Physiology and Molecular Biology of Plants, Год журнала: 2025, Номер 31(2), С. 199 - 209
Опубликована: Фев. 1, 2025
Язык: Английский
BioDesign Research, Год журнала: 2024, Номер 6, С. 0029 - 0029
Опубликована: Янв. 1, 2024
Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities
Язык: Английский
Процитировано
13
Journal of Experimental Botany, Год журнала: 2024, Номер 75(17), С. 5188 - 5203
Опубликована: Март 11, 2024
Biotic and abiotic environmental cues are major factors influencing plant growth productivity. Interactions with biotic (e.g. symbionts pathogens) changes in temperature, water, or nutrient availability) trigger signaling downstream transcriptome adjustments plants. While bulk RNA-sequencing technologies have traditionally been used to profile these transcriptional changes, tissue homogenization may mask heterogeneity of responses resulting from the cellular complexity organs. Thus, whether different cell types respond equally fluctuations, subsets cell-type specific, long-lasting questions biology. The recent breakthrough single-cell transcriptomics research offers an unprecedented view under changing conditions. In this review, we discuss contribution understanding cell-type-specific interactions. Besides biological findings, present some technical challenges coupled studies plant-environment interactions, proposing possible solutions exciting paths for future research.
Язык: Английский
Процитировано
11
Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2024, Номер 51(7), С. 680 - 690
Опубликована: Фев. 26, 2024
Язык: Английский
Процитировано
5
Molecular Plant, Год журнала: 2024, Номер 17(10), С. 1558 - 1572
Опубликована: Авг. 23, 2024
For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for basal and systemic acquired resistance. SA activates these responses by reprogramming ∼20% of the transcriptome through NPR1. However, components in NPR1 signaling hub, which appears nuclear condensates, cascade have remained elusive due to difficulties studying this transcriptional cofactor, whose chromatin association is indirect likely transient. To overcome challenge, we applied TurboID divulge proxiome, detected almost all interactors well new transcription-related complexes. Testing showed that remodeling histone demethylation contribute SA-induced Globally, proxiome striking similarity GBPL3 involved synthesis, except associated transcription factors (TFs), suggesting common regulatory modules are recruited reprogram specific transcriptomes cofactors, like NPR1, binding unique TFs. Stepwise green fluorescent protein-tagged factor cleavage under target release using nuclease (greenCUT&RUN) analyses that, upon induction, initiates primarily with TGACG-binding TFs induce expression secondary TFs, predominantly WRKYs. Further, WRKY54 WRKY70 were identified play major role inducing immune-output genes without interacting at chromatin. Moreover, loss condensate formation function decreases its activity, indicating importance condensates organizing hub initiating cascade. Collectively, study demonstrates how combinatorial applications stepwise greenCUT&RUN transcend traditional genetic methods globally map hubs cascades in-depth explorations.
Язык: Английский
Процитировано
5
Current Opinion in Plant Biology, Год журнала: 2023, Номер 76, С. 102444 - 102444
Опубликована: Сен. 9, 2023
Язык: Английский
Процитировано
12
Frontiers in Plant Science, Год журнала: 2024, Номер 15
Опубликована: Март 1, 2024
The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, tissues are made several distinct cell types with unique and differentiated functions, which limits ‘omics’-based studies to determine only an averaged molecular signature arising from multiple types. Advancements in spatial omics technologies provide opportunity understand mechanisms underlying responses WD cell-type levels. Here, we spatiotemporal metabolic two poplar ( Populus tremula× P. alba ) leaf -palisade vascular cells- using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified stress-mediated shifts each type when exposed early prolonged stresses recovery stress. During water-limited conditions, flavonoids phenolic metabolites were exclusively accumulated palisade cells. cells mainly sugars fatty acids during respectively, highlighting functional divergence response By comparing our MALDI-MSI data gas chromatography-mass (GC-MS)-based profile, a few including monosaccharides, hexose phosphates, palmitic acid that showed similar accumulation trend both Overall, this work highlights potential MSI approach complement tissue-based metabolomics techniques provides novel understanding This will help engineer specific pathways cellular level strategic perennial trees like poplars withstand future aberrations environmental conditions increase bioenergy sustainability.
Язык: Английский
Процитировано
4
Genomics Proteomics & Bioinformatics, Год журнала: 2024, Номер 22(2)
Опубликована: Март 15, 2024
Abstract Plants possess diverse cell types and intricate regulatory mechanisms to adapt the ever-changing environment of nature. Various strategies have been employed study their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs address biological concerns. In recent years, technologies in transcriptomics, epigenomics, proteomics, metabolomics, spatial transcriptomics increasingly used plant science reveal relationships at level. However, application plants is more limited due challenges posed by structure. This review outlines advancements omics technologies, implications systems, future research applications, systems.
Язык: Английский
Процитировано
4
Nature Communications, Год журнала: 2024, Номер 15(1)
Опубликована: Окт. 1, 2024
Язык: Английский
Процитировано
4
Horticulture Research, Год журнала: 2025, Номер 12(4)
Опубликована: Янв. 3, 2025
Abstract The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by accumulation viruses. Herein, we describe a single-cell transcriptomic atlas cloves with virus accumulation, comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells two clusters, clusters 7 (C7) and (C11), were inferred to be from meristem. Cell trajectory analysis suggested differentiation clove start meristem cells, along pseudo-time paths. Investigation into cell-specific activity invasive viruses demonstrated that genes showed relatively low-expression in There 2060 co-expressed genes, many an association defense response. Five glutathione synthase/reductase displayed up-regulated expression, related metabolites level alteration virus-invasive clove, implying role viral immunity garlic. Our study offers valuable insights organogenesis interaction between at resolution.
Язык: Английский
Процитировано
0
Microbiological Research, Год журнала: 2025, Номер 293, С. 128054 - 128054
Опубликована: Янв. 7, 2025
Язык: Английский
Процитировано
0