The exo-proteomic framework for nitrogen acquisition from proteinaceous organic matter in the model marine heterotroph Ruegeria pomeroyi DSS-3

Nitrogen-rich proteinaceous compounds are a key component of surface and upper mesopelagic particulate organic matter, and their rapid degradation by heterotrophic bacteria is an important process in releasing bioavailable nitrogen when other nitrogen containing substrates are deficient. Heterotrophs encode a wide variety of hydrolytic enzymes and nutrient transporters, which provide them with the ability to sustain nutrient stresses and inhabit protein-rich niche habitats such as sinking or suspended particles. Despite their important contribution to the oceanic nitrogen cycle, and marine biogeochemical cycles, the exact protein-level response of heterotrophic bacteria to nitrogen limitation in these environments remains unknown. In this study, Ruegeria pomeroyi strain DSS-3, a marine heterotrophic bacterium, served as model organism to investigate the shift in protein expression and secretion upon nitrogen limitation in the presence of extracellular protein. We tie these observations to extracellular protease rates determined from a fluorescence-based proteolysis assay. Our analyses reveal an increase in extracellular protease activity in response to nitrogen deficiency in DSS-3, due to increased production and secretion of type 1 secretion system dependent proteolytic enzymes into the extracellular environment. We found serine-, and metalloproteases to be important for periplasmic proteolysis, and propose an essential role for metalloproteases in the acquisition of proteinaceous nitrogen. Increased amino acid and oligopeptide uptake capabilities as well as higher abundance of amino acid dehydrogenases in the intracellular proteome further highlight this alternative process heterotrophic bacteria employ to challenge nitrogen limitation. Our study contributes to a better understanding of adaptation strategies of marine heterotrophic bacteria to proteinrich and inorganic nitrogen-limited niches, such as sinking and suspended particulate organic matter.

Grantor dc:publisher

Massachusetts Institute of Technology and Woods Hole Oceanographic Institution

Year dc:date.issued

2025

Author dc:creator

• Stemmer, Fadime Renée

Advisor dc:contributor.advisor

• Saito, Mak A.

• Proteomics
• Nitrogen
• Marine biochemistry

Statement dc:rights

• Attribution 4.0 International

Licence dc:rights.uri

• https://creativecommons.org/licenses/by-nc/4.0/

DOI

10.1575/1912/72176

OAI identifier oai:identifier

oai:darchive.mblwhoilibrary.org:1912/72176