PXD027843

PXD027843 is an original dataset announced via ProteomeXchange.

Title	Degradation of diatom protein in seawater: a peptide-level view
Description	Peptides were identified during degradation of the diatom Thalassiosira weissflogii with and without the use of the enzyme trypsin. This allows comparison of protein degradation occurring within the experiment (no trypsin added; peptides already present due to in situ degradation) and the protein still available for future degradation (peptides released from protein when trypsin is added during analysis). Over the 12-day degradation experiment 31% of the particulate organic carbon was depleted and there was no preferential degradation of the overall protein pool. However, there was distinct differentiation in the cellular location, secondary structure and modifications of the peptides that were either degraded or remained. During the initial period of rapid algal decay and bacterial growth, intracellular components from the cytoplasm were selectively consumed, resulting in the accumulation of membrane-associated proteins and peptides in the detrital pool. Accompanying this was an increase in the importance of membrane-bound ɑ-helix motifs. At the end of the 12 day experiment, the natural bacterial assemblage was focusing on degradation of membrane-associated proteins, which was the dominant source of peptides in both the residual pool (released by trypsin) and the actively degraded pool (no trypsin added). Methylated arginine, a post-translationally modified amino acid that is produced within the diatom prior to senescence, is found in high amounts within the detrital peptide pool, suggesting a link between in-cell modification and resistance to immediate degradation. Another modification - asparagine deamidation - appears to occur during degradation and deamidated peptides also accumulate within the detritus. The bacterial community decomposing the algal material was rich in proteobacteria, and employed a growth approach focusing on accumulation of solubilized material across their membranes and on DNA replication. At this early stage of diagenesis, no changes in bulk amino acids (THAA) were observed, yet a peptidomic approach allowed us to observe the differential changes in diatom protein preservation by discriminating between intracellular location, secondary structure, and modifications status.
HostingRepository	PRIDE
AnnounceDate	2021-12-20
AnnouncementXML	Submission_2021-12-20_11:27:05.777.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Keil
SpeciesList	scientific name: environmental samples
ModificationList	methylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-10 03:48:11	ID requested
⏵ 1	2021-12-20 11:27:06	announced

Dataset with its publication pending

submitter keyword: marine organic matter, marine metaproteomics, environmental peptidomics, protein cycling, phytoplankton bloom, particulate organic matter, amino acids, early diagenesis, peptidomics, peptide degradation

Richard Keil
contact affiliation	Oceanography, University of Washington, USA
contact email	rickkeil@uw.edu
lab head
Richard Keil
contact affiliation	University of Washington
contact email	keillab@uw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027843
     1. Label: PRIDE project
     2. Name: Degradation of diatom protein in seawater: a peptide-level view