Dataset Information

Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes.

ABSTRACT: Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.

SUBMITTER: Subong BJJ

PROVIDER: S-EPMC8706660 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes.

Subong Bryan John J BJJ Malto Zabrina Bernice L ZBL Lluisma Arturo O AO Azanza Rhodora V RV Salvador-Reyes Lilibeth A LA

International journal of molecular sciences 20211211 24

Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodiniu ...[more]

PMID: 34948131

Similar Datasets

Project description:BackgroundTransplantation of osteochondral allografts (OCAs) freshly preserved for ≥30 days has proven to be a reliable technique for cartilage resurfacing. However, the prolonged storage of allografts comes at the expense of chondrocyte viability, which declines precipitously after 14 days under refrigeration. Despite this, radiographic data indicate that most allograft cartilage remains stable for years after implantation. The apparent durability of partially devitalized cartilage begs the question of how the extracellular matrix is maintained.HypothesisCompared with patients' defect cartilage, replacement OCAs freshly preserved for 36 days on average contain significantly lower levels of cartilage matrix-destructive metalloproteinases, which may contribute to the long-term stability of implanted grafts.Study designDescriptive laboratory study.MethodsChondrocyte density was determined by the cell yield from digested cartilage and by double-strand DNA content quantified with PicoGreen assay. Chondrocyte viability was estimated by staining enzymatically isolated chondrocytes with calcein AM and ethidium homodimer-2. Cartilage proteoglycan (PG) content was analyzed with dimethylmethylene blue assay. The in vitro 48-hour release of PG-depleting metalloproteinases including matrix metalloproteinase (MMP)-1, -3, -13, and ADAMTS-5 from cartilage was examined with Western blotting. The data were compared between diseased cartilage from patients and samples from matched grafts. The relative amount of MMP-3 to its endogenous inhibitor, tissue inhibitor of MMP-1 (TIMP-1), was also determined with Western blotting.ResultsChondrocyte density decreased linearly with allograft storage time and declined by an average of 43%. PG content decreased while the percentage of nonviable chondrocytes increased with storage time, with the former showing less linearity. However, PG content remained in the normal range and was significantly higher than that in patients' defect cartilage. Correspondingly, significantly less PG-depleting metalloproteinases and a much lower MMP-3/TIMP-1 ratio were detected in allograft cartilage than in patients' diseased cartilage.ConclusionThese findings indicated that, at the time of implantation, fresh-preserved OCAs contained significantly lower levels of PG-depleting metalloproteinases compared with patients' defect cartilage, which might contribute to their long-term stability in vivo.Clinical relevanceThe comparatively low expression of cartilage-dissolving metalloproteinases in human OCAs freshly preserved over 30 days offers support to the long-term durability of implanted grafts. Based on study data that showed similarity in the response to inflammatory cytokines between patients' cartilage and OCA cartilage, strategies that can alleviate inflammation may provide extra benefit for the survival of implanted grafts. In terms of the practice of graft preservation, agents that can keep balance between the ATP supply and demand or stabilize the cell membrane or inhibit the activation of metalloproteinases may significantly improve cell viability in fresh-preserved OCAs with a storage time longer than 5 weeks.

Dataset Information

Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes.

Publications

Biochemical Mapping of <i>Pyrodinium bahamense</i> Unveils Molecular Underpinnings behind Organismal Processes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets