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PXD006417

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-05-19
  • AnnouncementXML: Submission_2017-05-19_02:21:41.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Brook Nunn
  • Title: Protein recycling in Bering Sea Algal incubations
  • Description: Protein present in phytoplankton represents a large fraction of the organic nitrogen and carbon transported from its synthesis in surface waters to marine sediments. Yet relatively little is known about the longevity of identifiable protein in situ, or the potential modifications to proteins that occur during bloom termination, protein recycling and degradation. To address this knowledge gap, diatom-dominated phytoplankton was collected during the Bering Sea spring blooms of 2009 and 2010, and incubated under darkness in separate shipboard degradation ex periments spanning 11 and 53 d, respectively. In each experiment, the protein distribution was monited over time using shotgun proteomics, along with total hydrolyzable amino acids (THAAs), total protein, particulate organic carbon (POC) and nitrogen (PN), and bacterial cell abundance. Identifiable proteins, total protein and THAAs were rapidly lost during the first 5 d of enclosure in darkness in both incubations. Thereafter the loss rate was slower, and it declined further after 22 d. The initial loss of identifiable biosynthetic, glycolysis, metabolism and translation proteins after 12 h may represent shutdown of cellular activity among algal cells. Additional peptides with glycan modifications were identified in early incubation time points, suggesting that such protein modifications could be used as a marker for internal recycling processes and possibly cell death. Protein recycling was not uniform, with a subset of algal proteins including fucoxanthin chlorophyll binding proteins and RuBisCO identified after 53 d of degradation. Non-metric multidimensional scaling was used to compare the incubations with previous environmental results. The results confirmed recent observations that some fraction of algal proteins can survive water column recycling and undergo transport to marine sediments, thus contributing organic nitrogen to the benthos.
  • SpeciesList: scientific name: Thalassiosira pseudonana; NCBI TaxID: 35128;
  • ModificationList: No PTMs are included in the dataset
  • Instrument: Finnigan MAT instrument model

Dataset History

VersionDatetimeStatusChangeLog Entry
02017-05-02 01:47:19ID requested
12017-05-19 02:21:41announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. curator keyword: Metaproteomics, Biological
  2. submitter keyword: Protein recycling, Bering Sea, Amino acid, Nitrogen cycle, Tandem mass spectrometry, Diatom, Cell death, Preservation

Contact List

    Brook L. Nunn
    • contact affiliation: University of Washington, Department of Genome Sciences
    • contact email: brookh@uw.edu
    • lab head:
    Brook Nunn
    • contact affiliation: University of Washington
    • contact email: brookh@uw.edu
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
Repository Record List
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