From the Journals: MCP

Protein acetylation helps plants adapt to light. Mapping protein locations in 3D tissues. Demystifying the glycan–protein interactome. Read about papers on these topics recently published in the journal Molecular & Cellular Proteomics.

Protein acetylation helps plants adapt to light

Acetylation is a posttranslational modification in which acetyl transferases add an acetyl group to a protein. This modification allows for the rapid and reversible regulation of protein activity. In plants, acetylation occurs in plastids, which include organelles like chloroplasts that are vital for processes such as photosynthesis.

Thale cress or Arabidopsis thaliana flowers.

In a recent Molecular & Cellular Proteomics paper, Jürgen Eirich of the University of Muenster, Germany, and a team of international researchers studied the role of plastid acetyl transferase, GNAT2, in light acclimation of Arabidopsis thaliana, a flowering plant of the mustard family. GNAT2 mediates two types of acetylation — N-terminal acetylation and lysine acetylation. N-terminal acetylation typically affects protein localization and interactions, while lysine acetylation regulates enzymatic activity and gene expression. The study focused on GNAT2 and its potential role in regulating plant responses to changing light conditions.

The researchers exposed both normal and plants lacking in GNAT2 to three different light conditions: standard or low light, high light and darkness, each for two hours. They analyzed the transcriptome, proteome, metabolome and acetylome to assess GNAT2’s role in light acclimation. While N-terminal acetylation remained unchanged, lysine acetylation was significantly deregulated in GNAT2-deficient plants compared to normal plants. These findings highlight the distinct regulatory functions of GNAT2-mediated acetylation in plant responses to changing light conditions.

By integrating acetylomics data with other omics data, the researchers obtained a comprehensive and dynamic view of how plants respond to light, a critical environmental trigger. This study enhances our understanding of acetylation’s role in plant adaptation to environmental stimuli, which is critical for the plant stress response. Furthermore, targeting lysine acetylation pathways could provide novel strategies to optimize photosynthesis, potentially aiding in the development of plant species better adapted to low or artificial light.

Mapping protein locations in 3D tissues

Like in real estate, location matters in biology. The location of proteins in tissues affects cellular processes like signaling and metabolism. Aberrant protein distribution can lead to cancer and neurodegenerative disorders. Mass spectrometry, or MS, is the gold standard in proteomics for precise analysis of protein composition. New approaches like spatial proteomics allow researchers to analyze proteins within their tissue context; thus, offering crucial insights into cellular organization and activity.

Researchers are evaluating the use of various MS techniques for improving spatial proteomics. In their Molecular & Cellular Proteomics paper, Yumi Kwon of the Pacific Northwest National Laboratory and colleagues analyzed thin slices of human pancreatic tissue using three MS-based techniques: label-free quantification, or LFQ, tandem mass tag MS-2, or TMT-MS2, and TMT-MS3. LFQ identified about 3,500 proteins with quantitative accuracy but low throughput. Both TMT methods achieved high throughput, generating 125 pixels per day. Conversely, TMT-MS3 performed poorly in detecting low-abundance proteins. Therefore, the researchers concluded that LFQ is best for achieving accurate quantification while TMT-MS2 is best suited for large experiments.

This study provides a framework to evaluate how to use traditional MS techniques for spatial proteomics. The researchers’ findings put forth robust methods that may be able to analyze diseased tissues with high spatial resolution and sensitivity, which will enhance our understanding of tissue heterogeneity.

Demystifying the glycan–protein interactome

Glycans are complex carbohydrates that bind to biomolecules like toxins, enzymes, proteins and lipids. They act as molecular beacons for glycan-binding proteins, or GBPs, which mediate processes such as cell communication, pathogen recognition, toxin neutralization and enzymatic regulation. Lectins, a type of GBP, help the immune system distinguish self from nonself molecules and facilitate cell adhesion, as antibodies can also bind glycans made by humans and infectious organisms.  

In their review in Molecular & Cellular Proteomics, Jamie Heimburg–Molinaro and colleagues from Harvard Medical School explored the role of glycan microarrays in studying glycan–protein interactions. These microarrays act like molecular jigsaw puzzles, with each glycan "key" binding to a specific protein "lock." One microarray enables the testing of hundreds of glycan–protein combinations simultaneously. The authors highlighted examples such as DNA-based and liquid glycan microarrays, which are useful in identifying molecular targets for diagnostics and treatments. Advancements in microarray technology have led to novel findings, including the binding of antibodies from parasite-infected individuals to core xylose and fucose and SARS-CoV-2 binding to phosphorylated glycans and glycosaminoglycans. Additionally, microarrays identified antibodies targeting laminaribioside and chitobioside markers for Crohn’s disease. While glycan microarrays have advanced our understanding of glycan biology, the authors concluded that overcoming challenges like the complexity of glycan–protein interactions and addressing cost and reusability limitations will be key to future progress.