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Distinct mechanisms orchestrate the contra-polarity of IRK and KOIN, two LRR-receptor-kinases controlling root cell division

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Cell polarity Plant polarity Root apical meristem

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Nature Communications

volume 13 , Article number: 235 ( 2022 )
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In plants, cell polarity plays key roles in coordinating developmental processes. Despite the characterization of several polarly localized plasma membrane proteins, the mechanisms connecting protein dynamics with cellular functions often remain unclear. Here, we introduce a polarized receptor, KOIN, that restricts cell divisions in the Arabidopsis root meristem. In the endodermis, KOIN polarity is opposite to IRK, a receptor that represses endodermal cell divisions. Their contra-polar localization facilitates dissection of polarity mechanisms and the links between polarity and function. We find that IRK and KOIN are recognized, sorted, and secreted through distinct pathways. IRK extracellular domains determine its polarity and partially rescue the mutant phenotype, whereas KOIN’s extracellular domains are insufficient for polar sorting and function. Endodermal expression of an IRK/KOIN chimera generates non-cell-autonomous misregulation of root cell divisions that impacts patterning. Altogether, we reveal two contrasting mechanisms determining these receptors’ polarity and link their polarity to cell divisions in root tissue patterning.
Asymmetric protein distribution along different plasma membrane (PM) domains can be guided by external cues from adjacent or distal cells and may define polar axes of a tissue or organ. This coordinated polarity facilitates oriented cell division, developmental patterning, cell growth, long-range signal transduction, and the transport of ions and other molecules 1 . Intrinsic cellular machinery generates polar protein distribution, but the process remains poorly understood 2 , 3 . However, research has been greatly aided by examining PM proteins with contrasting polar distribution 1 .
A well-studied example of proteins with asymmetric distribution at the PM is the PIN-FORMED (PIN) family of auxin efflux carriers that drive directional auxin flow, which is essential for root growth and development. When expressed under their endogenous promoters, PIN1 and PIN2 exhibit contrasting polar distribution. PIN1 accumulates at the rootward PM domain in vascular and endodermal cells, while PIN2 is located at the shootward domain in epidermal and cortex cells. PIN1 polar distribution changes in different cell types indicating cell type-specific localization mechanisms 4 . PIN2 rootward localization in cortex cells near the stem cell niche becomes shootward as cells mature, indicating its polarity is associated with developmental context 4 . PIN polarity is established after cytokinesis through distinct trafficking routes for shootward/rootward localization 4 , 5 , 6 , 7 . Once established, maintenance of PIN polarity occurs by hyper-polar secretion, endocytosis and recycling, restriction of lateral diffusion, and protein phosphorylation 8 . However, the sorting signals and regulatory mechanisms targeting these proteins in different cell types and developmental contexts are still being investigated.
Another well-studied, contrasting protein duo is the laterally localized boric acid channel NODULIN INTRINSIC PROTEIN 5;1 (NIP5;1) and the boric acid/borate exporter REQUIRES HIGH BORON 1 (BOR1) 9 . Contra-polar localization of BOR1 at the inner PM domain toward the stele and NIP5;1 at the outer domain away from the stele, is proposed to be determined by cues originating from the stele 10 . This polar distribution is maintained in different tissues indicating an organ-level, stele-oriented polar axis enabling directional boron transport. Under boron limiting conditions, BOR1 and NIP5;1 polar distribution in epidermal and cortical cells is regulated by targeted secretion of newly synthesized proteins, constant endocytosis and recycling, cytoskeleton components, and control of lateral diffusion 3 , 9 , 11 , 12 , 13 , 14 . However, in endodermal cells, once BOR1 and NIP5;1 are polarly secreted, maintenance of lateral polarity is independent of the actin or microtubule cytoskeleton 10 . Additionally, the polarity of NIP5;1, but not BOR1, depends on phosphoinsitol synthesis 10 . This suggests differential mechanisms for protein accumulation to the inner or outer PM domains in endodermal cells, yet these underlying mechanisms remain poorly understood.
The leucine-rich repeat receptor-like kinase (LRR-RLK) INFLORESCENCE AND ROOT APICES RECEPTOR KINASE (IRK) exhibits polar accumulation to distinct PM domains in different cell types 15 . It localizes to the outer PM domain in the endodermis and pericycle and the inner domain in epidermal and cortical cells, with its polar distribution informed locally by adjacent cells. IRK is downstream of SHORT ROOT (SHR) transcriptional regulation and SHR together with the transcription factor SCARECROW (SCR) control expression of a D-type cyclin, CYCD6;1 , restricting it to the cortex/endodermal initial (CEI) and the CEI daughter (CEID) leading to formative cell divisions that eventually generate endodermal and cortical cells. Strict regulation of gene expression in these cell types prevents the formation of additional ground tissue (GT) layers and maintains radial patterning 16 , 17 , 18 , 19 , 20 . CYCD6;1 promoter activity is altered in irk endodermal cells, which exhibit excess periclinal and longitudinal anticlinal cell divisions (LADs), leading to radial enlargement of the root. These phenotypes are rescued by endodermal IRK expression suggesting its polar distribution is functionally linked to repression of cell division in these cells upon a perception of extracellular cues 15 . However, the mechanistic basis for the establishment and maintenance of IRK polarity remains unknown.
Here, we introduce another LRR-RLK downstream of the SHR transcriptional network that, in contrast to IRK, is polarized to the inner PM domain regardless of cell type; therefore, we named it KINASE ON THE INSIDE (KOIN). The contrasting polarization of IRK and KOIN makes them a valuable pair to investigate the underlying mechanisms of LRR-RLK polarity. Our study reveals that polarization of IRK and KOIN relies mainly on the secretion of newly synthesized protein through distinct endomembrane trafficking routes. IRK and KOIN differentially accumulate during endodermal cell divisions, revealing targeted secretion to newly formed PMs. Using chimeric proteins and truncations, we found the protein domains necessary for IRK polar sorting are distinct from those of KOIN. Our results reveal coordination between LRR-RLK polarity and function to repress root cell division in the radial and longitudinal axes, adding to the growing body of work showing that polarized signal perception controls specific developmental events.
Analysis of genes expressed downstream of SHR activation in the GT led to the identification of IRK and another LRR–RLK we named KOIN (encoded by At5g58300), as candidate proteins involved in the regulation of GT cell divisions 15 , 20 , 21 , 22 . koin alleles have a larger root meristem with increased stele area and more numerous cells in the longitudinal axis, as measured by cortex cell number and T-junction length, phenotypes consistent with excessive cell divisions (Fig. 1a–c ; Supplementary Fig. 1 ). Although koin roots are larger than WT roots in the radial axis, we consistently observe the expected eight GT cells around the stele and no increase in overall root length (Supplementary Fig. 1f–h ). Thus, IRK and KOIN both function to repress root cell proliferation but IRK restrict GT cell number in the radial axis, while KOIN operates in the longitudinal axis.
a Confocal images of the median longitudinal sections of root tips with cells highlighted: quiescent center (QC, cyan), meristematic cortex (orange), and T-junctions (pink arrowheads). Quantification of b cortex cell number and c distance to the uppermost T-junction over time 5–7 days post-stratification (d.p.s.). Box plots show data from a single biological replicate representative of three with similar results ( n = 20 per genotype). Boxes delimit upper and lower quartiles, median values are indicated with a line, and single values are shown as dots. Bars indicate max/min values and **** statistical significance P value < 0.001 (two-way ANOVA using Turkey’s multiple comparison test). d , e Confocal images of WT root meristems at 6 d.p.s. Adjacent panels show merged images of green fluorescent protein (GFP, fluorescence intensity color scale) and stained with propidium iodide (PI, gray scale) followed by GFP alone. d Median longitudinal and e transverse sections showing accumulation of KOIN-GFP driven by KOINp . Inset in ( d ) KOIN-GFP accumulation in the CEI. f Schematics summarizing endogenously expressed IRK-GFP localization (green) and KOIN-GFP (purple). g Quantification of cortex cell number and distance to the uppermost T-junction at 7 d.p.s. in koin-1 expressing KOIN-GFP driven by KOINp or SCRp normalized to Col-0. Data from n = 20 per genotype for a single biological replicate representative of 3 with similar results. Boxes delimit upper and lower quartiles, median values are indicated with a line, and single values are sho
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