SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in Arabidopsis Roots

Kim, Hyoujin; Zhou, Jing; Kumar, Deepak; Jang, Geupil; Ryu, Kook Hui; Sebastián, José; Miyashima, Shunsuke; Helariutta, Yrjö; Lee, Ji-Young

doi:10.1105/tpc.19.00455

Cited by 35 publications

(40 citation statements)

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“…Similar changes are also detected for scr-4 (Fig 3c). These results are consistent with reports of shr-2 and scr-4 defects in stele development [38][39][40][41][42] but were not discernible in earlier shr-2 scRNAseq data 19 . Taken together, the resolution of the atlas annotation enables confident detection of major and subtle cell type changes in mutants.…”

Section: Scrna-seq Reveals Differentiation Pathways Of Cell Identity supporting

confidence: 92%

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Shahan

Hsu

Nolan

et al. 2020

Preprint

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SummaryCell fate acquisition is a fundamental developmental process in all multicellular organisms. Yet, much is unknown regarding how a cell traverses the pathway from stem cell to terminal differentiation. Advances in single cell genomics1 hold promise for unraveling developmental mechanisms2–3 in tissues4, organs5–6, and organisms7–8. However, lineage tracing can be challenging for some tissues9 and integration of high-quality datasets is often necessary to detect rare cell populations and developmental states10,11. Here, we harmonized single cell mRNA sequencing data from over 110,000 cells to construct a comprehensive atlas for a stereotypically developing organ with indeterminate growth, the Arabidopsis root. To test the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. Although both transcription factors are required for early specification of cell identity12, our results suggest the existence of an alternative pathway acting in mature cells to specify endodermal identity, for which SHORTROOT is required. Uncovering the architecture of this pathway will provide insight into specification and stabilization of the endodermis, a tissue analogous to the mammalian epithelium. Thus, the atlas is a pivotal advance for unraveling the transcriptional programs that specify and maintain cell identity to regulate organ development in space and time.

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Section: Scrna-seq Reveals Differentiation Pathways Of Cell Identity supporting

confidence: 92%

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Shahan

Hsu

Nolan

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…For some of them, existing reporter plasmids could be obtained, but for the majority we cloned promoter constructs that drive the expression of a nuclear localized fluorescent reporter (NLS-CITRINE). After their transformation into Col-0 wildtype plants, eight out of the 21 reporters showed activity in developing root phloem: the described SISTER OF ALTERED PHLOEM DEVELOPMENT (SAPL) (Ross-Elliott et al, 2017), EARLY NODULIN-LIKE 9 (ENODL9) (Khan et al, 2007), SIEVE ELEMENT OCCLUSION-RELATED 2 (SEOR2) (Anstead et al, 2012) and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN 2 (SND2) (Kim et al, 2020) reporters (Fig. 3A-D); and the new reporters DESIGUAL 2 (DEAL2) (Wilson-Sanchez et al, 2018), SIEVE ELEMENT MARKER 1 ( SEMA1 ; AT2G35585), SEMA2 (AT1G61760) and SEMA3 (AT3G26350) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Metaphloem development in the Arabidopsis root tip

Graeff

Hardtke

2021

Preprint

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The phloem transport network is a major evolutionary innovation that enabled plants to dominate terrestrial ecosystems. In the growth apices, the meristems, apical stem cells continuously produce early, so-called protophloem. This is easily observed in Arabidopsis root meristems, where the differentiation of individual protophloem sieve element precursors into interconnected, conducting sieve tubes is laid out in a spatio-temporal gradient. The mature protophloem eventually collapses as the neighboring metaphloem takes over its function further distal from the stem cell niche. Compared to protophloem, metaphloem ontogenesis is poorly characterized, primarily because its visualization is challenging. Here we describe an improved protocol to investigate metaphloem development in Arabidopsis root tips in combination with a set of new molecular markers. We found that mature metaphloem sieve elements are only observed in the late post-meristematic root although their specification is initiated as soon as protophloem sieve elements enucleate. Moreover, unlike protophloem sieve elements, metaphloem sieve elements only differentiate once they have fully elongated. Finally, our results suggest that metaphloem differentiation is not directly controlled by protophloem-derived cues but rather follows a distinct, robust developmental trajectory.Summary statementMetaphloem sieve element differentiation in Arabidopsis roots follows a robust developmental trajectory.

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“…Extensive studies have shown that exogenous NH 4 + triggers multiple specific changes in gene expression, metabolism, hormonal signaling, and root phenotype in rice and Arabidopsis [ 66 , 67 ] . Therefore, the fact that improving the affinity of crop roots to NH 4 + and NO 3 − can raise nitrogen utilization efficiency may be closely related to the regulation of the key enzymes involved in nitrogen metabolism [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings

et al. 2021

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Background Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mechanisms of how biochar affects nitrogen assimilation by crop seedlings have not been well elucidated. Results Here, we report changes in root system architecture, activities of the key enzymes involved in nitrogen assimilation, and cytokinin (CTK) at the seedling stage of cotton with reduced urea usage and biochar application at different soil layers (0–10 cm and 10–20 cm). Active root absorption area, fresh weight, and nitrogen agronomic efficiency increased significantly when urea usage was reduced by 25% and biochar was applied in the surface soil layer. Glutamine oxoglutarate amino transferase (GOGAT) activity was closely related to the application depth of urea/biochar, and it increased when urea/biochar was applied in the 0–10 cm layer. Glutamic-pyruvic transaminase activity (GPT) increased significantly as well. Nitrate reductase (NR) activity was stimulated by CTK in the very fine roots but inhibited in the fine roots. In addition, AMT1;1, gdh3, and gdh2 were significantly up-regulated in the very fine roots when urea usage was reduced by 25% and biochar was applied. Conclusion Nitrogen assimilation efficiency was significantly affected when urea usage was reduced by 25% and biochar was applied in the surface soil layer at the seedling stage of cotton. The co-expression of gdh3 and gdh2 in the fine roots increased nitrogen agronomic efficiency. The synergistic expression of the ammonium transporter gene and gdh3 suggests that biochar may be beneficial to amino acid metabolism.

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SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in Arabidopsis Roots

Abstract: Companion cells and sieve elements, two key cell types of sugar-conducting phloem, develop as a functional unit in the root via intercellular signals triggered by the SHORTROOT transcription factor.

Cited by 35 publications

References 50 publications

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Metaphloem development in the Arabidopsis root tip

Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings

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