Protein cycling in the eastern tropical North Pacific oxygen‐deficient zone: A de novo‐discovery peptidomic approach

peer-reviewed · Limnology and Oceanography · 2022

peer-reviewed · Limnology and Oceanography · 2022. Megan E. Duffy et al. Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the…
Date 2022-02-01
Type peer-reviewed
Venue Limnology and Oceanography
Publisher Wiley
Contribution downstream-application
DOI 10.1002/lno.12012
Citations (OpenAlex) 5

Abstract

Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the eastern tropical North Pacific oxygen‐deficient zone (ODZ) and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. The benchmarking experiment with Prochlorococcus shows de novo peptides to be taxonomically specific, and thus of value in augmenting database‐driven approaches. Analysis of the suspended and sinking particles using the de novo‐discovery approach reveals the presence of fungal proteins in deep sinking particles that were not in our original search database, contributing to growing recognition that fungi may play important roles in marine organic matter cycling. Cyanobacterial peptides that have been post‐translationally modified were tracked to depth, where they contribute ~ 1% of the phylum‐level identifiable peptide pool in the sediment trap sample. The majority of peptides found at depth in the detrital pool are associated with membranes, indicating that cellular location is associated with early preservation within the detrital pool. Modified amino acids in sinking and suspended particles include high levels of deamidation, suggesting that partial extracellular degradation of protein could fuel observed anammox and contribute to pools of refractory organic nitrogen.

Authors

  1. Megan E. Duffy · University of Washington
  2. Jacquelyn A. Neibauer · University of Washington
  3. Jamee Adams · University of Washington
  4. Rachel A. Lundeen · University of Washington
  5. Gabrielle Rocap · University of Washington
  6. Anitra E. Ingalls · University of Washington
  7. Clara A. Fuchsman · University of Washington
  8. Richard G. Keil · University of Washington

Methods and tools

  • Oxygen-deficient zone de novo peptidomics: De novo peptides from sinking and suspended particles in the eastern tropical North Pacific revealed fungal proteins and tracked modified cyanobacterial peptides with depth.

Methods it uses

  • PEAKS: Commercial DP-based de novo

Cites (9)

Seen in the charts

Back to the full map

Back to top