PXD053717-1

PXD053717 is an original dataset announced via ProteomeXchange.

Title	Quantitative contributions of cyanobacterial alkaline phosphatases to biogeochemical rates in the subtropical North Atlantic
Description	Microbial enzymes alter marine biogeochemical cycles by catalyzing chemical transformations that bring elements into and out of particulate organic pools. These processes are traditionally studied through enzyme rate-based estimates and nutrient-amendment bioassays, but these approaches lack the ability to resolve species-level contributions to enzymatic rates. Molecular methods including proteomics have the potential to link the contributions of specific populations to the overall community enzymatic rate; this is important because organisms will have distinct enzyme characteristics, feedbacks, and responses to perturbations. Integrating molecular methods with rate measurements can be achieved quantitatively through absolute quantitative proteomics. Here, we use the subtropical North Atlantic as a model system to probe how absolute quantitative proteomics can provide a more comprehensive understanding of nutrient limitation in marine environments. The experimental system is characterized by phosphorus stress and potential metal-phosphorus co-limitation due to dependence of the organic phosphorus scavenging enzyme alkaline phosphatase on metal cofactors; we performed nutrient amendment incubation experiments to investigate how alkaline phosphatase abundance and activity is affected by trace metal additions. We show that the two most abundant picocyanobacteria, Prochlorocccus and Synechococcus are minor contributors to total alkaline phosphatase activity as assessed by a widely used enzyme assay. This was true even when trace metals were added, despite both species having the genetic potential to utilize both the Fe and Zn containing enzymes, PhoX and PhoA respectively. Serendipitously, we also found that the alkaline phosphatases responded to cobalt additions suggesting possible substitution of the metal center by Co in natural populations of Prochloroccocus (substitution for Fe in PhoX) and Synechococcus (substitution for Zn in PhoA). This integrated approach allows for a nuanced interpretation of how nutrient limitation affects marine biogeochemical cycles and highlights the benefit of building quantitative connections between rate and “-omics” based measurements.
HostingRepository	PRIDE
AnnounceDate	2025-10-03
AnnouncementXML	Submission_2025-10-02_18:00:52.601.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Noelle Held
SpeciesList	scientific name: Prochlorococcus marinus subsp. pastoris; NCBI TaxID: NEWT:142479; scientific name: environmental samples
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-06 18:40:42	ID requested
⏵ 1	2025-10-02 18:00:52	announced

10.5194/EGUSPHERE-2024-3996;

submitter keyword: skyline lorococcus, PRM, prochitrap fusion,marine microbes, ocean, alkaline phosphatase, synechococcus, orb

Noelle Held
contact affiliation	University of Southern California
contact email	nheld@usc.edu
lab head
Noelle Held
contact affiliation	University of Southern California
contact email	nheld@usc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053717
     1. Label: PRIDE project
     2. Name: Quantitative contributions of cyanobacterial alkaline phosphatases to biogeochemical rates in the subtropical North Atlantic