{"id":{"repo_id":"woods-hole","oai_identifier":"oai:darchive.mblwhoilibrary.org:1912/72176"},"canonical_url":"https://search.dev.ndltd.org/etd/woods-hole/oai:darchive.mblwhoilibrary.org:1912/72176","repository":{"repo_id":"woods-hole","name":"Woods Hole Oceanographic Institute","base_url":"https://darchive.mblwhoilibrary.org/server/oai/request"},"display":{"title":"The exo-proteomic framework for nitrogen acquisition from proteinaceous organic matter in the model marine heterotroph Ruegeria pomeroyi DSS-3","abstract":"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.","abstract_html":"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.","abstract_has_math":false,"creators":["Stemmer, Fadime Renée"],"institution":"Massachusetts Institute of Technology and Woods Hole Oceanographic Institution","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Saito, Mak A."],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-09","date_published":"2025-09","updated_at":"2026-07-27T22:05:02Z","subjects":["Proteomics","Nitrogen","Marine biochemistry"],"languages":[],"rights":["Attribution 4.0 International"],"rights_urls":["https://creativecommons.org/licenses/by-nc/4.0/"],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.1575/1912/72176"],"render_values":[{"text":"10.1575/1912/72176","href":"https://doi.org/10.1575/1912/72176","code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/1912/72176","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Saito, Mak A."]},{"key":"dc:creator","label":"Author","values":["Stemmer, Fadime Renée"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-09-03T15:09:55Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-09-03T15:09:55Z"]},{"key":"dc:date.issued","label":"Date","values":["2025-09"]},{"key":"dc:publisher","label":"Institution","values":["Massachusetts Institute of Technology and Woods Hole Oceanographic Institution"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Proteomics","Nitrogen","Marine biochemistry"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["Attribution 4.0 International"]},{"key":"dc:rights.uri","label":"Rights URI","values":["https://creativecommons.org/licenses/by-nc/4.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.1575/1912/72176"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1912/72176"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submitted in partial fulfillment of the requirements for the degree of Master of Science in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2025."]},{"key":"dc:description.abstract","label":"Abstract","values":["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."]},{"key":"dc:title","label":"Title","values":["The exo-proteomic framework for nitrogen acquisition from proteinaceous organic matter in the model marine heterotroph Ruegeria pomeroyi DSS-3"]}]}],"canonical_facts":{"dc:contributor.advisor":["Saito, Mak A."],"dc:creator":["Stemmer, Fadime Renée"],"dc:date.accessioned":["2025-09-03T15:09:55Z"],"dc:date.available":["2025-09-03T15:09:55Z"],"dc:date.issued":["2025-09"],"dc:description":["Submitted in partial fulfillment of the requirements for the degree of Master of Science in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2025."],"dc:description.abstract":["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."],"dc:identifier.doi":["10.1575/1912/72176"],"dc:identifier.uri":["https://hdl.handle.net/1912/72176"],"dc:publisher":["Massachusetts Institute of Technology and Woods Hole Oceanographic Institution"],"dc:rights":["Attribution 4.0 International"],"dc:rights.uri":["https://creativecommons.org/licenses/by-nc/4.0/"],"dc:subject":["Proteomics","Nitrogen","Marine biochemistry"],"dc:title":["The exo-proteomic framework for nitrogen acquisition from proteinaceous organic matter in the model marine heterotroph Ruegeria pomeroyi DSS-3"],"dc:type":["Thesis"]},"updated_at":"2026-07-27T22:05:02Z"}