Proteomic characterization of pilot scale hot-water extracts from the industrial carrageenan red seaweed Eucheuma denticulatum
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Elsevier
Materia
Eucheuma denticulatum Hot-water protein extraction Quantitative proteomics De novo quantitative transcriptomics Bioinformatics Subcellular localization
Date
2022-01-05Referencia bibliográfica
Simon Gregersen... [et al.]. Proteomic characterization of pilot scale hot-water extracts from the industrial carrageenan red seaweed Eucheuma denticulatum, Algal Research, Volume 62, 2022, 102619, ISSN 2211-9264, [https://doi.org/10.1016/j.algal.2021.102619]
Sponsorship
Innovation Fund Denmark 7045-00021BAbstract
Seaweeds have a long history as a resource for polysaccharides/hydrocolloids extraction for use in the food
industry due to their functionality as stabilizing agents. In addition to the carbohydrate content, seaweeds also
contains a significant amount of protein, which may find application in food and feed. Here, we present a novel
combination of transcriptomics, proteomics, and bioinformatics to determine the protein composition in two
pilot-scale extracts from Eucheuma denticilatum (Spinosum) obtained via hot-water extraction. Although the
quality of extracted protein appeared quite poor based on SDS-PAGE analysis, extracts were characterized by
qualitative and quantitative proteomics using LC-MS/MS and a de-novo transcriptome assembly for construction
of a suitable protein database. A novel concept of length-normalization for relative quantification of sub-optimal
protein extracts with partial, non-specific digestion is introduced and validated against conventional methods for
relative quantification of proteins. Despite a limited number of protein identifications due to poor protein
quality, our data suggest that the majority of quantified protein in the extracts (>75%) is constituted by merely
three previously uncharacterized proteins. Putative subcellular localization for the quantified proteins was
determined by bioinformatic prediction using several predictors, and by correlating with the expected copy
number from the transcriptome analysis, we find that the extracts appear highly enriched in extracellular proteins.
This implies that the extraction method used predominantly extracts extracellular proteins, and thus
appear ineffective for cellular disruption and subsequent release of intracellular proteins. Nevertheless, the
highly abundant proteins may be potential substrates for targeted hydrolysis and release of bioactive peptides.
Ultimately, this study highlight the potential of quantitative proteomics for characterization of alternative
protein sources intended for use in foods and evaluating protein extraction process efficiency through novel
combinations with bioinformatic analysis.