黑料网

Plant Proteomics; Post-translational modifications; Protein-protein interactions; Stress response; Metabolomics; Crop improvement

Introduction

Plants, as primary producers in ecosystems, face an array of challenges throughout their life cycles, including fluctuating environmental conditions, biotic stress from pathogens and herbivores, and abiotic stress such as drought, salinity, and temperature extremes [1]. In order to survive and thrive, plants have evolved intricate molecular mechanisms to sense and respond to these challenges. Central to these responses is the plant proteome the full set of proteins expressed in a plant at any given time which drives critical physiological processes such as growth, development, and stress adaptation.

Proteins are the primary functional entities in cells, and their functions are determined not just by their sequences, but also by their interactions with other proteins and their post-translational modifications (PTMs) [2]. These dynamic and reversible modifications, such as phosphorylation, acetylation, and ubiquitination, regulate protein activity, stability, and localization, allowing plants to fine-tune their responses to environmental stimuli. In recent years, advances in proteomics have enabled researchers to probe the complexity of the plant proteome with unprecedented detail. Proteomics, particularly with the advent of high-throughput mass spectrometry (MS) and other advanced techniques, has allowed for the identification, quantification, and functional analysis of thousands of proteins from diverse plant species [3]. The application of proteomic approaches to plant science has greatly enhanced our understanding of protein functions in processes ranging from cellular metabolism and signal transduction to the regulation of stress responses and growth. This manuscript aims to provide a comprehensive overview of recent advancements in plant proteomics, emphasizing the insights gained into plant biology, the challenges faced, and the applications of these findings in crop improvement. We will discuss key methods in plant proteomics, including mass spectrometry-based approaches, the identification of protein functions, and the integration of proteomics with other omics technologies to provide a more holistic view of plant biology.

Materials and Methods

Proteomic analyses typically start with the collection of plant tissues exposed to specific environmental conditions or developmental stages [4]. Model plants like Arabidopsis thaliana, as well as crop species such as rice, maize, wheat, and soybean, are often used for these studies. Samples are usually collected from tissues such as leaves, roots, flowers, and seeds, depending on the focus of the research. Protein extraction from plant tissues can be challenging due to the presence of large amounts of polysaccharides, lipids, and secondary metabolites. However, various extraction protocols have been developed to ensure high-quality protein recovery. Proteins are typically extracted using buffer systems optimized for solubilizing plant proteins while preventing degradation or modification.

Mass spectrometry is the gold standard for protein identification and quantification. Proteins are digested into peptides using proteolytic enzymes, such as trypsin, and the resulting peptides are analyzed by LC-MS/MS. The mass spectrometer measures the mass-to-charge ratio of the peptides and generates spectra that can be used to identify the proteins by matching them against protein databases [5]. MS-based quantitative proteomics allows for the comparison of protein abundance under different experimental conditions, such as stress treatments or genetic modifications. Although less commonly used today due to the high resolution of MS techniques, 2-DE can be used to separate proteins based on their isoelectric point (pI) and molecular weight. This approach provides a global overview of the proteome and is particularly useful in identifying changes in protein abundance or isoform expression in response to environmental conditions. Label-free quantification is a mass spectrometry-based approach that does not require isotopic labeling of samples. It quantifies protein abundance by analyzing the intensity of peptide peaks in MS spectra. This technique is advantageous for high-throughput studies as it simplifies the workflow and avoids the complications associated with isotope labelling [6]. PTMs, such as phosphorylation, glycosylation, acetylation, and ubiquitination, are crucial for regulating protein activity and function in response to environmental changes. Proteomic methods that enrich for specific PTMs, such as phosphoproteomics for studying phosphorylation events, are widely used to uncover how plants modulate protein functions during stress responses or growth processes.

Results and Discussion

The use of MS-based proteomics has led to the identification of thousands of proteins in various plant species. The Arabidopsis proteome, for example, has been extensively characterized, revealing proteins involved in key biological processes such as photosynthesis, metabolism, signaling, and stress responses [7]. More recently, the proteomes of crop species have been mapped, with a particular emphasis on stress-responsive proteins that mediate tolerance to drought, salinity, heat, and cold. The identification of these proteins provides new opportunities for crop improvement through breeding or genetic modification.

Protein function is often determined by its interaction with other proteins, forming complex networks that regulate cellular processes. Recent advances in plant proteomics have enabled the mapping of protein-protein interactions (PPIs) on a large scale. For example, the identification of proteins involved in signaling pathways, such as the MAPK cascade in response to abiotic stress, has been facilitated by proteomic interaction studies. These studies provide insights into how proteins cooperate within signaling networks to mediate stress responses and other cellular functions [8]. PTMs play a central role in regulating protein function and modulating stress responses. Phosphorylation, for instance, is a key mechanism in stress signal transduction, where specific kinases and phosphatases regulate the activity of target proteins. Recent studies have highlighted the role of PTMs in regulating transcription factors involved in drought and heat stress responses, as well as enzymes responsible for antioxidant defense. Advances in proteomics have led to the identification of novel PTMs and their regulatory roles, shedding light on the dynamic regulation of protein functions during stress adaptation. The integration of proteomics with genomics, transcriptomics, and metabolomics offers a more comprehensive view of plant biology. While genomics provides the genetic blueprint of a plant, proteomics reveals how the plant’s proteins function and respond to environmental stimuli. Transcriptomics, on the other hand, informs us about gene expression patterns, while metabolomics uncovers the metabolic consequences of stress. By combining data from these different omics layers, researchers can gain a more holistic understanding of the molecular mechanisms that underlie plant responses to environmental challenges.

Advances in plant proteomics hold great promise for crop improvement, particularly in enhancing stress tolerance, disease resistance, and yield. For instance, by identifying key proteins involved in drought tolerance, researchers can develop crops that are better equipped to withstand water scarcity [9]. Similarly, the identification of proteins involved in pathogen resistance can lead to the development of crops with enhanced immunity. Furthermore, proteomic approaches can aid in improving photosynthesis efficiency, a critical factor for increasing crop productivity. While the potential of plant proteomics is immense, several challenges remain. The complexity and diversity of plant proteomes make it difficult to identify and quantify all proteins in a given sample. Proteins are expressed at different levels depending on the tissue type, developmental stage, and environmental conditions, which can complicate proteomic analyses. Moreover, the presence of highly abundant proteins, such as ribulose-1,5-bisphosphate carboxylase (RuBisCO) in leaves, can overshadow the detection of low-abundance stress-related proteins [10]. Overcoming these challenges requires improvements in sample preparation, protein extraction methods, and data analysis techniques.

Conclusion

Advances in plant proteomics have greatly enhanced our understanding of plant biology, providing insights into protein functions, interactions, and regulatory mechanisms. By identifying and characterizing proteins involved in key processes such as stress response, metabolism, and growth, proteomics has opened new avenues for crop improvement. As technologies continue to improve, plant proteomics will play an increasingly important role in addressing global agricultural challenges, such as climate change, food security, and sustainable farming. The integration.

Acknowledgment

None

Conflict of Interest

None

1. Morry J, Ngamcherdtrakul W, Yantasee W (2017) . Redox Biol 11: 240-253.

, ,

2. Heft H (1989) . J Theory Social Behav 19: 1-30.

,

3. Michaels CF, Carello C (1981) . Englewood Cliffs, NJ: Prentice-Hall.
4. Koffka K (1935) . New York: Harcourt, Brace & World.

,

5. Shaw RE, Bransford JD (1977) . Hillsdale, NJ: Lawrence Erlbaum Associates.

,

6. Costall A (1999) . Hillsdale, NJ: Lawrence Erlbaum Associates.

,

7. Warren WH (2006) . Psychological Review 113: 358-389.

,

8. Turvey MT, Shaw RE (1995) .
9. Lui PPY, Zhang X, Yao S, Sun H, Huang C, et al. (2022) . Int J Mol Sci 23: 3571.

, ,

10. Withagen R, Chemero A (2009). . Theory & Psychology 19: 363-389.

,