Stemmer Fadime Renée

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Last Name
Stemmer
First Name
Fadime Renée
ORCID
0009-0003-8294-9876

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  • Thesis
    The exo-proteomic framework for nitrogen acquisition from proteinaceous organic matter in the model marine heterotroph Ruegeria pomeroyi DSS-3
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2025-09) Stemmer, Fadime Renée ; Saito, Mak A.
    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.