
Alternative splicing, Arabidopsis thaliana, cold acclimation, heat acclimation, splicing factor, temperature adaptation, temperature response
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-202940 (URN)10.1093/jxb/erab234 (DOI)000744583700005 ()34105719 (PubMedID)2-s2.0-85123494432 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2018.0202
Available from: 2023-01-14 Created: 2023-01-14 Last updated: 2024-07-02Bibliographically approved
Yang, X., Zhang, L., Yang, Y., Schmid, M. & Wang, Y. (2021). Mirna mediated regulation and interaction between plants and pathogens. International Journal of Molecular Sciences, 22(6), 1-13, Article ID 2913.
Open this publication in new window or tab >>Mirna mediated regulation and interaction between plants and pathogens
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2021 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 22, no 6, p. 1-13, article id 2913Article, review/survey (Refereed) Published
Abstract [en]

Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.

Place, publisher, year, edition, pages
MDPI, 2021
Keywords
Arms race, Interaction, MiRNA, Pathogen, Plant
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-181718 (URN)10.3390/ijms22062913 (DOI)000645796000001 ()2-s2.0-85102351126 (Scopus ID)
Available from: 2021-03-25 Created: 2021-03-25 Last updated: 2024-07-02Bibliographically approved
Muralidhara, P., Weiste, C., Collani, S., Krischke, M., Kreisz, P., Draken, J., . . . Dröge-Laser, W. (2021). Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling. Proceedings of the National Academy of Sciences of the United States of America, 118(37), Article ID e2106961118.
Open this publication in new window or tab >>Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling
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2021 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 37, article id e2106961118Article in journal (Refereed) Published
Abstract [en]

Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.

Keywords
ARF19, BZIP63, Lateral root, Metabolic homeostasis, SnRK1
National Category
Cell Biology Genetics
Identifiers
urn:nbn:se:umu:diva-187723 (URN)10.1073/pnas.2106961118 (DOI)000705153400001 ()2-s2.0-85114731783 (Scopus ID)
Available from: 2021-09-20 Created: 2021-09-20 Last updated: 2024-07-02Bibliographically approved
Lee, J. E., Goretti, D., Neumann, M., Schmid, M. & You, Y. (2020). A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem. Physiologia Plantarum, 170(4), 474-487
Open this publication in new window or tab >>A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem
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2020 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 170, no 4, p. 474-487Article in journal (Refereed) Published
Abstract [en]

The transition from vegetative to reproductive growth is a key event in the plant life cycle. Plants therefore use a variety of environmental and endogenous signals to determine the optimal time for flowering to ensure reproductive success. These signals are integrated at the shoot apical meristem (SAM), which subsequently undergoes a shift in identity and begins producing flowers rather than leaves, while still maintaining pluripotency and meristematic function. Gibberellic acid (GA), an important hormone associated with cell growth and differentiation, has been shown to promote flowering in many plant species including Arabidopsis thaliana , but the details of how spatial and temporal regulation of GAs in the SAM contribute to floral transition are poorly understood. In this study, we show that the gene GIBBERELLIC ACID METHYLTRANSFERASE 2 (GAMT2 ), which encodes a GA‐inactivating enzyme, is significantly upregulated at the SAM during floral transition and contributes to the regulation of flowering time. Loss of GAMT2 function leads to early flowering, whereas transgenic misexpression of GAMT2 in specific regions around the SAM delays flowering. We also found that GAMT2 expression is independent of the key floral regulator LEAFY but is strongly increased by the application of exogenous GA. Our results indicate that GAMT2 is a repressor of flowering that may act as a buffer of GA levels at the SAM to help prevent premature flowering.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-173310 (URN)10.1111/ppl.13146 (DOI)000540372800001 ()32483836 (PubMedID)2-s2.0-85096285583 (Scopus ID)
Funder
Vinnova, 2016-00504Knut and Alice Wallenberg Foundation, 2016.0025Knut and Alice Wallenberg Foundation, 2016.0341Max Planck Society
Available from: 2020-07-03 Created: 2020-07-03 Last updated: 2023-03-23Bibliographically approved
Brunoni, F., Collani, S., Casanova-Saez, R., Simura, J., Karady, M., Schmid, M., . . . Bellini, C. (2020). Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. New Phytologist, 226(6), 1753-1765
Open this publication in new window or tab >>Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis
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2020 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 226, no 6, p. 1753-1765Article in journal (Refereed) Published
Abstract [en]

Dynamic regulation of the concentration of the natural auxin (IAA) is essential to coordinate most of the physiological and developmental processes and responses to environmental changes. Oxidation of IAA is a major pathway to control auxin concentrations in angiosperms and, along with IAA conjugation, to respond to perturbation of IAA homeostasis. However, these regulatory mechanisms remain poorly investigated in conifers. To reduce this knowledge gap, we investigated the different contributions of the IAA inactivation pathways in conifers. MS-based quantification of IAA metabolites under steady-state conditions and after perturbation was investigated to evaluate IAA homeostasis in conifers. Putative Picea abies GH3 genes (PaGH3) were identified based on a comprehensive phylogenetic analysis including angiosperms and basal land plants. Auxin-inducible PaGH3 genes were identified by expression analysis and their IAA-conjugating activity was explored. Compared to Arabidopsis, oxidative and conjugative pathways differentially contribute to reduce IAA concentrations in conifers. We demonstrated that the oxidation pathway plays a marginal role in controlling IAA homeostasis in spruce. By contrast, an excess of IAA rapidly activates GH3-mediated irreversible conjugation pathways. Taken together, these data indicate that a diversification of IAA inactivation mechanisms evolved specifically in conifers.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
Keywords
auxin conjugates, auxin homeostasis, conifers, GH3 genes, indole-3-acetic acid (IAA), Picea abies
National Category
Developmental Biology
Identifiers
urn:nbn:se:umu:diva-171948 (URN)10.1111/nph.16463 (DOI)000533328500021 ()32004385 (PubMedID)2-s2.0-85080875275 (Scopus ID)
Available from: 2020-06-18 Created: 2020-06-18 Last updated: 2023-03-24Bibliographically approved
Projects
Reglering av blomningsprocessen via trehalos-6-fosfat signalering [2015-04617_VR]; Umeå UniversityBinding of Arabidopsis FD to an Unusual cis-Regulatory Element – A new Role for the Master Floral Regulator LEAFY? [2019-04372_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-0068-2967

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