Plant Vacuoles Research Articles

Vacuolar phosphate efflux transporter ZmVPEs mediate phosphate homeostasis and remobilization in maize leaves.

Phosphorus (P) is an essential macronutrient for plant growth and development. Vacuoles play a crucial role in inorganic phosphate (Pi) storage and remobilization in plants. However, the physiological function of vacuolar phosphate efflux transporters in plant Pi remobilization remains obscure. Here, we identified three ZmVPE genes (ZmVPE1, ZmVPE2a, ZmVPE2b) by combining them with transcriptome and quantitative real-time polymerase chain reaction (PCR) analyses, showing a relatively higher expression in older leaves than in younger leaves in maize. Moreover, the expression of the ZmVPEs was triggered by Pi deficiency and abscisic acid. ZmVPEs were localized to the vacuolar membrane and responsible for vacuolar Pi efflux. Compared with the wild-type, Pi remobilization from older to younger leaves was enhanced in ZmVPE-overexpression lines. zmvpe2a mutants displayed an increase in the total P and Pi concentrations in older leaves, but a decrease in younger leaves. In rice, Pi remobilization was impaired in the osvpe1osvpe2 double mutant and enhanced in OsVPE-overexpression plants, suggesting conserved functions of VPEs in modulating Pi homeostasis and remobilization in crop plants. Taken together, our findings revealed a novel mechanism underlying Pi remobilization from older to younger leaves mediated by plant vacuolar Pi efflux transporters, facilitating the development of Pi-efficient crop plants.

The MON1-CCZ1 complex plays dual roles in autophagic degradation and vacuolar protein transport in rice.

Autophagy is a highly conserved cellular program in eukaryotic cells which mediates the degradation of cytoplasmic components through the lysosome, also named the vacuole in plants. However, the molecular mechanisms underlying the fusion of autophagosomes with the vacuole remain unclear. Here, we report the functional characterization of a rice (Oryza sativa) mutant with defects in storage protein transport in endosperm cells and accumulation of numerous autophagosomes in root cells. Cytological and immunocytochemical experiments showed that this mutant exhibits a defect in the fusion between autophagosomes and vacuoles. The mutant harbors a loss-of-function mutation in the rice homolog of Arabidopsis thaliana MONENSIN SENSITIVITY1 (MON1). Biochemical and genetic evidence revealed a synergistic interaction between rice MON1 and AUTOPHAGY-RELATED 8a in maintaining normal growth and development. In addition, the rice mon1 mutant disrupted storage protein sorting to protein storage vacuoles. Furthermore, quantitative proteomics verified that the loss of MON1 function influenced diverse biological pathways including autophagy and vacuolar transport, thus decreasing the transport of autophagic and vacuolar cargoes to vacuoles. Together, our findings establish a molecular link between autophagy and vacuolar protein transport, and offer insights into the dual functions of the MON1-CCZ1 (CAFFEINE ZINC SENSITIVITY1) complex in plants.

The Complexity of the Influence of Growth Substances, Heavy Metals, and Their Combination on the Volume Dynamics of Vacuoles Isolated from Red Beet (Beta vulgaris L.) Taproot Cells

The plant vacuole is a very dynamic organelle that can occupy more than 90% of the cell volume and is essential to plant cell growth and development, the processes in which auxin (indole-3-acetic acid, IAA) is a central player. It was found that when IAA or FC (fusicoccin) was present in the control medium of vacuoles isolated from red beet taproots at a final concentration of 1 µM, it increased their volume to a level that was 26% or 36% higher than that observed in the control medium without growth regulators, respectively. In the presence of IAA and FC, the time after which most vacuoles ruptured was about 10 min longer for IAA than for FC. However, when cadmium (Cd) or lead (Pb) was present in the control medium at a final concentration of 100 µM, it increased the volume of the vacuoles by about 26% or 80% compared to the control, respectively. The time after which the vacuoles ruptured was similar for both metals. The combined effect of IAA and Pb on the volume of the vacuoles was comparable with that observed in the presence of Pb only, while for FC combined with Pb, it was additive. The use of IAA or FC together with Cd caused in both cases a decrease in the vacuole volumes by about 50%. The data presented in this study are discussed, taking into account the structure and function of the vacuolar membrane (tonoplast) and their changes in the presence of growth substances, heavy metals, and their combination.

Light at the end of the tunnel: FRAP assays combined with super resolution microscopy confirm the presence of a tubular vacuole network in meristematic plant cells.

Plant vacuoles play key roles in cellular homeostasis, performing catabolic and storage functions, and regulating pH and ion balance. Despite their essential role, there is still no consensus on how vacuoles are established. A model proposing that the endoplasmic reticulum is the main contributor of membrane for growing vacuoles in meristematic cells has been challenged by a study proposing that plant vacuoles are formed de novo by homotypic fusion of multivesicular bodies (MVBs). Here, we use the Arabidopsis thaliana root as a model system to provide a systematic overview of successive vacuole biogenesis stages, starting from the youngest cells proximate to the quiescent center. We combine in vivo high- and super-resolution (STED) microscopy to demonstrate the presence of tubular and connected vacuolar structures in all meristematic cells. Using customized fluorescence recovery after photobleaching (FRAP) assays, we establish different modes of connectivity and demonstrate that thin, tubular vacuoles, as observed in cells near the quiescent center, form an interconnected network. Finally, we argue that a growing body of evidence indicates that vacuolar structures cannot originate from MVBs alone but receive membrane material from different sources simultaneously.

Red beet betalains extraction process: A comprehensive review of methods, applications, and physicochemical properties.

Red beet extract is rich in bioactive compounds and possesses health-promoting properties. Moreover, the stability of red beet extract over a broad acidic pH range has given them great potential in developing new functional foods and drinks. The choice of extraction solvent and methodology significantly influences the efficiency of betalain extraction from plant vacuoles. Although the conventional solvent extraction method has been widely employed for betalain extraction, recent innovations have introduced alternative methods that offer advantages, such as reduced solvent consumption, energy efficiency, and minimized exposure to high temperatures. This paper aims to summarize the current knowledge about conventional and novel extraction methods, applications, biological activities, and purification of red beet betalains. Furthermore, the physicochemical properties of betalain-rich extract of red beet and associated safety considerations have been investigated.

A dominant-negative Arabidopsis cation exchanger 1 (CAX1): N-terminal autoinhibition and membrane topology.

Calcium (Ca2+) is essential for plant growth and cellular homeostasis, with cation exchangers (CAXs) regulating Ca2+ transport into plant vacuoles. In Arabidopsis, multiple CAXs feature a common structural arrangement, comprising an N-terminal autoinhibitory domain followed by two pseudosymmetrical modules. Mutations in CAX1 enhance stress tolerance, notably tolerance to anoxia (a condition marked by oxygen depletion), crucial for flood resilience. Here we engineered a dominant-negative CAX1 variant, named ½N-CAX1, incorporating the autoinhibitory domain and the N-terminal pseudosymmetrical module, which, when expressed in wild-type Arabidopsis plants, phenocopied the anoxia tolerance of cax1. Physiological evaluations, yeast assays, and calcium imaging demonstrated that wild-type plants expressing ½N-CAX1 have phenotypes consistent with inhibition of CAX1, which is likely through direct interaction of ½N-CAX1 with CAX1. Eliminating segments within the N-terminal pseudosymmetrical module, as well as incorporating modules from other plant CAXs and expressing these variants into wild-type plants, failed to produce anoxia tolerance. This underscores the requirement for both the CAX1 autoinhibitory domain and the intact pseudosymmetrical module to produce the dominant-negative phenotype. Our study elucidates the interaction of this ½N-CAX1 variant with CAX1 and its impact on anoxia tolerance, offering insights into further approaches for engineering plant stress tolerance.

Chlorophyll Degradation and its Physiological Function.

Research on chlorophyll degradation has progressed significantly in recent decades. In the 1990s, the structure of linear tetrapyrrole, which is unambiguously a chlorophyll degradation product, was determined. From the 2000s until the 2010s, the major enzymes involved in chlorophyll degradation were identified, and the pheophorbide a oxygenase/phyllobilin pathway was established. This degradation pathway encompasses several steps: (1) initial conversion of chlorophyll b to 7-hydroxymethyl chlorophyll a; (2) conversion of 7-hydroxymethyl chlorophyll a to chlorophyll a; (3) dechelation of chlorophyll a to pheophytin a; (4) dephytylation of pheophytin a to pheophorbide a; (5) opening of the macrocycle to yield a red chlorophyll catabolite; and (6) conversion of red chlorophyll catabolite to phyllobilins. This pathway converts potentially harmful chlorophyll into safe molecules of phyllobilins, which are stored in the central vacuole of terrestrial plants. The expression of chlorophyll-degrading enzymes is mediated by various transcription factors and influenced by light conditions, stress, and plant hormones. Chlorophyll degradation is differently regulated in different organs and developmental stages of plants. The initiation of chlorophyll degradation induces the further expression of chlorophyll-degrading enzymes, resulting in the acceleration of chlorophyll degradation. Chlorophyll degradation was initially considered the last reaction in senescence; however, chlorophyll degradation plays crucial roles in enhancing senescence, degrading chlorophyll-protein complexes, forming photosystem II, and maintaining seed quality. Therefore, controlling chlorophyll degradation has important agricultural applications.

Effector Protein Serine Carboxypeptidase FgSCP Is Essential for Full Virulence in Fusarium graminearum and Is Involved in Modulating Plant Immune Responses.

Fusarium head blight caused by Fusarium graminearum is a significant pathogen affecting wheat crops. During the infection process, effector proteins are secreted to modulate plant immunity and promote infection. The toxin deoxynivalenol is produced in infected wheat grains, posing a threat to human and animal health. Serine carboxypeptidases (SCPs) belong to the α/β hydrolase family of proteases and are widely distributed in plant and fungal vacuoles, as well as animal lysosomes. Research on SCPs mainly focuses on the isolation, purification, and production of a small number of fungi. The role of SCPs in plant secretion, growth and development, and stress resistance has also been extensively studied. However, their functions in F. graminearum, a fungal pathogen, remain relatively unknown. In this study, the biological functions of the FgSCP gene in F. graminearum were investigated. The study revealed that mutations in FgSCP affected the nutritional growth, sexual reproduction, and stress tolerance of F. graminearum. Furthermore, the deletion of FgSCP resulted in reduced pathogenicity and hindered the biosynthesis of deoxynivalenol. The upregulation of FgSCP expression 3 days after infection indicated its involvement in host invasion, possibly acting as a "smokescreen" to deceive the host and suppress the expression of host defensive genes. Subsequently, we confirmed the secretion ability of FgSCP and its ability to inhibit the cell death induced by INF1 in Nicotiana benthamiana cells, indicating its potential role as an effector protein in suppressing plant immune responses and promoting infection. In summary, we have identified FgSCP as an essential effector protein in F. graminearum, playing critical roles in growth, virulence, secondary metabolism, and host invasion.

PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset

Plant vacuoles, play a crucial role in maintaining cellular stability, adapting to environmental changes, and responding to external pressures. The accurate identification of vacuolar proteins (PVPs) is crucial for understanding the biosynthetic mechanisms of intracellular vacuoles and the adaptive mechanisms of plants. In order to more accurately identify vacuole proteins, this study developed a new predictive model PEL-PVP based on ESM-2. Through this study, the feasibility and effectiveness of using advanced pre-training models and fine-tuning techniques for bioinformatics tasks were demonstrated, providing new methods and ideas for plant vacuolar protein research. In addition, previous datasets for vacuolar proteins were balanced, but imbalance is more closely related to the actual situation. Therefore, this study constructed an imbalanced dataset UB-PVP from the UniProt database，helping the model better adapt to the complexity and uncertainty in real environments, thereby improving the model's generalization ability and practicality. The experimental results show that compared with existing recognition techniques, achieving significant improvements in multiple indicators, with 6.08 %, 13.51 %, 11.9 %, and 5 % improvements in ACC, SP, MCC, and AUC, respectively. The accuracy reaches 94.59 %, significantly higher than the previous best model GraphIdn. This provides an efficient and precise tool for the study of plant vacuole proteins.

CAX control: multiple roles of vacuolar cation/H+ exchangers in metal tolerance, mineral nutrition and environmental signalling.

Plant vacuolar transporters, particularly CAX (Cation/H+ Exchangers) responsible for Ca2+/H+ exchange on the vacuole tonoplast, play a central role in governing cellular pH, ion balance, nutrient storage, metal accumulation, and stress responses. Furthermore, CAX variants have been employed to enhance the calcium content of crops, contributing to biofortification efforts. Recent research has uncovered the broader significance of these transporters in plant signal transduction and element partitioning. The use of genetically encoded Ca2+ sensors has begun to highlight the crucial role of CAX isoforms in generating cytosolic Ca2+ signals, underscoring their function as pivotal hubs in diverse environmental and developmental signalling networks. Interestingly, it has been observed that the loss of CAX function can be advantageous in specific stress conditions, both for biotic and abiotic stressors. Determining the optimal timing and approach for modulating the expression of CAX is a critical concern. In the future, strategically manipulating the temporal loss of CAX function in agriculturally important crops holds promise to bolster plant immunity, enhance cold tolerance, and fortify resilience against one of agriculture's most significant challenges, namely flooding.

Model-based inference of a dual role for HOPS in regulating guard cell vacuole fusion.

Guard cell movements depend, in part, on the remodelling of vacuoles from a highly fragmented state to a fused morphology during stomata opening. Indeed, full opening of plant stomata requires vacuole fusion to occur. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. In plants, recruitment of HOPS subunits to the tonoplast has been shown to require the presence of the phosphoinositide phosphatidylinositol 3-phosphate. However, chemically depleting this lipid induces vacuole fusion. To resolve this counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we defined a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by using simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening-as induced by two distinct chemical treatments-we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signalling pathway, promoting the formation of SNARE complexes, but limiting their activity.

LATEX AGGLOMERATION AND COAGULATION IN LATICIFERS OF LIVE TARAXACUM KOK-SAGHYZ (RUBBER DANDELION) ROOTS

ABSTRACT The commercialization of Taraxacum kok-saghyz (rubber dandelion) as an alternative rubber crop requires fundamental knowledge of latex, an aqueous suspension of rubber particles, and rubber yield and quality. Rubber particles are formed in the root laticifers from Golgi bodies via the vesicular trafficking system in the cytosol and are then translocated into the vacuoles for storage. However, when freshly harvested roots are processed to extract the latex, much of the latex has already coagulated into solid rubber, reducing the commercial viability of latex extraction from this species. The process of in vivo loss of the latex fraction was investigated histologically, by transmission electron microscopy, in roots of plants grown in soil or hydroponically. In both root types, some rubber particles agglomerated in the cytosol as a precursor to coagulation. Other rubber particles agglomerated and then coagulated after rubber particles were translocated into vacuoles, and also after the cell internal cytoplasmic structure degraded. Uniquely large rubber particles were formed in the vacuoles of hydroponically grown plants by particle coalescence, but were not found in soil-grown roots. Eventually, some root laticifers of both root types filled with solid rubber. The instability of the aqueous latex phase postontogeny through rubber particle agglomeration, coalescence, and coagulation suggests that commercial processes likely would involve root drying to convert residual latex into solid rubber followed by aqueous- or solvent-based extraction.

Mitophagy in plants: Emerging regulators of mitochondrial targeting for selective autophagy.

The degradation and turnover of mitochondria is fundamental to Eukaryotes and is a key homeostatic mechanism for maintaining functional mitochondrial populations. Autophagy is an important pathway by which mitochondria are degraded, involving their sequestration into membrane-bound autophagosomes and targeting to lytic endosomal compartments (the lysosome in animals, the vacuole in plants and yeast). Selective targeting of mitochondria for autophagy, also known as mitophagy, distinguishes mitochondria from other cell components for degradation and is necessary for the regulation of mitochondria-specific cell processes. In mammals and yeast, mitophagy has been well characterised and is regulated by numerous pathways with diverse and important functions in the regulation of cell homeostasis, metabolism and responses to specific stresses. In contrast, we are only just beginning to understand the importance and functions of mitophagy in plants, chiefly as the proteins that target mitochondria for autophagy in plants are only recently emerging. Here, we discuss the current progress of our understanding of mitophagy in plants, the importance of mitophagy for plant life and the regulatory autophagy proteins involved in mitochondrial degradation. In particular, we will discuss the recent emergence of mitophagy receptor proteins that selectively target mitochondria for autophagy, and discuss the missing links in our knowledge of mitophagy-regulatory proteins in plants compared to animals and yeast.

Potential of Salvinia molesta as a Copper Phytoremediation Agent based on Gene Expression Analysis

This research explores the rapid environmental impact of the batik industry, particularly concerning batik waste pollution, especially from the heavy metal copper (Cu). Untreated batik waste can have adverse effects on the environment. The study highlights the potential of the water fern plant (Salvinia molesta) as a heavy metal phytoremediator, specifically for Cu, by activating phytochelatin synthase. The research aims to determine the most effective waste concentration for Cu absorption by water ferns, measure the reduction in Cu levels after phytoremediation treatment, evaluate post-phytoremediation water quality, and observe PCS gene expression in the roots and leaves of water ferns. A static method is employed with variations in waste concentrations. Data analysis utilizes one-way ANOVA for Cu level reduction and changes in water quality. The results indicate that the most effective wastewater concentration for absorbing heavy metal copper (Cu) using water fern (Salvinia molesta) is 2%. The highest reduction in heavy metal copper (Cu) concentration after phytoremediation treatment with water fern (Salvinia molesta) is 41.48%. Water quality post-phytoremediation treatment using water fern (Salvinia molesta) at all concentrations exhibits improvement with an increase in dissolved oxygen (DO) levels. The expression of the phytochelatin synthase (PCS) gene in the leaves and roots of water fern (Salvinia molesta) confirms the role of the PCS gene in binding heavy metal copper (Cu) to the plant's vacuole.

Whole-Cell Electron Tomography Analysis of Vacuole Biogenesis.

Vacuoles in plant cells are the most prominent organelles that harbor distinctive features, including lytic function, storage of proteins and sugars, balance of cell volume, and defense responses. Despite their dominant size and functional versatility, the nature and biogenesis of vacuoles in plants per se remain elusive and several models have been proposed. Recently, we used the whole-cell 3D electron tomography (ET) technique to study vacuole formation and distribution at nanometer resolution and demonstrated that small vacuoles are derived from multivesicular body maturation and fusion. Good sample preparation is a critical step to get high-quality electron tomography images. In this chapter, we provide detailed sample preparation methods for high-resolution ET in Arabidopsis thaliana root cells, including high-pressure freezing, subsequent freeze-substitution fixation, embedding, and serial sectioning.

A DUF3844 domain-containing protein is required for vacuolar protein sorting in Schizosaccharomyces pombe.

Protein trafficking to vacuoles in plants and fungi, and to lysosomes in animals, is essential for the maintenance of cellular homeostasis. In Saccharomyces cerevisiae, the vacuolar protein sorting (VPS) pathway has been well studied by using vacuolar carboxypeptidase Y (CPY) as a model, and many VPS genes have been identified. By contrast, the vacuolar protein trafficking pathway in Schizosaccharomyces pombe remains poorly understood. In this study, we identified a novel VPS gene (SPBC1709.03) in S. pombe that is broadly conserved in fungi, but not in S. cerevisiae. Owing to its DUF3844 domain of unknown function, the gene was named vps3844. Disruption mutants of vps3844 had defects in both CPY sorting and incorporation of FM4-64 dye into the vacuolar membrane. Partial deletion analysis of the Vps3844 protein revealed that, within the DUF3844 domain, the region comprising amino acids 354 to 380 is important for protein trafficking to the vacuole. Our findings represent the first report of a VPS gene involved in vacuolar transport that is conserved in fungi, particularly S. pombe, but lacks representation in S. cerevisiae.

Unraveling the Molecular Functions of Multifaced Plant‐Vacuolar Processing Enzymes

AbstractIn the plant development cycle, different types of proteases play essential functions. Plant vacuolar processing enzymes (VPEs) are a group of cysteine proteases localized in the cell vacuoles that process and regulate several larger proprotein precursors. VPEs activate the proteolytic cleavage of proproteins precursors within aspartic acid and asparagine residues to trigger the tightly controlled programmed cell death process induced by different stages of plant development and environmental cues, impacting myriad plant physiological processes. In plants, VPEs are categorized into embryo, vegetative, and seed coat‐types, in which embryo and seed coat‐type VPEs are mainly involved in processing the seed storage protein precursors to provide nutrients for early growth, while the vegetative type induces programmed cell death in a varied range of vegetative tissues. Recently, several plant VPEs exhibited transpeptidase activity, which is essential for the cyclization mechanism during the production of cyclotides. In this review, we explore and understand the complex functions of plant VPEs, which can lead to the production of stress‐tolerant and higher‐yield crops, and provide the recent advances in the application of VPEs in molecular pharming, which highlights the significant implications of VPEs in protein science and agriculture.

Identification and Potential Participation of Lipases in Autophagic Body Degradation in Embryonic Axes of Lupin (Lupinus spp.) Germinating Seeds.

Autophagy is a fundamental process for plants that plays a crucial role in maintaining cellular homeostasis and promoting survival in response to various environmental stresses. One of the lesser-known stages of plant autophagy is the degradation of autophagic bodies in vacuoles. To this day, no plant vacuolar enzyme has been confirmed to be involved in this process. On the other hand, several enzymes have been described in yeast (Saccharomyces cerevisiae), including Atg15, that possess lipolytic activity. In this preliminary study, which was conducted on isolated embryonic axes of the white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet), the potential involvement of plant vacuolar lipases in the degradation of autophagic bodies was investigated. We identified in transcriptomes (using next-generation sequencing (NGS)) of white and Andean lupin embryonic axes 38 lipases with predicted vacuolar localization, and for three of them, similarities in amino acid sequences with yeast Atg15 were found. A comparative transcriptome analysis of lupin isolated embryonic axes cultured in vitro under different sucrose and asparagine nutrition, evaluating the relations in the levels of the transcripts of lipase genes, was also carried out. A clear decrease in lipase gene transcript levels caused by asparagine, a key amino acid in lupin seed metabolism which retards the degradation of autophagic bodies during sugar-starvation-induced autophagy in lupin embryonic axes, was detected. Although the question of whether lipases are involved in the degradation of autophagic bodies during plant autophagy is still open, our findings strongly support such a hypothesis.

The structure of anthocyanins and the copigmentation by common micromolecular copigments: A review

Under natural physiological conditions, anthocyanins can keep bright and stable color for a long time due to the relatively stable acid-base environment of plant vacuoles and the copigmentation from various copigment substances, such as polyphenols, nucleotides, metallic ions and other substances. Therefore, the copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale yellow organic molecules (copigments). These interactions are usually manifested in both hyperchromic effect and bathochromic shifts. In addition to making anthocyanins more stable, the copigmentation also could make an important contribution to the diversification of their tone. Based on the molecular structure of anthocyanins, this review focuses on the interaction mode of auxochrome groups or copigments with anthocyanins and their effects on the chemical and color stability of anthocyanins.

ProSE-Pero: Peroxisomal Protein Localization Identification Model Based on Self-Supervised Multi-Task Language Pre-Training Model.

Peroxisomes are membrane-bound organelles that contain one or more types of oxidative enzymes. Aberrant localization of peroxisomal proteins can contribute to the development of various diseases. To more accurately identify and locate peroxisomal proteins, we developed the ProSE-Pero model. We employed three methods based on deep representation learning models to extract the characteristics of peroxisomal proteins and compared their performance. Furthermore, we used the SVMSMOTE balanced dataset, SHAP interpretation model, variance analysis (ANOVA), and light gradient boosting machine (LightGBM) to select and compare the extracted features. We also constructed several traditional machine learning methods and four deep learning models to train and test our model on a dataset of 160 peroxisomal proteins using tenfold cross-validation. Our proposed ProSE-Pero model achieves high performance with a specificity (Sp) of 93.37%, a sensitivity (Sn) of 82.41%, an accuracy (Acc) of 95.77%, a Matthews correlation coefficient (MCC) of 0.8241, an F1 score of 0.8996, and an area under the curve (AUC) of 0.9818. Additionally, we extended our method to identify plant vacuole proteins and achieved an accuracy of 91.90% on the independent test set, which is approximately 5% higher than the latest iPVP-DRLF model. Our model surpasses the existing In-Pero model in terms of peroxisomal protein localization and identification. Additionally, our study showcases the proficient performance of the pre-trained multitasking language model ProSE in extracting features from protein sequences. With its established validity and broad generalization, our model holds considerable potential for expanding its application to the localization and identification of proteins in other organelles, such as mitochondria and Golgi proteins, in future investigations.