Plant Cell Nucleus

This is the primary and most obvious function. Within the nucleus, in the form of chromatin (a complex of DNA with histone proteins), nearly the entire genome of the cell is stored. Unlike prokaryotes, where DNA resides in the cytoplasm, the nuclear envelope creates a protective environment that prevents damage to the genetic material (Mauseth, 2017; Evert, 2006). In plants, the nucleus stores a significantly larger genome than in animals, often rich in repetitive sequences. At the same time, plant cells exhibit a high tolerance to polyploidy — an increase in the number of copies of the entire genome. In many agricultural crops (e.g., wheat, potato), polyploidy not only does not lead to pathology but is an evolutionarily fixed norm, often associated with larger cell sizes and increased yield (Bidlack & Jansky, 2021; von Denffer et al., 1971).

The nucleus controls the synthesis of all cellular proteins, but does so indirectly. Transcription — the synthesis of messenger RNA (mRNA) molecules on a DNA template — occurs in the nucleus. After processing (maturation, which includes the removal of non‑coding introns), these mRNA molecules are exported through nuclear pores into the cytoplasm, where translation — the assembly of the protein chain — takes place on ribosomes (Evert, 2006).

The processes of transcription and subsequent RNA processing are tightly regulated by the nucleus in response to external and internal signals. Inside the nucleus reside special proteins — transcription factors — that recognise specific DNA regions (promoters) and activate or suppress the reading of particular genes. This allows the plant to flexibly adapt the protein composition of its cells to changing environmental conditions (light, drought, pathogen attack) (Lee et al., 2024; Beck, 2010).

The nucleus is the main organiser of its own division (mitosis) and, consequently, of whole‑cell division. It is within the nucleus during interphase that precise DNA replication (duplication) occurs. During mitosis, the nucleus ensures the accurate distribution of copies of genetic material between two daughter cells. The processes of chromatin condensation into chromosomes, attachment of spindle microtubules to centromeres, and segregation of chromatids are all controlled by nuclear structures (Beck, 2010; Stern’s Introductory Plant Biology, 2021). This function has direct agronomic relevance: understanding the cell cycle allows us to manage the growth and reproduction of crop plants.

In contrast to "classical" views, the nucleus not only issues commands but also actively receives signals about the cell’s state. Under various stresses (heat shock, salinity, pathogen attack, DNA damage), signalling molecules arrive in the nucleus from the cytoplasm and other organelles (mitochondria, chloroplasts). The nucleus analyses this information and triggers the appropriate gene expression programme, leading to the synthesis of protective proteins, DNA repair, or — in the case of irreversible damage — programmed cell death (PCD) (Lee et al., 2024; Groves et al., 2025). For example, during xylem (wood) differentiation, the nucleus initiates its own death in a strictly controlled programme, which is necessary for the formation of hollow water‑conducting vessels. Here, the nucleus is not a passive observer but an active executor, organising the destruction of its own envelope and other cellular structures (Chustecki & Johnston, 2024; Abe & Numata, 2024).

Thus, the functions of the nucleus are not limited to the passive storage of the genetic "blueprint." It represents an active and dynamic system that reads, interprets, and implements genetic information while simultaneously receiving and processing feedback signals about the state of the cell and its environment. In the following sections, we will examine how the architecture of the nucleus and its molecular components allow it to perform such complex tasks.

In a typical young meristematic cell (a cell of the generative tissue), the nucleus is spherical or slightly ellipsoid and occupies a central position, often accounting for up to half of the protoplast volume. It is surrounded by dense cytoplasm rich in ribosomes and organelles (Mauseth, 2017; Evert, 2006).

As the cell matures and a large central vacuole forms, the position of the nucleus changes. Displaced by the growing vacuole, the nucleus usually shifts to the periphery, located in the parietal layer of cytoplasm pressed against the cell wall. However, it never loses connection with the central part of the cell; the nucleus is often "suspended" on cytoplasmic strands that cross the vacuole (Bidlack & Jansky, 2021; Graham et al., 2014). In some specialised cell types (e.g., sieve tube elements of the phloem), the mature nucleus may completely degrade, and the cell functions without it — a rare exception to the general rule (Evert, 2006).

Nuclear size varies depending on tissue type, ploidy, and metabolic activity. On average, the nuclear diameter ranges from 5 to 25 µm, although in giant cells of some algae (e.g., Acetabularia), the nucleus can reach tens or even hundreds of micrometres (von Denffer et al., 1971). The nuclear volume generally remains relatively constant as the cell grows, while the volume of the cytoplasm and vacuole increases, so the relative nuclear size (the "nuclear‑cytoplasmic ratio") in mature cells is significantly smaller than in young ones (Mauseth, 2017).

The plant nucleus is a complexly organised system consisting of several key structural units, each performing specific functions. Here is a brief characterisation.

Nuclear envelope (karyolemma). Separates the nucleoplasm from the cytoplasm, creating a unique environment for transcription and replication. The inner membrane serves as a scaffold for chromatin organisation and the nuclear lamina (Groves et al., 2025).

Nuclear pores (nuclear pore complexes). Provide selective bidirectional transport between the nucleus and the cytoplasm. Small molecules and ions diffuse freely through the pores; transport of large macromolecules (mRNA, ribosomal subunits, transcription factor proteins) requires energy and is carried out by specialised transport proteins (Lee et al., 2024).

Nuclear lamina (nucleoskeleton). Maintains nuclear shape, serves as a scaffold for chromatin organisation, and is an attachment point for telomeres and certain genes, participating in their regulation. It interacts with the LINC complex, linking the nucleus to the cytoskeleton (actin and microtubule filaments) (Chustecki & Johnston, 2024).

Chromatin. The repository of genetic information. The three‑dimensional organisation of chromatin within the nucleus (topologically associating domains, nuclear domains) is critically important for precise regulation of gene expression. During interphase, chromosomes are decondensed and occupy specific territories.

Nucleolus. The centre for ribosomal RNA (rRNA) synthesis and assembly of ribosomal precursors. Here, rRNA genes are transcribed, processed, and combined with ribosomal proteins imported from the cytoplasm to form the small and large ribosomal subunits (Evert, 2006).

Karyoplasm (nucleoplasm). Provides the internal environment for all nuclear processes. It serves as a solvent and transport medium for macromolecules.

All these components function not in isolation but as a single, dynamically reorganising system capable of rapidly changing its architecture in response to signals and during the cell cycle (Santos et al., 2020; Groves et al., 2025).

Although the basic structural plan of the nucleus is conserved across all eukaryotes, the plant nucleus possesses a number of distinctive features that reflect the metabolism, lifestyle, and phylogeny of plants (Table).

A crucial difference is the absence in higher plants of centrioles — organelles that in animal cells organise the microtubule‑organising centres of the division spindle. In plants, their function is taken over by the so‑called "spindle poles", whose structure is not yet fully understood, but they effectively ensure chromosome segregation (Evert, 2006; Mauseth, 2017). This difference serves as another reminder that the plant cell has evolved independently, developing a number of unique mechanisms for fundamental cellular processes.

Thus, the plant nucleus is not simply an analogue of the animal nucleus but an organelle with its own distinct characteristics, determined by the plant’s lifestyle and the specifics of its cell biology.

The nuclear envelope (synonyms: karyolemma, nuclear envelope) is a double‑membrane structure that physically separates the nuclear contents (nucleoplasm) from the cytoplasm. Its main function is to create an isolated environment for the storage and expression of genetic material and to ensure selective transport of substances (Evert, 2006; Beck, 2010).

The karyolemma consists of two parallel bilipid membranes, each about 6–8 nm thick:

Between the outer and inner membranes lies the perinuclear space (20–40 nm wide), which is continuous with the ER lumen. This space acts as a buffer zone and may participate in the transport of certain molecules (Graham et al., 2014).

This construction — the direct fusion of the outer nuclear membrane with ER membranes — is unique to eukaryotic cells and underscores the functional unity of the nuclear compartment and the endomembrane system. It provides not only a barrier function but also a degree of mechanical stability.

The nuclear envelope is not continuous; it contains specialised openings — nuclear pores — where the outer and inner membranes merge to form a through‑channel. However, these pores are not mere "holes" but elaborate protein assemblies known as nuclear pore complexes (NPCs). These are among the largest and most complex protein complexes in the eukaryotic cell, with molecular masses reaching 100–120 MDa (Evert, 2006; Beck, 2010).

Structure of the pore complex (generalised): In the central part of the channel lies a transport barrier formed by proteins with flexible, unstructured domains that create a selective filter. A ring‑like structure surrounds this channel and is anchored in the nuclear envelope. From the inner ring, a "basket" extends into the nucleoplasm, and cytoplasmic fibrils extend into the cytoplasm. These elements participate in recognising and docking transport particles (Graham et al., 2014; Stern’s Introductory Plant Biology, 2021).

Functions of nuclear pores:

The number of nuclear pores in a single cell can reach several thousand, and their density varies depending on the transcriptional activity of the cell. In cells with high RNA synthesis (e.g., meristems), the number of pores is significantly higher. Thus, the nuclear pore complex is not just an opening but a dynamic molecular gateway that strictly controls the informational and metabolic exchange between the nucleus and the cytoplasm, serving as a central regulator of gene expression (Bidlack & Jansky, 2021).

In the following sections, we will continue our exploration of the structural units of the nucleus and examine the internal components: the nuclear lamina, chromatin, nucleolus, and karyoplasm.

The inner nuclear membrane does not remain unsupported. On its nucleoplasmic side lies a protein network known as the nuclear lamina (or nucleoskeleton). In animals, it is built from lamin proteins (type V intermediate filaments) that form an ordered meshwork, giving the nucleus mechanical strength, serving as a platform for chromatin attachment, and participating in nuclear envelope assembly/disassembly during cell division (Evert, 2006; Beck, 2010).

In plants, the situation is different. Their genomes contain no direct homologues of animal lamins. However, this does not mean that plants lack a nucleoskeleton. The functional analogue of the nuclear lamina is formed by proteins of the NMCP/CRWN family (Nuclear Matrix Constituent Proteins / CROWDED NUCLEI). These proteins have long α-helical domains characteristic of filamentous proteins and are capable of forming a fibrillar network along the inner nuclear membrane (Groves et al., 2025; Evert, 2006).

In Arabidopsis thaliana, the CRWN family includes four proteins (CRWN1–CRWN4), which interact with each other and with other nuclear envelope components, including SUN proteins (part of the LINC complex) and KAKU4 (an angiosperm‑specific protein also involved in maintaining nuclear shape) (Serebryakova et al., 2006; Groves et al., 2025).

Main functions of the nuclear lamina in plants:

Thus, the plant nuclear lamina is not merely an analogue but an independently evolved structure that combines scaffolding and regulatory functions, ensuring the dynamic organisation of the nucleus.

If the nuclear envelope is the “fortress wall” and the lamina is its “internal framework”, then chromatin is the “state archive” and simultaneously the “working office” of the nucleus. It is within chromatin that genetic information is stored, replicated, and read.

Chemical composition and structure

Chromatin is a complex of deoxyribonucleic acid (DNA) with proteins, as well as a small amount of RNA. The main protein components of chromatin are histones. These are small proteins rich in basic amino acids (lysine, arginine) that form “spools” around which the DNA molecule winds. The basic unit of chromatin packaging is the nucleosome, consisting of a histone octamer (two molecules each of histones H2A, H2B, H3, and H4) with about 1.65 turns of DNA (approximately 146 base pairs) wrapped around it (Evert, 2006; Mauseth, 2017).

In addition to histones, chromatin contains non‑histone proteins — a vast array of transcription factors, replication enzymes, repair enzymes, histone modifiers, and others. It is these proteins that provide the regulatory function of chromatin.

Euchromatin and heterochromatin

In the interphase nucleus, chromatin is not uniform. Under a light microscope, two types of staining can be distinguished:

In plants, especially in species with large genomes (e.g., cereals), heterochromatin constitutes a significant part of the nucleus and often forms noticeable chromocentres — clumps of intensely staining material visible even under a light microscope (Serebryakova et al., 2006; Santos et al., 2020). Chromocentres typically contain repetitive DNA sequences and inactive genes.

Chromosomes: chromatin during division

When a cell prepares to divide (in mitosis or meiosis), chromatin undergoes condensation (spiralisation). Chromatin threads repeatedly coil and shorten, becoming visible under a light microscope as distinct rod‑like structures — chromosomes. Each chromosome consists of two identical copies — chromatids — joined at the centromere (primary constriction) (Mauseth, 2017; Bidlack & Jansky, 2021). The centromere serves as the attachment site for spindle fibres, ensuring the segregation of chromatids to opposite poles of the cell. At the ends of chromosomes are telomeres — specialised structures that protect DNA ends from degradation and fusion.

After division is complete, chromosomes decondense and return to the chromatin state characteristic of the interphase nucleus.

Dynamics and epigenetic regulation

It is important to understand that the state of chromatin (its degree of condensation) is not fixed once and for all. It is dynamically regulated through chemical modifications of histones (acetylation, methylation, phosphorylation, etc.) and methylation of DNA itself. These modifications, known as epigenetic marks, determine the accessibility of genes to transcription factors without changing the primary DNA sequence (Santos et al., 2020; Evert, 2006). Thanks to epigenetic regulation, a single cell can differentiate into a root, leaf, or flower cell while possessing an absolutely identical genome.

If chromatin is the “archive” of genetic information, then the nucleolus is the largest and most conspicuous “factory” of the nucleus under a light microscope. It is a dense, membrane‑less body within the nucleoplasm. The number of nucleoli per nucleus varies (usually one to several) and depends on cell ploidy and the number of nucleolar organisers — chromosome regions that contain ribosomal RNA (rRNA) genes (Evert, 2006; Mauseth, 2017).

Concluding the overview of the structural units of the nucleus, we must mention the medium in which they reside. Karyoplasm (or nuclear sap) is the semi‑fluid, colloidal content of the nucleus that fills the space between chromatin, the nucleolus, and other structures (von Denffer et al., 1971; Serebryakova et al., 2006).

All somatic plant cells go through the cell cycle — an ordered sequence of events leading to cell division. Classically, the cell cycle is divided into interphase (the period between divisions) and mitosis (nuclear division), usually followed by cytokinesis (cytoplasmic division) (Bidlack & Jansky, 2021; Evert, 2006).

Interphase occupies up to 90% of the cycle time and is itself divided into three phases:

Interphase is followed by mitosis (M‑phase). In higher plants, mitosis has a number of features that distinguish it from animal mitosis (von Denffer et al., 1971; Mauseth, 2017).

DNA replication is the key event of S‑phase. It is carried out by specialised enzyme complexes that “unwind” the DNA double helix and synthesise two new strands on each of the parental strands (Evert, 2006). Replication occurs simultaneously at many sites on chromosomes (replicons), ensuring the high speed of copying gigantic plant genomes.

Transcription — synthesis of RNA molecules on a DNA template. Three main RNA polymerases work in the nucleus (Evert, 2006; Mauseth, 2017):

Transcription in plants, as in other eukaryotes, is tightly regulated. Specific transcription factors (proteins that recognise specific DNA sequences in gene promoters) determine which gene is activated and when (Lee et al., 2024). A unique feature of plant genes is their high sensitivity to external signals (light, temperature, drought, pathogen attack), requiring rapid and flexible tuning of transcription.

Primary transcripts synthesised by RNA polymerase II (pre‑mRNA) are not mature functional molecules. In the nucleus, they undergo processing (maturation), which includes three main steps (Evert, 2006; Lee et al., 2024):

Alternative splicing is also widespread in plants, whereby different mature mRNAs can be produced from a single primary transcript (by excising different combinations of exons). This significantly increases the diversity of proteins encoded by a limited number of genes and plays an important role in stress adaptation (Lee et al., 2024).

Mature mRNAs, tRNAs, and ribosomal subunits are transported from the nucleus to the cytoplasm through nuclear pores. This process is active, energy‑dependent, and requires the participation of special exportin receptors that recognise nuclear export signals (NES) on RNA molecules (in complex with proteins) (Evert, 2006; Beck, 2010).

In many plant cells during differentiation, complete mitosis and cytokinesis do not occur. Instead, nuclei may repeatedly replicate DNA without subsequent division — a process called endopolyploidy (or endomitosis) (Mauseth, 2017; Chustecki & Johnston, 2024). As a result, the nucleus becomes polyploid (containing 4C, 8C, 16C or more copies of the genome), but the cell remains uninucleate. Endopolyploidy is widespread in specialised plant tissues: in endosperm cells, leaf parenchyma, trichomes, phloem cells, and mature fruits (e.g., tomatoes). Large polyploid nuclei often have larger size and increased transcriptional activity, allowing cells to more efficiently synthesise proteins and secondary metabolites. This property is used in breeding: polyploid varieties of crop plants often have larger fruits and increased yield (Bidlack & Jansky, 2021).

The nucleus is an extremely dynamic system. In response to stress (heat shock, drought, salinity, pathogen attack), rapid changes occur in nuclear organisation:

Thus, biogenesis and dynamic processes in the nucleus are a continuously operating conveyor that ensures the storage, replication, and implementation of genetic information, as well as rapid adaptation of the plant to changing conditions. In the next section, we will examine how the nucleus interacts with other organelles of the cell (cytoplasm, endoplasmic reticulum, vacuole, chloroplasts, and mitochondria), forming a unified metabolic and signalling network.

The most obvious and intense connection of the nucleus is with the cytoplasm. This exchange occurs through nuclear pores (detailed in section 3.2). Transport through the pores includes:

However, the connection of the nucleus with the cytoplasm is not limited to molecular transport. The cytoplasm constantly “probes” the state of the nucleus and sends signals to it. For example, the concentration of calcium (Ca²⁺) in the cytoplasm influences the activity of nuclear transcription factors; the metabolic status of the cell (ATP, NADPH levels) can modulate gene expression through nuclear sensors. This two‑way information exchange underlies all adaptive responses of the plant (Chustecki & Johnston, 2024).

As noted in section 3.1, the outer membrane of the nuclear envelope is a direct continuation of the membranes of the rough endoplasmic reticulum (ER). The perinuclear space is continuous with the ER lumen (Evert, 2006; von Denffer et al., 1971). This structural continuity has fundamental importance:

The nucleus is physically connected to the cytoskeleton — microtubules and actin filaments — via the LINC complex (Linker of Nucleoskeleton and Cytoskeleton). In plant cells, the LINC complex consists of SUN proteins on the inner nuclear membrane (e.g., AtSUN1, AtSUN2) and KASH proteins on the outer membrane (e.g., WIP/WIT or SINE) (Groves et al., 2025; Chustecki & Johnston, 2024).

This connection provides:

The relationship of the nucleus with semi‑autonomous organelles — chloroplasts and mitochondria — is two‑way (Evert, 2006; Mauseth, 2017). Direct anterograde signalling (from nucleus to organelles) is well studied: nuclear genes encode the vast majority of chloroplast and mitochondrial proteins. But there is also a reverse connection — retrograde signalling (from organelles to the nucleus). When chloroplasts or mitochondria experience stress (excess light, ATP deficiency, oxidative stress), they generate signalling molecules (e.g., reactive oxygen species, metabolites, changes in redox status). These signals are perceived by the nucleus, which adjusts the expression of appropriate genes for adaptation (Lee et al., 2024; Chustecki & Johnston, 2024).

Example: when the photosynthetic apparatus is damaged, chloroplasts send a signal to the nucleus, leading to activation of genes encoding antioxidant enzymes and repair proteins. This process helps maintain homeostasis and ensures plant survival under adverse conditions (Santos et al., 2020).

Although direct physical contact between the nucleus and the vacuole is less pronounced, their interrelationship is important for cell growth. As noted earlier, in mature plant cells the nucleus is often displaced by the vacuole to the periphery. However, the nucleus can influence vacuole development and tone through regulation of aquaporin (water channel) and ion transporter gene expression (Neuhaus & Trentmann, 2014; Zhang et al., 2015). In turn, changes in turgor pressure caused by osmotic stresses are transmitted to the nucleus via the cytoskeleton and can modulate its position and activity. Thus, the nucleus and vacuole participate in a unified system that maintains water balance and cell size.

The nucleus is the central integrator of signals coming from all cellular compartments. It does not simply react passively to each signal individually. Signals from the ER, mitochondria, chloroplasts, cytoskeleton, and the external environment are processed together (cross‑talk). The nucleus “decides” to launch a comprehensive gene expression programme that optimises the functioning of the entire cell under given conditions (Lee et al., 2024; Santos et al., 2020).

Thus, the plant cell nucleus is not an isolated “command centre” but an active participant in a complex, multi‑channel dialogue inside the cell. It both dictates and listens, adjusting its commands based on incoming information. This capacity for signal integration forms the basis of the remarkable plasticity and adaptability of plants, allowing them to survive in constantly changing environmental conditions.

In the next, concluding section of the article, we will examine the applied significance of knowledge about the cell nucleus in agriculture and biotechnology.

The basis of most breeding programmes is the analysis and modification of hereditary material. The cell nucleus provides the breeder with key tools:

The state of the nucleus is a sensitive indicator of the physiological status of the cell and the whole plant. The following approaches are used in agronomy:

Modern biotechnologies are impossible without manipulations of the nuclear genome.

Many pathogens (viruses, bacteria, fungi, oomycetes) have learned to manipulate the nuclear processes of the host plant to suppress its defence responses.

Finally, deep knowledge of cytology, anatomy, and morphology of the nucleus is an essential part of the training of agronomists, breeders, biotechnologists, and phytopathologists. Only by understanding how the “command centre” of the plant cell is built and functions can a specialist competently use modern biotechnological methods, interpret the results of cytogenetic analysis, and make informed decisions in breeding and seed production.