Bioinformatic Prediction and Characterization of Proteins in Porphyra dentata by Shotgun Proteomics

Abstract

Porphyra dentata is an edible red seaweed with high nutritional value. It is widely cultivated and consumed in East Asia and has vast economic benefits. Studies have found that P. dentata is rich in bioactive substances and is a potential natural resource. In this study, label-free shotgun proteomics was first applied to identify and characterize different harvest proteins in P. dentata. A total of 13,046 different peptides were identified and 419 co-expression target proteins were characterized. Bioinformatics was used to study protein characteristics, functional expression, and interaction of two important functional annotations, amino acid, and carbohydrate metabolism. Potential bioactive peptides, protein structure, and potential ligand conformations were predicted, and the results suggest that bioactive peptides may be utilized as high-quality active fermentation substances and potential targets for drug production. Our research integrated the global protein database, the first time bioinformatic analysis of the P. dentata proteome during different harvest periods, improves the information database construction and provides a framework for future research based on a comprehensive understanding.

Conjoint transcriptomic and proteogenomic analysis of quality formation in various Porphyra dentata harvests: Photosynthesis acts as a stressor

“…Total protein was extracted from P. dentata using a method previously described by Yang et al. (2022b). Bradford's method was used to determine protein concentration, bicinchoninic acid was used as a quantitative standard to evaluate the extraction quality, and the integrity of the extracted proteins was analyzed using SDS–PAGE.…”

“…Red algae are multicellular macroalgae belonging to the clade of eukaryotes, mainly distributed in the intertidal and subtidal zones of the ocean. Due to its superior nutritional value, it has become an excellent source of raw materials for human diet and disease treatment (Rawiwan et al., 2022; Yang et al., 2022b). Porphyra , a member of the red algae, is rich in high‐quality proteins, amino acids, dietary fibers, vitamins, minerals, and potentially bioactive peptides.…”