#METABOLOMICS WORKBENCH katherine_heal_20251106_111613 DATATRACK_ID:6630 STUDY_ID:ST004352 ANALYSIS_ID:AN007266 PROJECT_ID:PR002738 VERSION 1 CREATED_ON November 11, 2025, 9:09 am #PROJECT PR:PROJECT_TITLE Conserved pathway for homarine catabolism in environmental bacteria PR:PROJECT_SUMMARY Homarine (N-methylpicolinic acid) is a ubiquitous marine metabolite produced by PR:PROJECT_SUMMARY phytoplankton and noted for its bioactivity in marine animals, yet its microbial PR:PROJECT_SUMMARY degradation pathways are uncharacterized. Here, we identify a conserved operon PR:PROJECT_SUMMARY (homABCDER) that mediates homarine catabolism in bacteria using comparative PR:PROJECT_SUMMARY transcriptomics, mutagenesis, and targeted knockouts. Phylogenetic and genomic PR:PROJECT_SUMMARY analyses show this operon distributed across abundant bacterial clades, PR:PROJECT_SUMMARY including coastal copiotrophs (e.g., Rhodobacterales) and open-ocean oligotrophs PR:PROJECT_SUMMARY (e.g., SAR11, SAR116). High-resolution mass spectrometry revealed PR:PROJECT_SUMMARY N-methylglutamic acid and glutamic acid as key metabolic products of homarine in PR:PROJECT_SUMMARY both model and natural systems, with N-methylglutamate dehydrogenase catalyzing PR:PROJECT_SUMMARY their conversion. Metatranscriptomics showed responsive and in situ expression PR:PROJECT_SUMMARY of hom genes aligned with homarine availability. These findings uncover the PR:PROJECT_SUMMARY genetic and metabolic basis of homarine degradation, establish its ecological PR:PROJECT_SUMMARY relevance, and highlight homarine as a versatile growth substrate that feeds PR:PROJECT_SUMMARY into central metabolism via glutamic acid in diverse marine bacteria. PR:INSTITUTE University of Washington, School of Oceanography PR:LAST_NAME Heal PR:FIRST_NAME Katherine PR:ADDRESS 1501 NE Boat Street, Marine Science Building, Room G, Seattle PR:EMAIL katherine.heal@pnnl.gov PR:PHONE 612-616-4840 PR:PUBLICATIONS DOI 10.21203/rs.3.rs-7359689/v1 #STUDY ST:STUDY_TITLE Homarine catabolism: Isotope-tracing metabolomics experiments for cruise TN397 ST:STUDY_SUMMARY Stable-isotope probing was performed to track homarine degradation products in ST:STUDY_SUMMARY natural marine microbial communities from three locations (Figure 2D of DOI ST:STUDY_SUMMARY 10.21203/rs.3.rs-7359689/v1). Seawater incubated with isotopically-labeled ST:STUDY_SUMMARY 2H3-homarine was analyzed for the compounds enriched in our model organisms (see ST:STUDY_SUMMARY other studies within this project), with the isotopic labels. ST:INSTITUTE University of Washington, School of Oceanography ST:LAST_NAME Heal ST:FIRST_NAME Katherine ST:ADDRESS 1501 NE Boat Street, Marine Science Building, Room G, Seattle ST:EMAIL katherine.heal@pnnl.gov ST:PHONE 612-616-4840 ST:STUDY_COMMENTS Part of project 6620 ST:PUBLICATIONS DOI 10.21203/rs.3.rs-7359689/v1 #SUBJECT SU:SUBJECT_TYPE Water sample #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - 230724_Smp_G4_1_C-H_t0_A Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 experiment_id=G4_1; RAW_FILE_NAME(raw_file_name)=230724_Smp_G4_1_C-H_t0_A.mzML SUBJECT_SAMPLE_FACTORS - 230724_Smp_G4_1_C-H_t0_B Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 experiment_id=G4_1; RAW_FILE_NAME(raw_file_name)=230724_Smp_G4_1_C-H_t0_B.mzML SUBJECT_SAMPLE_FACTORS - 230724_Smp_G4_1_C-H_t0_C Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 experiment_id=G4_1; 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RAW_FILE_NAME(raw_file_name)=230724_Std_4uMStdsMix2InH2O_3.mzML SUBJECT_SAMPLE_FACTORS - 230724_Std_4uMStdsMix2InH2O_4 Sample source:Standards | treatment:N/A | timepoint:N/A | lat_collected:N/A | lon_collected:N/A | date_collected:N/A experiment_id=N/A; RAW_FILE_NAME(raw_file_name)=230724_Std_4uMStdsMix2InH2O_4.mzML SUBJECT_SAMPLE_FACTORS - 230724_Std_4uMStdsMix2InH2O_5 Sample source:Standards | treatment:N/A | timepoint:N/A | lat_collected:N/A | lon_collected:N/A | date_collected:N/A experiment_id=N/A; RAW_FILE_NAME(raw_file_name)=230724_Std_4uMStdsMix2InH2O_5.mzML SUBJECT_SAMPLE_FACTORS - 230724_Std_4uMStdsMix2InH2O_6 Sample source:Standards | treatment:N/A | timepoint:N/A | lat_collected:N/A | lon_collected:N/A | date_collected:N/A experiment_id=N/A; RAW_FILE_NAME(raw_file_name)=230724_Std_4uMStdsMix2InH2O_6.mzML #COLLECTION CO:COLLECTION_SUMMARY Experiments using 2H3-homarine were performed on research cruise TN397 in the CO:COLLECTION_SUMMARY Fall of 2021 at two different stations in the North Pacific (described in Table CO:COLLECTION_SUMMARY S8 and displayed in Figure 2 of 10.21203/rs.3.rs-7359689/v1). 2H3-homarine was CO:COLLECTION_SUMMARY purchased from Toronto Research Chemicals and was injected onto a Q-Exactive HF CO:COLLECTION_SUMMARY Orbitrap Mass Spectrometer (QE-HF) to confirm the mass of the deuterium label CO:COLLECTION_SUMMARY (141.0743 m/z) and the retention time (6.4 minutes, same as non-labeled CO:COLLECTION_SUMMARY homarine). Seawater was collected into 21 acid washed 10 L polycarbonate carboys CO:COLLECTION_SUMMARY from a trace metal clean stayfish system suspended at a depth of 8 m and CO:COLLECTION_SUMMARY prefiltered through 100 µm nylon mesh. Three unamended samples were collected CO:COLLECTION_SUMMARY immediately after seawater collection to provide samples of the starting CO:COLLECTION_SUMMARY community. Nine treatment bottles were spiked with 500 nM 2H3-homarine with nine CO:COLLECTION_SUMMARY control bottles receiving no additions. Bottles were incubated in blue-shaded CO:COLLECTION_SUMMARY temperature and light-controlled incubators designed to mimic mixed-layer CO:COLLECTION_SUMMARY conditions of the sampling location. Triplicate bottles with and without CO:COLLECTION_SUMMARY homarine addition were harvested at 2, 24, and 48 hours. All particulate samples CO:COLLECTION_SUMMARY (4 L) were collected using peristaltic pumps onto Durapore® 0.22 μm, 47 mm, CO:COLLECTION_SUMMARY hydrophilic PVDF membrane filters, flash frozen in liquid nitrogen, and stored CO:COLLECTION_SUMMARY at -80°C. CO:SAMPLE_TYPE Marine particulate matter #TREATMENT TR:TREATMENT_SUMMARY Nine treatment bottles were spiked with 500 nM 2H3-homarine with nine control TR:TREATMENT_SUMMARY bottles receiving no additions. Bottles were incubated in blue-shaded TR:TREATMENT_SUMMARY temperature and light-controlled incubators designed to mimic mixed-layer TR:TREATMENT_SUMMARY conditions of the sampling location. Triplicate bottles with and without TR:TREATMENT_SUMMARY homarine addition were harvested at 2, 24, and 48 hours. The experiment was TR:TREATMENT_SUMMARY repeated with the same treatments at a second location. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY For particulate metabolomics, cell pellets were extracted using a combination of SP:SAMPLEPREP_SUMMARY mechanical and chemical disruption techniques as described in previous work SP:SAMPLEPREP_SUMMARY (Boysen et al 2018). Metabolites from the supernatant were extracted using a SP:SAMPLEPREP_SUMMARY cation-exchange-based solid phase extraction technique as described previously SP:SAMPLEPREP_SUMMARY (Sacks et al 2022), with 1 mL of supernatant diluted into 10 mL of HPLC grade SP:SAMPLEPREP_SUMMARY water. To prevent confusion using the isotope labels, we used a subset of SP:SAMPLEPREP_SUMMARY isotopically-labeled internal standards, as reported in Table S17 of SP:SAMPLEPREP_SUMMARY https://doi.org/10.21203/rs.3.rs-7359689/v1. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY For HILIC chromatography, a SeQuant ZIC-pHILIC column (5 um particle size, 2.1 CH:CHROMATOGRAPHY_SUMMARY mm x 150 mm, from Millipore) was used with 10 mM ammonium carbonate in 85:15 CH:CHROMATOGRAPHY_SUMMARY acetonitrile to water (Solvent A) and 10 mM ammonium carbonate in 85:15 water to CH:CHROMATOGRAPHY_SUMMARY acetonitrile (Solvent B) at a flow rate of 0.15 mL/min. This column was compared CH:CHROMATOGRAPHY_SUMMARY with a Waters UPLC BEH amide and a Millipore cHILIC column; the pHILIC showed CH:CHROMATOGRAPHY_SUMMARY superior reproducibility and peak shapes. The column was held at 100% A for 2 CH:CHROMATOGRAPHY_SUMMARY minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held CH:CHROMATOGRAPHY_SUMMARY at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes CH:CHROMATOGRAPHY_SUMMARY total). The column was maintained at 30 C. The injection volume was 2 µL for CH:CHROMATOGRAPHY_SUMMARY samples and standard mixes. When starting a batch, the column was equilibrated CH:CHROMATOGRAPHY_SUMMARY at the starting conditions for at least 30 minutes. To improve the performance CH:CHROMATOGRAPHY_SUMMARY of the HILIC column, we maintained the same injection volume, kept the CH:CHROMATOGRAPHY_SUMMARY instrument running water blanks between samples as necessary, and injected CH:CHROMATOGRAPHY_SUMMARY standards in a representative matrix in addition to standards in water. After CH:CHROMATOGRAPHY_SUMMARY each batch, the column was flushed with 10 mM ammonium carbonate in 85:15 water CH:CHROMATOGRAPHY_SUMMARY to acetonitrile for 20 to 30 minutes. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Waters Acquity I-Class CH:COLUMN_NAME SeQuant ZIC- pHILIC (150 x 2.1mm,5um) CH:SOLVENT_A 85% acetonitrile/15% water; 10 mM ammonium carbonate CH:SOLVENT_B 15% acetonitrile/85% water; 10 mM ammonium carbonate CH:FLOW_GRADIENT The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, CH:FLOW_GRADIENT ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated CH:FLOW_GRADIENT at 100% A for 25 minutes CH:FLOW_RATE 0.15 mL/min CH:COLUMN_TEMPERATURE 30 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF-X Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS MS acquisition Comments: Polarity switching was used with a scan range of 60 to MS:MS_COMMENTS 900 m/z and a resolution of 60,000. MS parameters were as follows: capillary MS:MS_COMMENTS temperature was 320 ∞C, the H-ESI spray voltage was 3.3 kV, and the auxiliary MS:MS_COMMENTS gas heater temperature was 100 ∞C. The S-lens RF level was 65. Sheath gas, MS:MS_COMMENTS auxiliary gas, and sweep gas flow rates were maintained at 16, 3, and 1, MS:MS_COMMENTS respectively. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS normalized peak area MS_METABOLITE_DATA_START Samples 230724_Smp_G4_1_C-H_t0_A 230724_Smp_G4_1_C-H_t0_B 230724_Smp_G4_1_C-H_t0_C 230724_Smp_G4_1_C-H_t2_A 230724_Smp_G4_1_C-H_t2_B 230724_Smp_G4_1_C-H_t2_C 230724_Smp_G4_1_C-H_t24_A 230724_Smp_G4_1_C-H_t24_B 230724_Smp_G4_1_C-H_t24_C 230724_Smp_G4_1_C-H_t48_A 230724_Smp_G4_1_C-H_t48_B 230724_Smp_G4_1_C-H_t48_C 230724_Smp_G4_1_H_t2_A 230724_Smp_G4_1_H_t2_B 230724_Smp_G4_1_H_t2_C 230724_Smp_G4_1_H_t24_A 230724_Smp_G4_1_H_t24_B 230724_Smp_G4_1_H_t24_C 230724_Smp_G4_1_H_t48_A 230724_Smp_G4_1_H_t48_B 230724_Smp_G4_1_H_t48_C 230724_Smp_G4_2_C-H_t0_A 230724_Smp_G4_2_C-H_t0_B 230724_Smp_G4_2_C-H_t0_C 230724_Smp_G4_2_C-H_t2_A 230724_Smp_G4_2_C-H_t2_B 230724_Smp_G4_2_C-H_t2_C 230724_Smp_G4_2_C-H_t24_A 230724_Smp_G4_2_C-H_t24_B 230724_Smp_G4_2_C-H_t24_C 230724_Smp_G4_2_C-H_t48_A 230724_Smp_G4_2_C-H_t48_B 230724_Smp_G4_2_C-H_t48_C 230724_Smp_G4_2_H_t2_A 230724_Smp_G4_2_H_t2_B 230724_Smp_G4_2_H_t2_C 230724_Smp_G4_2_H_t24_A 230724_Smp_G4_2_H_t24_B 230724_Smp_G4_2_H_t24_C 230724_Smp_G4_2_H_t48_A 230724_Smp_G4_2_H_t48_B 230724_Smp_G4_2_H_t48_C Factors Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:27.0673 | lon_collected:-126.6739 | date_collected:20211123 Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:0 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Control | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:2 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:24 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 Sample source:Filtered Cells | treatment:Homarine (2H3-labelled) | timepoint:48 | lat_collected:0.1812 | lon_collected:-141.9465 | date_collected:20211208 UDP-N-acetylglucosamine 47390 144040 40632 86567 43450 79056 216530 199671 232584 624135 429910 619025 379460 550804 459559 663950 755529 550079 626461 562127 604609 327069 466075 564500 620984 791100 373312 L-Cysteic acid 74340 43684 69331 71383 48072 97496 68196 142124 89607 73055 125895 178838 129767 52071 202613 73696 958714 914160 844601 992792 904234 838837 1767737 1878656 2328518 3663385 2862927 3357297 1193931 1303540 901808 1920775 1856256 1897580 6519472 5029075 2002001 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name molecule_id stable_isotope_version retention_time mz UDP-N-acetylglucosamine UDP-N-acetylglucosamine 12.75 606.0738 L-Cysteic acid Cysteic acid 12.15 167.9967 METABOLITES_END #END