A glossary of plant cell structures: Current insights and future questions

Abstract

In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Figure 1

The nucleus and its constituents. A, A fluorescence micrograph of a nucleus in a N. benthamiana epidermal cell. The NE-localized CPR5 protein (pseudo-colored in green) was coexpressed with the nucleoplasmic-localized cyclin kinase inhibitor structure illumination microscopy (SIM) (pseudo-colored in magenta). B, An electron micrograph of a nucleus in an Arabidopsis root cell. Arrowheads indicate the ONM and the INM of the NE. C, An electron micrograph showing a tangential section through the NE in an Arabidopsis root cell. Arrowheads indicate nuclear pores distributed at the surface of the NE. Scale bars are 10 μm in (A) and 500 nm in (B) and (C). D, The nucleus is defined by the double-layered NE composed of the ONM and the INM, which join at the nuclear pore membrane. The NE hosts a specific population of proteins. SUN and KASH proteins comprise the LINC complex and function in various aspects of plant cell biology and physiology, as discussed in the main text. CPR5, PNET1, GP210, and NDC1 are structural components of the plant NPC membrane ring. CNGC15, DMI1, and MCA8 regulate nuclear calcium transport and signaling and affect symbiotic interaction with arbuscular mycorrhiza. GCP3 and GIP proteins are part of the microtubule nucleation complex and regulate nuclear stiffness. CRWN and KAKU4 proteins assemble the plant nuclear skeleton and also function as a platform to interact with INM proteins and regulate chromatin organization by binding to chromatin-associating proteins (such as the PRC2 complex). NEAP proteins bind to the transcription factor bZIP18 and may also influence chromatin organization. The CDC48–UFD1–NPL4 trimeric complex and PUX3/4/5 proteins mediate plant INM-associated protein degradation. The nuclear interior is organized heterogeneously. Heterochromatic regions and chromocenters are typically located near the nuclear periphery and the nucleolus. Other multivalent biomolecules (e.g. proteins and RNAs) aggregate to form various types of membrane-less condensates via the liquid–liquid phase separation mechanism.

Figure 2

The plant ER forms a distinctive network of membranes at the cell cortex. Left: Confocal microscopy image of a N. benthamiana leaf epidermal cell transiently expressing the fluorescent lumenal marker ER-mCherry (Nelson et al., 2007), which labels the lumen of the bulk ER network. Scale bar = 40 mm. Right: magnified view of the boxed region in the left part highlighting some of the characteristic ER structures discussed in the main text.

Figure 3

Plant Golgi stacks. A, Transmission electron micrograph showing a cluster of Golgi stacks in an Arabidopsis root tip cell. Plastids (P), mitochondria (M), and vacuoles (V) are marked. B, Confocal laser scanning micrograph of Arabidopsis root tip cells expressing a Golgi-localized green fluorescent protein. The PM was counterstained. C, ET slice image of a Golgi stack. The cis-side, trans-side, and TGN are labeled. D, ET model of an Arabidopsis Golgi stack associated with the ER. The entire Golgi and TGN are encompassed by a ribosome–ribosome excluding matrix (Golgi matrix). E, ET slice image of a Golgi stack in a root cap border cell. F, ET model of the Golgi in E. Swollen cisternal margins containing mucilage are marked with arrowheads in (E) and (F). Scale bars in (A), (B), (D), (E), and (F): 500 nm. Scale bar in (C): 10 μm.

Figure 4

Plant endosomes. A, Diagram of plant endosomes and the major associated pathways, highlighting the effects on MVE mis-sorting in ESCRT mutants. B, Tomographic reconstructions of a Golgi stack, GA-TGN, and free/ GI-TGN in an Arabidopsis embryo cells. C and D, Confocal images of MVE-localized RabF2a/RHA1-GFP (C) and TGN-localized VHAa1-GFP (D) in Arabidopsis root cells. Scale bar = 200 nm in (B) and 5 mm in (C) and (D).

Figure 5

The multifunctional roles of the plant vacuole. A, There are various trafficking routes toward the vacuole, including pathways from the PVC, TGN, Golgi, ER, and autophagosomes. The vacuole carries out numerous indispensable functions as indicated. B, Confocal-based 3D reconstruction of the cell (in purple, based on CW staining with propidium iodide) and the vacuole (in green, based on BCECF-AM staining) visualizes the vacuolar occupancy of meristematic (left) and elongating cells (right). Scale bars: 6 µm.

Figure 6

Spatial association of LDs with the ER and a model of LD biogenesis. A, Enhanced-resolution fluorescence imaging of the relationship of the ER to LDs in leaf mesophyll cells of N. benthamiana infiltrated with an ER marker and stained with the LD-specific fluorescent dye BODIPY 493/503. The ER network was marked in cyan with the ER-lumen marker protein Kar2-CFP-HDEL, and LDs are false-colored in yellow (white arrows). In leaves, small LDs are normally associated with the ER (top row). In this system, LDs were induced to proliferate by expressing lipogenic factors to study LD proteins and their roles in LD formation (second row). Here this process is illustrated by expressing LEAFY COTYLEDON2 in these leaves; this transcription factor is preferentially expressed in developing seeds and promotes storage lipid synthesis and LD formation. Under semi-normal conditions, the LD phenotype of tobacco shows few small LDs intimately connected to the ER. Scale bars: 5 µm. B, TEM micrographs showing LDs (labeled as OB for oil body) emerging from the ER in cells of developing soybean (Glycine max) cotyledons. Left to right freeze-fracture; cryofixation; chemical fixation. Arrows mark ER–LD junctions. For scale, ribosomes on the ER membrane are approximately 20 nm in diameter. Electron micrographs are courtesy of Dr Eliot Herman, University of Arizona. C, Diagram illustrating the current, general model for LD biogenesis. Initial LD formation begins with the coalescence of the “lipid lens” within the ER bilayer. Various LD-associated proteins such as SEIPINs, LDIP, LDAPs, VAP27-1, oleosins (in seeds), and LDIP are recruited, which together facilitate the formation and stabilization of the nascent LD as it emerges into the cytoplasm. Adapted in part from a model presented and described in Greer et al. (2020).

Figure 7

Microscopic images of peroxisomal structures in Arabidopsis cells. A, Microscopic image of 4-day-old Arabidopsis cotyledons expressing mNeonGreen with a membrane peroxisomal targeting signal (mNeonGree-mPTSPEX26; green) and mRuby with a matrix-bound peroxisomal targeting signal (mRuby3-PTS1; magenta) showing the presence of ILVs in peroxisomes. The close-up image highlights the variable sizes of the vesicles. B, Separate images of fluorescent molecules in the membrane (green) and matrix (magenta) highlight the different substructures within the peroxisome, including ILVs with (yellow arrowheads) or without (blue arrowheads) matrix proteins and a separate area with denser membrane accumulation. Images in (A) and (B) are Figures 1, G and , A from Wright and Bartel (2020; reprinted with permission). C, ET slice image of a young root cell highlighting the interactions between a peroxisome (P), LDs (asterisks), and other organelles. Scale bar: 500 nm.

Figure 8

Microscopy imaging of plant mitochondrial dynamics. A, An apparent mitochondrial outer-membrane-derived vesicle (MDV) (arrow) in an Arabidopsis cell. On the right is a mitochondrion whose outer membrane was stained with ELM1-GFP and whose matrix was stained with RFP. The MDV contains only the outer membranes and no matrix (Yamashita et al., 2016, reprinted with permission). B, Heterogeneity of DNA contents in mitochondria. The mitochondria were stained red with MitoTracker Red and DNA was stained with SYBR Green I. Green signals in red regions are shown in yellow. Therefore, red particles with yellow dots represent mitochondria containing DNA, and red mitochondria without yellow dots represent mitochondria lacking DNA (Arimura et al., 2004a, , reprinted with permission). C, Fusion of mitochondria in an onion bulb epidermal cell. The cell contains thousands of mitochondria. The mitochondria on the left and right sides of the cell were labeled green and red, respectively, by the (irreversibly) color-changing fluorescent protein Kaede. The photographs show the movement and mixing of the mitochondria after 10 min (upper), 1 h (middle), and 2 h (bottom). Yellow mitochondria are the result of fusion between green and red mitochondria (Arimura et al., 2004a, , reprinted with permission). D, Five consecutive frames showing mitochondria fission in a tobacco BY-2 cell. The mitochondria were stained with MitoTracker Red and dynamin-related protein 3A was labeled with GFP (Arimura, 2018, reprinted with permission). E, Progression of mitophagy in an Arabidopsis cell, in which the mitochondria were stained with MitoTracker Red and autophagosomes were visualized by expression of YFP-ATG8e. The autophagosome on the right (arrowhead) is shown engulfing a mitochondrion over a 300-s interval (Ma et al., 2021, reprinted with permission). F, ET image of a mitochondrion in an Arabidopsis root meristematic cell. Black dots in the cytosol and mitochondrial matrix are ribosomes. Scale bars. (A), (D), and €, 2 μm; (B) 1 μm; (C) 40 μm; (F) 500 nm.

Figure 9

Chloroplast morphogenesis is a highly regulated process. A, ET slice image of a normal-sized wild-type (WT) chloroplast with typical thylakoid differentiation into stacked (grana) and unstacked domains. B, 3D model based on the chloroplast in (A). Green represents thylakoid membranes, blue represents starch grains. C, ET slice image of an oversized chloroplast (compare scale bars) with aberrant thylakoid membrane organization in an Arabidopsis flz mutant (Liang et al., 2018b). FLZ is a dynamin-like protein, and thylakoid fusion is inhibited in the mutant (Gao et al., 2006; Findinier et al., 2019). Instead of a stroma-wide network, thylakoids form discrete spirals in the mutant. D, 3D model based on the chloroplast in (C). Scale bars = 500 nm.

Figure 10

Examples of membrane contact sites in plants. A-B, ET slice images showing different MCS present in plant cells; an ER-PM contact site (A) and an ER-mitochondrion contact site (B) are shown. Arrowheads mark plasmodesmata. CW: cell wall, M: mitochondrion. Scale bars = 500 nm. C-D, The distribution of SYT1-GFP- and VAP27-1-YFP-labelled tethering assemblies in different regions of the cortical ER (indicated by the RFP-HDEL or GFP-HDEL markers) highlights the presence of spatially separated ER-PM MCS within the cell. E, The co-expression of the actin-associated NET3C cytoskeletal adaptor, the microtubule-associated IQ67-domain 2 (IQD2) bridging component, and the VAP27-1 tether highlights the interaction of the Arabidopsis ER-PM MCS with the cortical cytoskeleton. Scale bars in (C-E) = 10 μM. F, The appearance of putative SYT1-GFP labelled ER-PM contact sites changes depending on the microscopy technique used. The intermembrane distances at MCS are below the light diffraction limit and are not properly resolved using conventional confocal microscopy (Laser Scanning/Spinning Disc, left two panels). More accurate visualizations are obtained using super-resolution techniques (TIRF/SIM, right two panels). Scale bar in (F) = 20 μM. G, Advances in electron tomography techniques are enabling accurate 3D reconstructions of PD MCS. In the current functional models, the cytosolic space between the ER and the PM inside the PD serves as a trafficking conduit for mobile molecules, and the adjustment of its width is believed to regulate their flow rate, effectively controlling inter-cellular trafficking. Dark blue: Plasma Membrane. Light Blue: Cortical ER across the PD pore. (Panel E is from Zang et al. 2021, reprinted with permission.)

Figure 11

Structural diversity in PD and their constituents. A, A cartoon depiction of a simple plasmodesma showing details of the PM, lipid composition, and select protein constituents as described in the text. B, Cartoons depicting some PD morphologies. (1) is a branched PD with a “Y” shape, (2) represents a simple pore with constrictions near the openings (necks) and dilation of the central region of the DT, (3) is a funnel plasmodesma. A and B were drawn with BioRender. C and D, Structure of branched PD in Arabidopsis leaf tissue revealed by ET. C, Four representative individual frames from a tomogram (1/4–4/4). While the PM is readily visible in these images, the DT is difficult to discern. Central cavities are found in the vicinity of the middle lamella. D, 3D model of PD generated by tracing the inner (yellow) and outer (blue) leaflets of the PM in the tomogram in (C). The PD on the left consists of two pores in Cell 2 and one in Cell 1. The PD on the left has two openings to Cell 2 but three to Cell 1. Ribosomes (red) are shown for scale. C and D were generated in the author’s lab.

Figure 12

Micrograph and model of the plant CW, showing wall patterning at the tissue and nanometer scales. A, Cellulose labeled with Pontamine Fast Scarlet 4B (S4B, magenta) and newly synthesized pectin labeled with fucose-alkyne and Alexa488-azide (green) in epidermal cells of the root differentiation zone in a 5-day-old Arabidopsis seedling. Note oblique, punctate labeling of the Alexa488 signal, predominantly longitudinal labeling of the S4B signal, and variation in intensity of the Alexa488 signal between different cells. Bar = 10 µm. B, Model of CW assembly viewed from outside the PM (yellow), showing Cellulose Synthase Complexes (purple) producing cellulose microfibrils (magenta) and a vesicle (orange) fusing with the PM to deliver pectin (green) and hemicellulose (cyan) to the wall. Cortical microtubules and an intracellular vesicle are shown in gray in the background. Objects are drawn approximately to scale, bar = 25 nm. Part (B) of this figure was inspired by a dynamic model of CW assembly created by Drew Berry for the Australian Research Council Center of Excellence in Plant Cell Walls and directed by Tony Bacic (University of Melbourne), Monika Doblin (University of Melbourne), and Mike Gidley (University of Queensland), which can be viewed on YouTube (https://youtu.be/zp2WW2TYcng).