The Plant Cell Atlas: focusing new technologies on the kingdom that nourishes the planet

Birnbaum, Kenneth D.; Otegui, Marisa S.; Bailey‐Serres, Julia; Rhee, Seung Y.

doi:10.1093/plphys/kiab584

Cited by 12 publications

(8 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While such proof-of-concepts are important, there is now a need to accelerate the engineering of crop plants for agriculture. The recent, rapid uptake of single-cell omics by the plant community is already producing a wealth of information about cellular functions in a wide range of agriculturally and industrially important species . Advances in synthetic biosensors and DNA-recording devices (Figure and ) are also likely to provide novel insights into the molecular events that lead to cell differentiation and cell-type-specific functions.…”

Section: Discussionmentioning

confidence: 99%

“…The recent, rapid uptake of single-cell omics by the plant community is already producing a wealth of information about cellular functions in a wide range of agriculturally and industrially important species. 16 Advances in synthetic biosensors and DNA-recording devices ( Figure 2 and 3 ) are also likely to provide novel insights into the molecular events that lead to cell differentiation and cell-type-specific functions. Currently, the plant synthetic biology community experiences bottlenecks imposed by low-efficiency and laborious plant transformation protocols.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, single-cell omics of protoplasts and isolated nuclei has led to an explosion in data. However, the identification and comparison of cell types across the diversity of plant lineages from gene-expression signatures remains a significant challenge . The advent of spatial genomics, which allows high-throughput fluorescent in situ hybridization (FISH) is beginning to address this, though to date it has only been applied to a few plant species. , To understand how metabolic pathways are organized across cell-types, single cell transcriptomics and metabolomics have been integrated to link gene expression with the presence of specific compounds …”

Section: Synthetic Biology Approaches For Elucidating Plant Cellular ...mentioning

confidence: 99%

See 2 more Smart Citations

Engineering Plant Cell Fates and Functions for Agriculture and Industry

Tansley,

Patron,

Guiziou

2024

ACS Synth. Biol.

View full text Add to dashboard Cite

Many plant species are grown to enable access to specific organs or tissues, such as seeds, fruits, or stems. In some cases, a value is associated with a molecule that accumulates in a single type of cell. Domestication and subsequent breeding have often increased the yields of these target products by increasing the size, number, and quality of harvested organs and tissues but also via changes to overall plant growth architecture to suit large-scale cultivation. Many of the mutations that underlie these changes have been identified in key regulators of cellular identity and function. As key determinants of yield, these regulators are key targets for synthetic biology approaches to engineer new forms and functions. However, our understanding of many plant developmental programs and cell-type specific functions is still incomplete. In this Perspective, we discuss how advances in cellular genomics together with synthetic biology tools such as biosensors and DNA-recording devices are advancing our understanding of cell-specific programs and cell fates. We then discuss advances and emerging opportunities for cell-type-specific engineering to optimize plant morphology, responses to the environment, and the production of valuable compounds.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Synthetic Biology Approaches For Elucidating Plant Cellular ...mentioning

confidence: 99%

See 1 more Smart Citation

Engineering Plant Cell Fates and Functions for Agriculture and Industry

Tansley,

Patron,

Guiziou

2024

ACS Synth. Biol.

View full text Add to dashboard Cite

show abstract

“…Beside animals, the Plant Cell Atlas ( https://www.plantcellatlas.org ) project was also proposed to create a community resource that incorporates information on nucleic acids, proteins, and metabolites to comprehensively describe the states of various cell types at increasing higher resolutions. 95 , 96 , 97 To illustrate the mechanisms of plant development and stress response, plant scientists have not stopped their steps to trace the gene expression profiles from the whole plant, different organs, specific cell types, and single cells. At the level of nucleic acids, with the newly developed scATAC-seq and scCUT&Tag approaches, 98 , 99 , 100 integrated multi-omics analysis would be the next direction for plant single-cell studies.…”

Section: Bioinformatics Analysis Of Single-cell Sequencing Datamentioning

confidence: 99%

Single-cell technologies: From research to application

Wen

Huang

et al. 2022

The Innovation

View full text Add to dashboard Cite

“…The machine learning model outputs will help design optimal and targeted experimental strategies to detect these unobserved proteins. Finally, this second PeptideAtlas release, including its associated metadata and our machine learning output, provides an ideal platform to contribute to a community Arabidopsis proteome cell atlas , and also contribute to the ongoing reannotation of the Arabidopsis genome. The new PeptideAtlas release is integrated into TAIR () and linked to JBrowse (), PPDB, SUBA, UniProtKB, ATHENA, PhosPhat, and Plant PTM Viewer …”

Section: Introductionmentioning

confidence: 99%

Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas

van Wijk,

Leppert,

Sun

et al. 2023

J. Proteome Res.

View full text Add to dashboard Cite

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023−10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.

show abstract

The Plant Cell Atlas: focusing new technologies on the kingdom that nourishes the planet

Cited by 12 publications

References 33 publications

Engineering Plant Cell Fates and Functions for Agriculture and Industry

Engineering Plant Cell Fates and Functions for Agriculture and Industry

Single-cell technologies: From research to application

Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas

Contact Info

Product

Resources

About