Distinct identities of leaf phloem cells revealed by single cell transcriptomics

The Plant Cell, Год журнала: 2021, Номер 33(3), С. 511 - 530

Опубликована: Янв. 1, 2021

The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles transport, metabolism, and signaling. Little is known about vascular cells, particular the phloem parenchyma (PP). PP effluxes sucrose into apoplasm as basis for loading, yet has been characterized only microscopically. Here, we enriched cells from Arabidopsis leaves to generate single-cell transcriptome atlas vasculature. We identified 19 clusters, encompassing epidermis, guard hydathodes, mesophyll, all used metabolic pathway analysis define their roles. Clusters comprising were transporters, including SWEET11 SWEET12 UmamiT amino acid efflux carriers. provide evidence that development occurs independently ALTERED PHLOEM DEVELOPMENT, transcription factor required differentiation. have unique pattern metabolism activity companion (CCs), explaining differential distribution/metabolism acids veins. kinship relation clusters strikingly similar vein morphology, except clear separation CC other PP. In summary, our RNA-sequencing provides wide range information relationship types.

Язык: Английский

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A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

Developmental Cell, Год журнала: 2022, Номер 57(4), С. 543 - 560.e9

Опубликована: Фев. 1, 2022

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal signatures underlying developmental trajectories. To map gene expression dynamics across root cell types time, we built a comprehensive, organ-scale atlas at single-cell resolution. addition to estimating progressions in pseudotime, employed mathematical concept of optimal transport infer trajectories identify their regulators. demonstrate utility interpret new datasets, profiled mutants two key regulators resolution, shortroot scarecrow. We report transcriptomic vivo evidence tissue trans-differentiation mixed identity phenotype Our results support as rich community resource unraveling programs that specify maintain regulate

Язык: Английский

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A single-cell analysis of the Arabidopsis vegetative shoot apex

Developmental Cell, Год журнала: 2021, Номер 56(7), С. 1056 - 1074.e8

Опубликована: Март 18, 2021

Язык: Английский

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Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

Molecular Plant, Год журнала: 2020, Номер 14(1), С. 115 - 126

Опубликована: Ноя. 2, 2020

Язык: Английский

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Plant Metabolic Network 15: A resource of genome‐wide metabolism databases for 126 plants and algae

Journal of Integrative Plant Biology, Год журнала: 2021, Номер 63(11), С. 1888 - 1905

Опубликована: Авг. 17, 2021

To understand and engineer plant metabolism, we need a comprehensive accurate annotation of all metabolic information across species. As step towards this goal, generated genome-scale pathway databases 126 algal genomes, ranging from model organisms to crops medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality databases, which revealed that our semi-automated validation pipeline dramatically improves quality. then compared content using multiple correspondence analysis found Brassicaceae, Poaceae, Chlorophyta appeared as metabolically distinct groups. demonstrate utility resource, used recently published sorghum transcriptomics data discover previously unreported trends metabolism underlying drought tolerance. also single-cell Arabidopsis root infer cell type-specific pathways. This work shows quantity resource demonstrates its wide-ranging in integrating with other areas biology.

Язык: Английский

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Advances and Opportunities in Single-Cell Transcriptomics for Plant Research

Annual Review of Plant Biology, Год журнала: 2021, Номер 72(1), С. 847 - 866

Опубликована: Март 17, 2021

Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of analyses to level individual cell. The field plant biology has fully embraced single-cell transcriptomics and is rapidly expanding portfolio available technologies applications. In this review, we give an overview main advances in over past few years provide reader with accessible guideline covering all steps, from sample preparation data analysis. We end offering a glimpse how these will shape accelerate plant-specific research near future.

Язык: Английский

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Single-cell transcriptome atlas of the leaf and root of rice seedlings

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2021, Номер 48(10), С. 881 - 898

Опубликована: Июнь 18, 2021

As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses environmental stimuli. In this study, we apply single-cell RNA sequencing both shoot and root seedlings growing in Kimura B nutrient solution or exposed abiotic stresses characterize transcriptomes for total 237,431 individual cells. We identify 15 9 cell types the leaf root, respectively, observe that common often shared between leaves roots same tissue layer, except endodermis epidermis. Abiotic stress stimuli alter largely type-specific manner, but given type, different trigger regulation roughly set genes. Besides, detect proportional changes populations response investigate underlying molecular mechanisms through reconstruction developmental trajectory. Collectively, our study represents benchmark-setting data resource atlas an illustration exploiting such resources drive discoveries plant biology.

Язык: Английский

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Transport mechanisms of plant hormones

Current Opinion in Plant Biology, Год журнала: 2021, Номер 63, С. 102055 - 102055

Опубликована: Июнь 5, 2021

Язык: Английский

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Nutrient–hormone relations: Driving root plasticity in plants

Molecular Plant, Год журнала: 2021, Номер 15(1), С. 86 - 103

Опубликована: Дек. 16, 2021

Optimal plant development requires root uptake of 14 essential mineral elements from the soil. Since bioavailability these nutrients underlies large variation in space and time, plants must dynamically adjust their architecture to optimize nutrient access acquisition. The information on external availability whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates trigger a systemic or locally restricted developmental response. Timing extent such local responses depend overall nutritional status transmitted shoots roots form other long-distance signals. integration then determines cell division elongation rates primary lateral roots, initiation, emergence, well formation hairs. Here, we review cascades nutrient-related sensing signaling events hormones highlight nutrient–hormone relations coordinate plasticity plants.

Язык: Английский

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How roots and shoots communicate through stressful times

Trends in Plant Science, Год журнала: 2021, Номер 26(9), С. 940 - 952

Опубликована: Апрель 22, 2021

Limitations in water uptake roots and sucrose supply from shoots under abiotic stress can be encoded into signals that regulate the growth development of distant tissues.Root-localized trigger changes xylem hydraulics, mobile peptides, reactive oxygen species (ROS), Ca2+, which lead to remote effects induce shoot stomatal closure.The mobility HY5 protein its downstream targets via phloem conveys shoot-sensed light temperature information affect both primary lateral root growth.Shoot-derived loading/unloading is highly responsive environmental changes, triggers signaling pathways development.Developmental plasticity vasculature response stresses key importance for long-distance transport substances assist plant resilience. When plants face an such as deficit, soil salinity, high temperature, or shade, good communication between above- belowground organs necessary coordinate development. Various including hormones, proteins, hydraulic signals, metabolites are transported mostly through tissues. How synchronize their using emerging field research. We summarize recent advances on regulating movement localized cues. In addition, we highlight how vascular system not only a conduit but also flexible stress. Tissues higher specialized. The captures solar energy by photosynthesis carries out reproduction, whereas extracts minerals soil. coordination these specialized functions critical thrive. system, comprising (see Glossary), supports body while transporting many molecules vice versa. Hormones well-studied integrators Abscisic acid (ABA) [1.Kuromori T. et al.ABA responses.Trends Plant Sci. 2018; 23: 513-522Abstract Full Text PDF PubMed Scopus (130) Google Scholar], auxin [2.Korver R.A. al.Out shape during stress: role auxin.Trends 783-793Abstract (50) gibberellins [3.Camut L. al.Root-derived GA12 contributes temperature-induced Arabidopsis.Nat. Plants. 2019; 5: 1216-1221Crossref (8) cytokinins (CKs) [4.Daviere J.M. Achard P. Organ communication: move.Nat. 2017; 3: 17116Crossref (7) jasmonic relatives [5.Schulze A. al.Wound-induced shoot-to-root relocation JA-Ile precursors coordinates Arabidopsis growth.Mol. Plant. 12: 1383-1394Abstract (0) Scholar] known travel act tissues (Figure 1, Key figure). More recently, several small RNA have been found nutrient distal responses [6.Fan H. al.Phloem sap proteome studied iTRAQ provides integrated insight salinity mechanisms cucumber plants.J. Proteom. 2015; 125: 54-67Crossref (25) Scholar, 7.Ko D. Helariutta Y. Shoot–root flowering plants.Curr. Biol. 27: R973-R978Abstract 8.Thieme C.J. al.Endogenous messenger RNAs tissues.Nat. 1: 15025Crossref 9.Takahashi F. al.A peptide modulates control abscisic signalling.Nature. 556: 235-238Crossref (164) 10.Ota R. al.Shoot-to-root CEPD-like 2 integrates nitrogen status systemically nitrate Commun. 2020; 11: 641Crossref 1). Localized require controlled elicit acclimation at whole-plant level [11.Choi W.G. al.Salt stress-induced Ca2+ waves associated with rapid, root-to-shoot plants.Proc. Natl. Acad. U. S. 2014; 111: 6497-6502Crossref (318) Scholar,12.Devireddy A.R. al.Coordinating overall plants: Rapid leaf-to-leaf stress.Sci. Signal. 11eaam9514Crossref (67) Scholar]. Understanding activate stress-responsive local developmental reprogrammed important aspect tolerance. mediates has recently reviewed [7.Ko this review focus developments different movements water-related stresses, changes. Furthermore, central transportation path allows over long distances times Water limitation profound impact [13.Aroca drought From morphological molecular features. Springer-Verlag, Berlin Heidelberg2012Crossref (58) absorbed moves radially apoplastic pathway cell-to-cell transcellular symplastic pathway. Subsequently, axially along towards following potential gradient, generally lowest present leaves [14.Christmann al.Hydraulic signaling.Curr. Opin. 2013; 16: 293-300Crossref (91) Scholar,15.Christmann signal signalling shortage.Plant J. 2007; 52: 167-174Crossref (369) turgor pressure leaf cells rapidly declines when experience shortage, causing drop potential, propagated [15.Christmann Root were able ABA near bundles well accumulation closure indicating correlated signaling. However, rapid observed biosynthesis mutants aba2 abi1-1, respectively, may ABA-independent So far, it unclear perceived subsequently linked signaling, although putative sensing postulated Reduced availability surroundings, caused salt osmotic stress, shown reduce conductivity (Lpr) – ability across gradient [16.Tang N. al.Natural variation XND1 impacts hydraulics trade-off 9: 3884Crossref (17) 17.Thompson A.J. al.Overproduction tomato increases transpiration efficiency influences expansion.Plant Physiol. 143: 1905-1917Crossref 18.Vitali V. al.Root adjustments conductance: strategy halotolerant species.AoB 7plv136Crossref 19.Kaneko al.Dynamic regulation barley salinity/osmotic stress.Plant Cell 56: 875-882Crossref (14) Under water-limitation conditions, Lpr rice (Oryza sativum) arabidopsis (Arabidopsis thaliana) was positively dry weight, suggesting increase could improve performance Scholar,20.Matsuo al.Genotypic differences conductance sativa L.) regimes.Plant Soil. 2009; 316: 25-34Crossref (45) Recently, XYLEM NAC DOMAIN 1 (XND1) transcription factor identified negative regulator Loss function increased fresh weight weight. Conversely, overexpression reduced negatively regulated tolerance Aquaporins classic channels gate radial transcellularly therefore [21.Postaire O. PIP1 aquaporin hydrostatic pressure-induced rosette Arabidopsis.Plant 2010; 152: 1418-1430Crossref (163) Scholar,22.Javot al.Role single isoform uptake.Plant Cell. 2003; 15: 509-522Crossref (265) Silencing PLASMA MEMBRANE INTRINSIC PROTEIN (PIP) aquaporins application blockers significantly Lpr, PIP-type resulted Scholar,21.Postaire Scholar,23.Katsuhara M. al.Over-expression shoot/root ratio raised sensitivity transgenic plants.Cell 44: 1378-1383Crossref (138) Scholar,24.Siefritz al.PIP1 plasma membrane tobacco: cellular plants.Plant 2002; 14: 869-876Crossref (269) always accompanied consistent transcriptional aquaporins, there additional levels aquaporin-mediated post-transcriptional trafficking [25.Horie al.Mechanisms mediated PIP phosphorylation events roots.Plant 2011; 663-675Crossref 26.Prak al.Multiple phosphorylations C-terminal tail aquaporins: subcellular AtPIP2;1 stress.Mol. Proteomics. 2008; 7: 1019-1030Abstract (175) 27.Boursiac al.Early roots. Molecular features expression.Plant 2005; 139: 790-805Crossref (391) 28.Suga al.Aquaporin isoforms phytohormones radish seedlings.Plant 43: 1229-1237Crossref (119) 29.Boursiac al.Stimulus-induced downregulation involves species-activated cell intrinsic internalization.Plant 207-218Crossref (166) reduction commonly hypoxia chilling Raf-like MAP kinase gene HYDRAULIC CONDUCTIVITY OF ROOT (HCR1) modulate quantitative trait locus mapping approach [30.Shahzad Z. potassium-dependent regulates hydraulics.Cell. 2016; 167: 87-98Abstract (42) HCR1 reduces K+-replete O2-deficient (referred hypoxia) conditions upregulation abundance RELATED TO AP2.12, mediating Consistent positive connection growth, less content hcr1 than wild-type (WT) exposed hypoxia, A chilling-tolerant variety restore faster sensitive challenged cold [31.Yu X. al.Water relations expression analysis proteins tolerant recovery.Cell Res. 2006; 599-608Crossref (83) attributed recovery stage. Taken together, obstruction adaptations, often modulation, conditions. once considered candidate hormone travels closure. This assumption supported fact accumulates deficit occurs 1A) Elegant grafting experiments WT aba2-1 (ABA-deficient) showed impaired did By contrast, grafts unable close stomata shoot-derived sufficient Recent studies water-stress interacting other root-derived signals. CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 25 (CLE25) ABA-dependent manner [9.Takahashi cle25 mutant grafted onto (cle25/WT), still induced NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) dehydrated WT/cle25 no longer NCED3 shoots. CLE25 two receptor-like kinases BARELY ANY MERISTEM (BAM1 3). Local loss BAM1 BAM3 abolished CLE25. Notably, rate already within h dehydration differ time These results imply together addition ABA, Both (ROS) work closely guard [33.Medeiros D.B. al.Eating away ROS opening.Trends 25: 220-223Abstract Beyond action closure, RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) elicits heat [12.Devireddy Scholar,34.Zandalinas S.I. al.Vascular mediate systemic 32: 3425-3435Crossref Scholar,35.Zandalinas al.Systemic combination 117: 13810-13820Crossref prevented either blocking response. Salt transient cytosolic ([Ca2+]i) influx roots, induces subsequent wave release progresses cortex endodermis layers MONOCATION-INDUCED [Ca2+]i INCREASES (MOCA1) REDUCED HYPEROSMOLALITY-INDUCED INCREASE1 (OSCA1) sensors ionic respectively [36.Yuan al.OSCA1 osmotic-stress-evoked vital osmosensing Arabidopsis.Nature. 514: 367-371Crossref Scholar,37.Jiang al.Plant cell-surface GIPC sphingolipids sense influx.Nature. 572: 341-346Crossref required elevation stress-specific manner. -activated slow vacuolar (SV) channel TWO-PORE CHANNEL 1(TPC1) salt-evoked induction genes Interestingly, propagation slowed down ROS-defective atrbohD mutants, line modeling showing TPC1-mediated alone insufficient explain velocity transmission, model ROS-triggered elements quantitatively [38.Evans M.J. ROS-assisted calcium dependent AtRBOHD NADPH oxidase TPC1 cation propagates 171: 1771-1784Crossref (113) HYDROGEN PEROXIDE-INDUCED (HPCA1), membrane-localized leucine-rich repeat (LRR-RLK), sensor extracellular (eH2O2) [39.Wu al.Hydrogen peroxide HPCA1 LRR receptor 578: 577-581Crossref (81) Because broadly expressed throughout plant, detect burst neighboring produced RBOHD, resulting progress 1B) Scholar,38.Evans Scholar,39.Wu cells, eH2O2, likely activation Ca2+-permeable membrane, leads LRR-RLK, GUARD CELL PEROXIDE-RESISTANT (GHR1), interact Ca2+-dependent (CPK) anion leading eH2O2 [40.Sierla al.The pseudokinase GHR1 closure.Plant 30: 2813-2837Crossref (35) Given eH2O2-assisted directly sulfate poplar maize (Zea mays) [41.Malcheska al.Drought-enhanced closes affecting ALMT12 synthesis.Plant 174: 798-814Crossref (36) Scholar,42.Ernst al.Sulphate xylem-borne chemical precedes biosynthetic roots.J. Exp. Bot. 61: 3395-3405Crossref 1C). Sulfate detached led promoted leaves, 42.Ernst 43.Batool al.Sulfate incorporated cysteine production 2973-2987Crossref (27) It possible acts direct evidence intact lacking. Light extreme temperatures detrimental plants, development, circadian rhythms. To activities crucial transduce ELONGATED HYPOCOTYL 5 (HY5) component photoperception photomorphogenesis [44.Gangappa S.N. Botto J.F. multifaceted roles development.Mol. 1353-1365Abstract (169) Phytochrome B (phyB) promote [45.Legris al.Phytochrome Arabidopsis.Science. 354: 897-900Crossref 46.Jung J.-H. al.Phytochromes thermosensors 886-889Crossref 47.Osterlund M.T. al.Targeted destabilization light-regulated 2000; 405: 462-466Crossref (867) shoot-accumulated HY5–GFP translocate light-promoted elongation 2A ) [48.Chen carbon acquisition.Curr. 26: 640-646Abstract (192) light, activates upregulates (N) transporter NRT2.1 N promotes sugar export promoting SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS (SWEET) 11 12. metabolism distribution cues Scholar,49.Chen L.Q. al.Sucrose efflux SWEET step transport.Science. 2012; 335: 207-211Crossref (597) During shade-avoidance response, far-red (FR) detected HY5–YFP primordia, represses outgrowth inhibiting transporters PIN-FORMED (PIN3) LIKE-AUXIN TRANSPORTER1 (LAX3) downregulating ARF19 2A) [50.van Gelderen K. al.Far-red detection factor.Plant 101-116Crossref (63)

Язык: Английский

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