Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO): A long-lived protein in the deep ocean

We demonstrate that the distribution of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in the deep North Pacific is a unique tracer for the accumulation of biochemically identifiable organic residue of the export flux. RuBisCO is found both dissolved and assembled in microgels in a dynamic gel-to-dissolved-to-gel continuum that may protect RuBisCO from degradation in the water column. High concentrations are located below biologically productive equatorial and subarctic systems, and low concentrations are associated with the subtropical gyre. RuBisCO tracks the advective transport of export products along deep circulation pathways of the ocean interior, serving as a quantifiable biochemical tracer of modern organic carbon exported to and resident in the deep ocean. The fate of most organic matter exported by sinking to the deep ocean interior is mineralization, which contributes to the elevated concentrations of inorganic carbon and nutrients found there. These mineralization products are returned to the ocean surface with the vertical circulation of the ocean, either to be re-assimilated into biomass and eventually returned to depth to complete the cycle or, in the case of dissolved inorganic carbon, to be exchanged with the atmosphere as CO2. A different and poorly understood fate of the exported material is to accumulate in the suspended particulate, gel, and dissolved phases as organic matter that is highly resistant to biological decay. In its most refractory form, the carbon is locked in the ocean in a stable state, unavailable for exchange with the atmosphere for periods longer than the circulation time of the ocean (Williams and Druffel 1987). The accumulated organic matter holds molecular information on the ocean’s major biogeochemical processes that has proven difficult to extract (Hansell et al. 2009); most of the organic material undergoes chemical and/or structural modifications that disguise much of the information originally held in its biochemical composition. Our limited ability to trace major biogeochemical processes and their pools has slowed assessment of the roles these processes play in the ocean carbon and nitrogen cycles. 15N-nuclear magnetic resonance spectroscopy shows that an important subset of the nitrogen (N) containing refractory material in the ocean’s interior appears in the form of amides that resist chemical hydrolysis and biological degradation for reasons that are not well understood (Aluwihare et al. 2005). Amides are found in living organisms as proteins and N-acetyl amino sugars (e.g., chitin, peptidoglycan). In surface waters, half of the materials containing amides are proteins; however, in deep oceanic waters, nearly all amides are present in the form of proteins (Aluwihare et al. 2005). Proteins are valuable as biomarkers because their amino acid sequence provides a direct link to the coding deoxyribonucleic acid (DNA) of an organism. Proteins represent the catalytic potential and reactivity of an organism and, collectively, of an ecosystem, providing a direct link between the ocean’s biology and chemistry. Thus, the identification and quantification of biogeochemically relevant proteins in the water column provides a powerful approach to understanding the cycling of major elements such as carbon (C) and N.