Summary of project PR002738
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002738. The data can be accessed directly via it's Project DOI: 10.21228/M8R54Z This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR002738 |
| Project DOI: | doi: 10.21228/M8R54Z |
| Project Title: | Conserved pathway for homarine catabolism in environmental bacteria |
| Project Summary: | Homarine (N-methylpicolinic acid) is a ubiquitous marine metabolite produced by phytoplankton and noted for its bioactivity in marine animals, yet its microbial degradation pathways are uncharacterized. Here, we identify a conserved operon (homABCDER) that mediates homarine catabolism in bacteria using comparative transcriptomics, mutagenesis, and targeted knockouts. Phylogenetic and genomic analyses show this operon distributed across abundant bacterial clades, including coastal copiotrophs (e.g., Rhodobacterales) and open-ocean oligotrophs (e.g., SAR11, SAR116). High-resolution mass spectrometry revealed N-methylglutamic acid and glutamic acid as key metabolic products of homarine in both model and natural systems, with N-methylglutamate dehydrogenase catalyzing their conversion. Metatranscriptomics showed responsive and in situ expression of hom genes aligned with homarine availability. These findings uncover the genetic and metabolic basis of homarine degradation, establish its ecological relevance, and highlight homarine as a versatile growth substrate that feeds into central metabolism via glutamic acid in diverse marine bacteria. |
| Institute: | University of Washington, School of Oceanography |
| Last Name: | Heal |
| First Name: | Katherine |
| Address: | 1501 NE Boat Street, Marine Science Building, Room G, Seattle |
| Email: | katherine.heal@pnnl.gov |
| Phone: | 612-616-4840 |
Summary of all studies in project PR002738
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST004324 | Homarine catabolism: Cobetia sp. OBi1 comparative metabolomics under homarine and glucose supported growth | Cobetia marina | University of Washington, School of Oceanography | MS | 2026-01-02 | 1 | 18 | Uploaded data (241.7M)* |
| ST004337 | Homarine catabolism: Ruegeria pomeroyi DSS-3 comparative metabolomics under homarine and glucose supported growth | Ruegeria pomeroyi | University of Washington, School of Oceanography | MS | 2026-01-02 | 1 | 26 | Uploaded data (496.1M)* |
| ST004347 | Homarine Catabolism: In situ metabolomics from KM1906, surface samples along a transect in the North Pacific | University of Washington | MS | 2026-01-02 | 1 | 140 | Uploaded data (1.5G)* | |
| ST004352 | Homarine catabolism: Marine microbial isotope-tracing metabolomics experiments for cruise TN397 in the Fall of 2021 at two different stations in the North Pacific | University of Washington, School of Oceanography | MS | 2026-01-02 | 1 | 74 | Uploaded data (0.9G)* | |
| ST004353 | Homarine catabolism: Marine microbial isotope-tracing metabolomics experiments for cruise TN412 in the Winter of 2023 at two different stations in the North Pacific | University of Washington, School of Oceanography | MS | 2026-01-02 | 1 | 68 | Uploaded data (797.1M)* | |
| ST004354 | Homarine catabolism: Marine microbial isotope-tracing metabolomics experiments for cruise RC104 in the Summer of 2023 in Puget Sound | University of Washington, School of Oceanography | MS | 2026-01-02 | 1 | 66 | Uploaded data (642.9M)* |
