Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0009039 urease activity	IEA GO_REF:0000120	ACCEPT	Summary: ACCEPT. UreC is the catalytic alpha subunit of urease, EC 3.5.1.5. Reason: The UniProt record names ureC1 as urease subunit alpha and assigns EC 3.5.1.5. NCBIfam TIGR01792 and PANTHER PTHR43440 support conserved urease alpha-subunit function. Falcon research also found organism-specific literature mapping NVIE_014740 to the regulated EN76 urease locus. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt RecName: Full=Urease subunit alpha; EC=3.5.1.5. file:9ARCH/ureC1/ureC1-uniprot.txt NCBIfam; TIGR01792; urease_alph; 1. file:9ARCH/ureC1/ureC1-deep-research-falcon.md Recent EN76 literature explicitly identifies ureC/NVIE_014740 as the urease alpha subunit in a urea transporter-urease operon.
GO:0016151 nickel cation binding	IEA GO_REF:0000120	ACCEPT	Summary: ACCEPT. Urease is a nickel metalloenzyme, so nickel binding is expected. Reason: Nickel binding is part of the urease catalytic mechanism. The UniProt record explicitly states that the enzyme binds two nickel ions per subunit. Family research notes that rare iron ureases exist, so nickel binding should be supported by gene-specific evidence rather than propagated blindly from urease-family membership. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt Binds 2 nickel ions per subunit. file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md PTHR43440 family research supports nickel-dependent urease annotations for canonical UreC homologs with explicit Ni-binding evidence, while warning that iron urease paralogs make blanket nickel propagation unsafe.
GO:0016787 hydrolase activity	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: KEEP_AS_NON_CORE. Correct but less informative than urease activity. Reason: Urease is a hydrolase, but this parent term is less informative than GO:0009039 urease activity and should not be treated as the core MF. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt RecName: Full=Urease subunit alpha; EC=3.5.1.5.
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: KEEP_AS_NON_CORE. Correct parent activity for urease, but the specific urease activity is the core molecular function. Reason: This parent C-N hydrolase term is technically consistent with urease chemistry, but GO:0009039 is the supported specific activity. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt RecName: Full=Urease subunit alpha; EC=3.5.1.5.
GO:0019627 urea metabolic process	IEA GO_REF:0000104	ACCEPT	Summary: ACCEPT. Urease directly metabolizes urea. Reason: ureC1 encodes the catalytic urease subunit, so urea metabolic process is a direct biological-process annotation, not merely pathway context. In EN76, urea utilization is regulated by nitrogen source and ureC/ut transcripts respond to urea versus ammonia. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md Family research identifies canonical UreC/large-subunit ureases as the catalytic subunits for urea hydrolysis, supporting urea catabolism for conserved UreC proteins. file:9ARCH/ureC1/ureC1-deep-research-falcon.md In N. viennensis EN76, ut and ureC/NVIE_014740 transcripts change about tenfold after urea versus ammonia addition, supporting regulated urea utilization by this locus.
GO:0043419 urea catabolic process	IEA GO_REF:0000041	ACCEPT	Summary: ACCEPT. The UniPathway annotation is specific and useful for this nitrogen-metabolism gene: ureC1 is a urease catalytic subunit that directly catalyzes urea degradation. Reason: UniPathway adds the correct process for the catalytic reaction. Urease hydrolyzes urea to ammonium and hydrogencarbonate/CO2, making urea catabolism direct rather than regulatory or downstream context. The Falcon report further supports intracellular urea hydrolysis rather than an extracellular urease model for EN76. Supporting Evidence: file:9ARCH/ureC1/ureC1-uniprot.txt PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. file:9ARCH/ureC1/ureC1-deep-research-falcon.md Culture studies found no extracellular urease activity and no secretion signal context for the urease genes, supporting intracellular urea catabolism in ammonia-oxidizing archaea including EN76.

Core Functions

Catalyzes urea hydrolysis as a nickel-dependent urease alpha subunit, contributing to urea catabolism in Nitrososphaera viennensis.

Molecular Function:

urease activity

Directly Involved In:

urea catabolic process

Supporting Evidence:

file:9ARCH/ureC1/ureC1-uniprot.txt
RecName: Full=Urease subunit alpha; EC=3.5.1.5.
file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md
Canonical urease large/alpha subunits house the dinuclear active site and catalyze urea hydrolysis; ureC1 has explicit EC and nickel-binding support.
file:9ARCH/ureC1/ureC1-deep-research-falcon.md
Falcon deep research supports ureC1/NVIE_014740 as the EN76 urease alpha subunit in an intracellular urea-utilization system; culture evidence indicates urea is transported into the cell, hydrolyzed by urease, and used as an ammonia source when ammonia is limiting.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000041

Gene Ontology annotation based on UniPathway vocabulary mapping

GO_REF:0000104

Automatic assignment of GO terms by UniProt keyword mapping

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

file:9ARCH/ureC1/ureC1-uniprot.txt

UniProt record for ureC1

UniProt names A0A060HK93 as urease subunit alpha, EC 3.5.1.5.

file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md

Falcon family deep research for PTHR43440 urease alpha subunits

Family research supports urease activity and urea catabolism for conserved UreC catalytic subunits, but highlights rare iron-dependent ureases as a reason not to infer nickel binding without gene-specific metal evidence.

file:9ARCH/ureC1/ureC1-deep-research-falcon.md

Falcon deep research for ureC1

Falcon deep research for ureC1 identified organism-specific support for NVIE_014740 as ureC in a regulated urea transporter-urease operon in Nitrososphaera viennensis EN76. Urea oxidation has lower apparent affinity than ammonia oxidation, and ut/ureC transcripts change about tenfold after urea versus ammonia addition.

Deep Research

Falcon

(ureC1-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 29 citations 3 artifacts 2026-05-21T18:44:49.487391

Edison artifact artifact-00 (text/markdown)

Edison artifact artifact-01 (text/markdown)

## Context ID: pqac-00000021 Figure 3 (on page 36) provides the Michaelis-Menten kinetic constants for *Nitrososphaera viennensis*, showing an apparent half-sat (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional annotation of ureC1 (UniProt A0A060HK93; locus NVIE_014740) in Nitrososphaera viennensis EN76 (9ARCH)

1) Target verification (avoid gene-symbol ambiguity)

The UniProt target (A0A060HK93) corresponds to the urease alpha (catalytic) subunit in the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76, with locus tag NVIE_014740 (gene symbol ureC/ureC1). In recent primary literature, ureC (NVIE_014740) is explicitly annotated as the urease alpha subunit in N. viennensis, and it is reported to be in the same operon as a urea transporter gene (ut; NVIE_014780), matching the UniProt-provided ORF name and functional description. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)

Earlier genomic characterization of strain EN76 also identified a contig containing a “potential urease operon”/“urease gene cluster,” supporting the presence of a urease system in this specific organism (and not a different ureC from bacteria or other archaea). (tourna2011nitrososphaeraviennensisan pages 2-3, tourna2011nitrososphaeraviennensisan pages 3-4)

2) Key concepts and current understanding (definitions and mechanistic role)

2.1 Urease and the meaning of ureC/ureC1

Urease is the enzyme that hydrolyzes urea; ureC (urease subunit alpha) encodes the catalytic subunit (often used as the functional marker gene “ureC” in environmental studies). In N. viennensis EN76, ureC1 (NVIE_014740) is part of the genetic capacity for urea utilization, which supplies intracellular ammonia that can support both biosynthesis and ammonia oxidation-derived energy metabolism in ammonia-oxidizing archaea (AOA). (qin2024ammoniaoxidizingbacteriaand pages 8-11, tourna2011nitrososphaeraviennensisan pages 3-4)

2.2 Pathway context in nitrifying archaea: urea as an ammonia precursor

Cultured AOA, including N. viennensis, can use urea such that urea hydrolysis in the cytoplasm releases ammonia that is then oxidized (and/or assimilated). Evidence supporting the intracellular coupling is that, across tested ammonia oxidizers including N. viennensis, extracellular urease activity was not detected and urease genes lacked secretion signals, supporting a model where urea is transported into the cell and hydrolyzed internally. (qin2023differentialsubstrateaffinity pages 4-7, qin2023differentialsubstrateaffinity pages 7-10)

3) Molecular function, substrate specificity, and operon/regulatory context (organism-specific)

3.1 Reaction and substrate specificity

Although the reaction chemistry is not explicitly written in the extracted text, the physiological and kinetic measurements directly establish that N. viennensis couples urea use to nitrification, and that urea is a secondary/less-preferred substrate relative to ammonia.

In N. viennensis EN76, measured apparent affinities show:
- Km(app) for ammonia oxidation: 0.68 ± 0.16 µM
- Km(app) for urea-dependent oxidation: 8.97 ± 1.27 µM

This indicates substantially lower affinity for urea (and ~10-fold lower specific affinity) than for ammonia. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 7-10, qin2024ammoniaoxidizingbacteriaand media 2caafcb9)

These organism-specific kinetic parameters are critical for functional annotation because they constrain when ureC1-mediated urea use is likely to contribute in situ (e.g., when urea is available and ammonia is scarce). (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2024ammoniaoxidizingbacteriaand media 2caafcb9)

3.2 Operon context and accessory functions (transport + urease)

In N. viennensis, ureC (NVIE_014740) is reported to be located in the same operon as a urea transporter gene ut (NVIE_014780), supporting a linked import + hydrolysis module for urea utilization. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)

Comparative genomics across nitrifiers indicates that AOA commonly encode urease structural genes (ureABC) plus accessory genes (ureDEFG), and they typically use archaeal-type urea transporters (e.g., dur3, utp/ut) rather than the bacterial high-affinity ABC transporter urtABCDE. This context supports that Nitrososphaera spp. (Group I.1b AOA, including N. viennensis) generally have the full intracellular machinery for urea uptake and urease activation. (liu2023genomicinsightinto pages 9-11, liu2023genomicinsightinto pages 1-2)

3.3 Regulation: inducible urea utilization and repression by ammonia

Multiple complementary observations show that ureC1-linked urea use is regulated by nitrogen source:

1) Transcriptomics (24 h after substrate switch): In N. viennensis, transcripts of ut and ureC (NVIE_014740) changed by ~tenfold in response to urea vs ammonia addition, indicating a strongly inducible operon responsive to N source. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)

2) Physiology / microrespirometry: When urea-grown N. viennensis cells were amended with low urea (10–20 µM) or ammonia (20–40 µM), O2 consumption responded immediately; however, when ammonia-grown cells were given 10 µM urea, there was no immediate O2 uptake for hours after ammonia depletion, consistent with repression of urea utilization during ammonia-based growth and a required adaptation period. (qin2024ammoniaoxidizingbacteriaand pages 55-58)

3) Mechanistic interpretation: The broader experimental framework supports that ammonia oxidizers can repress oxidation of extracellular ammonia when cytoplasmic urea hydrolysis satisfies N needs, consistent with regulated coupling between transport and downstream oxidation. (qin2023differentialsubstrateaffinity pages 7-10, qin2024ammoniaoxidizingbacteriaand pages 11-16)

4) Subcellular localization (where ureC1 functions)

Direct evidence supports cytoplasmic/intracellular localization of the urease system in N. viennensis and related ammonia oxidizers:
- No extracellular urease activity was detected for tested ammonia oxidizers including N. viennensis.
- Urease genes lacked signal peptides and urease operons were not flanked by secretion-system genes.

Together, these observations support that ureC1 (urease alpha subunit) acts inside the cell, consistent with an intracellular urea-to-ammonia conversion that then feeds ammonia oxidation/assimilation. (qin2023differentialsubstrateaffinity pages 4-7, qin2023differentialsubstrateaffinity pages 7-10)

5) Biological role in cellular metabolism and nitrogen cycling

5.1 Role in N. viennensis physiology

Initial genome-based characterization suggested N. viennensis EN76 “might be able to use urea instead of ammonia as sole energy source,” indicating ureC1 supports metabolic flexibility in soil environments. (tourna2011nitrososphaeraviennensisan pages 3-4)

At the single-cell level, isotopic measurements show urea is used mainly as an N source rather than a major C source: for N. viennensis, urea-derived carbon incorporation was very low (~0.1% during ammonia growth and 0.5–1.1% after urea depletion), while bicarbonate-derived carbon incorporation remained much higher, consistent with chemoautotrophic carbon fixation dominating. (qin2024ammoniaoxidizingbacteriaand pages 58-62)

5.2 Broader ecological context (soil and ocean)

Recent (2023–2024) ecosystem studies highlight how ureC/urease capacity shapes archaeal nitrifier niches:

Soils: Across major soil Nitrososphaeria lineages, 85.7–89.8% of AOA in surveyed soils were estimated to encode urease (based on ureC relative to amoA/rpoB), suggesting that urea utilization potential is widespread among soil archaeal nitrifiers related to Nitrososphaera. (liu2023genomicinsightinto pages 1-2)
Dark ocean: Quantitative metagenomic and rate measurements indicate urea is a major N source below the photic zone. UreC prevalence was estimated at 39% of deep-sea cells in one region, and 10–46% globally; on average 25% of deep-sea cells assimilated urea-derived N (or 60% of detectably active cells). Urea concentrations ranged 21 nM–1.1 µM, and urea-based nitrification could be comparable to ammonia-based nitrification at some depths/sites. (arandiagorostidi2024ureaassimilationand pages 1-2, arandiagorostidi2024ureaassimilationanda pages 8-13, arandiagorostidi2024ureaassimilationanda pages 17-20)
Quantitative nitrification example: At 150 m depth in one dataset, nitrification product accumulation reached 16.1 nmol N L−1 from ammonium and 11.8 nmol N L−1 from urea incubations, and urea-based nitrification rates were reported as statistically indistinguishable from ammonia-based rates (t-test > 0.1). (arandiagorostidi2024ureaassimilationanda pages 8-13)

These data support the interpretation that ureC-like systems, including those in Nitrososphaeria, can materially contribute to nitrogen cycling under certain substrate regimes, even if ammonia remains the preferred substrate in many settings. (arandiagorostidi2024ureaassimilationanda pages 8-13, qin2024ammoniaoxidizingbacteriaand pages 8-11)

6) Recent developments (2023–2024) and expert analysis

A key 2024 synthesis from controlled cultures is that ammonia-oxidizing archaea and bacteria differ in nitrogen-source preference strategies. For N. viennensis, this includes: (i) higher affinity for ammonia than urea, (ii) inducible ut–ureC expression, and (iii) physiological repression of urea use during ammonia growth—features that collectively support niche differentiation and help explain coexistence patterns where multiple nitrifiers share environments but exploit different nitrogen pools over time. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2024ammoniaoxidizingbacteriaand pages 55-58)

From a genomic/evolutionary perspective, a 2023 comparative genomics analysis argues urea is the most widely encoded LDON substrate among nitrifiers and that AOA urea metabolic genes (including ureC and certain transporters) show evolutionary patterns consistent with archaeal-specific trajectories and/or lateral gene transfer for some transport components. This supports ongoing research emphasis on transport and regulation as central determinants of urea utilization efficiency. (liu2023genomicinsightinto pages 1-2)

7) Current applications and real-world implementations

7.1 Environmental monitoring and biogeochemical modeling

Because ureC is a widely used marker for urease potential, quantitative evidence that ureC is present in large fractions of deep-sea cells (10–46% globally) and that urea assimilation can involve ~25% of deep-sea cells supports incorporating urea-driven processes into models of ocean nitrogen cycling and chemoautotrophic production. (arandiagorostidi2024ureaassimilationand pages 1-2, arandiagorostidi2024ureaassimilationanda pages 8-13)

Similarly, soil results indicating 85.7–89.8% of AOA in diverse soils encode urease suggest ureC-based functional profiling is useful for predicting archaeal nitrogen acquisition strategies and niche partitioning in terrestrial ecosystems, including those influenced by fertilizer-derived urea. (liu2023genomicinsightinto pages 1-2)

7.2 Interpreting ureC as an activity proxy (limitations)

Recent field observations caution that ureC abundance does not always predict urea oxidation rates. For example, Southern Ocean work reported variable Thaumarchaeota ureC abundance (highest mean 1.2 × 10^6 copies L−1 in one water mass) but found urea oxidation rates generally lower than ammonia oxidation and not well correlated with marker gene ratios, indicating regulation and community context must be considered in applications that infer function from gene abundance alone. (hollibaugh2023contributionofurean pages 14-18)

8) Evidence tables

The following tables compile organism-specific ureC1 evidence and 2023–2024 quantitative developments with URLs and publication dates.

Claim/Topic	Key findings (include quantitative values)	Evidence type	Source (full citation short)	Publication date	URL
Target identity verification	In Nitrososphaera viennensis EN76, ureC / NVIE_014740 is explicitly identified as the urease alpha subunit; it is reported in the same operon as a urea transporter gene ut / NVIE_014780, matching UniProt A0A060HK93 annotation (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)	Transcriptomics / genome-linked annotation	Qin et al., Nat Microbiol	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Primary function and substrate preference in EN76	N. viennensis uses urea as an alternative N/energy source precursor but prefers ammonia over urea: apparent Km(app) for ammonia 0.68 ± 0.16 µM versus urea 8.97 ± 1.27 µM; specific affinity for urea is ~10-fold lower than for ammonia (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 7-10, qin2024ammoniaoxidizingbacteriaand media 2caafcb9)	Culture kinetics	Qin et al., Nat Microbiol	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Regulation of ureC1 by nitrogen source	After substrate switching, ut and ureC (NVIE_014740) transcripts changed by about 10-fold within 24 h: induced after urea addition and reduced after ammonia addition; by contrast amt1 remained similar (1,379 TPM on ammonia vs 1,348 TPM on urea; P = 0.84) (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)	Transcriptomics	Qin et al., Nat Microbiol	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Physiological switching behavior	Urea-grown EN76 showed immediate O2 consumption when low urea (10–20 µM) or ammonia (20–40 µM) was added, but ammonia-grown cells given 10 µM urea showed no immediate O2 uptake until after ammonia depletion, indicating repression of urea use during ammonia growth; EN76 maintained growth without a pronounced lag during transition (qin2024ammoniaoxidizingbacteriaand pages 55-58)	Physiology / microrespirometry	Qin et al., Nat Microbiol	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Cellular role of urea in EN76	NanoSIMS-based single-cell data indicate AOM use urea mainly as an N source rather than C source; in soil AOA N. viennensis, urea-derived C was only ~0.1% during ammonia growth, increasing to 0.5–1.1% after urea depletion, while bicarbonate-derived C remained much larger (13 ± 4.5% → 8.0 ± 3.5%) (qin2024ammoniaoxidizingbacteriaand pages 58-62)	Single-cell isotope tracing	Qin et al., Nat Microbiol	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Localization of urease system	Across tested ammonia oxidizers including EN76, no extracellular urease activity was detected; no signal peptides were found in urease genes and no nearby secretion-system genes were found, supporting cytoplasmic localization of urease/ureC1 (qin2023differentialsubstrateaffinity pages 4-7)	Enzyme assay + comparative genomics	Qin et al., bioRxiv	Aug 2023	https://doi.org/10.1101/2023.08.04.551995
Broader AOA genomic context	Review/genomic survey of 70 nitrifier genomes found urea to be the most commonly encoded LDON substrate; AOA generally carry ureABC plus ureDEFG and use archaeal transporter types dur3 and/or utp rather than bacterial urtABCDE; experimental urea use is confirmed for N. viennensis EN76 (liu2023genomicinsightinto pages 9-11, liu2023genomicinsightinto pages 1-2)	Comparative genomics / review	Liu et al., Front Microbiol	Dec 2023	https://doi.org/10.3389/fmicb.2023.1273211
Initial discovery of urease capacity in EN76	Draft genome of EN76 contained a contig with a potential urease operon/urease gene cluster, leading the authors to propose that this soil AOA could use urea instead of ammonia as sole energy source; this provided the first genome-based indication for ureC1 function in this organism (tourna2011nitrososphaeraviennensisan pages 3-4, tourna2011nitrososphaeraviennensisan pages 2-3)	Genomics / culture characterization	Tourna et al., PNAS	Apr 2011	https://doi.org/10.1073/pnas.1013488108
Soil archaeal prevalence of urease potential	Across 12 major soil Nitrososphaeria lineages, 85.7–89.8% of AOA in surveyed soils were estimated to encode urease (based on ureC relative to amoA/rpoB), indicating urea use is widespread among soil archaeal nitrifiers related to Nitrososphaera (liu2023genomicinsightinto pages 1-2)	Soil metagenomics / expression-focused ecology	Zhao et al., ISME J	Aug 2023	https://doi.org/10.1038/s41396-023-01493-y
Environmental significance of archaeal ureC	In dark-ocean metagenomes, ureC occurred in 39% of deep-sea cells regionally and 10–46% globally (median ~36%); on average 25% of deep-sea cells assimilated urea-derived N (or 60% of active cells), and urea-based nitrification occurred at all sampled depths at one site (arandiagorostidi2024ureaassimilationanda pages 13-17, arandiagorostidi2024ureaassimilationand pages 1-2, arandiagorostidi2024ureaassimilationanda pages 17-20, arandiagorostidi2024ureaassimilationanda pages 8-13)	Environmental metagenomics + rates	Arandia-Gorostidi et al., ISME J	Jan 2024	https://doi.org/10.1093/ismejo/wrae230
Quantitative urea contribution to marine nitrification	Southern Ocean data showed Thaumarchaeota-associated ureC abundance was variable (highest mean 1.2 × 10^6 copies L^-1 in CDW); mean ureC/rrs ~0.14 overall. Ammonia oxidation averaged 10.9 nmol L^-1 d^-1 versus urea oxidation 2.6 nmol L^-1 d^-1 (or 1.5 excluding outliers), suggesting urea makes a significant but smaller, context-dependent contribution to nitrification (hollibaugh2023contributionofurean pages 14-18)	Environmental rates + qPCR/metagenetics	Hollibaugh et al., preprint/2023 study	2023	URL not available in retrieved context

Table: This table compiles organism-specific and ecosystem-level evidence relevant to ureC1 (NVIE_014740) in Nitrososphaera viennensis EN76, emphasizing verified identity, biochemical role, regulation, localization, and recent quantitative findings from 2023–2024 literature.

Study/system	Key quantitative results	Implication/application	Publication date	URL
Qin et al. 2024 — Nitrososphaera viennensis EN76 culture physiology and regulation	In N. viennensis, ureC (NVIE_014740) and adjacent ut (NVIE_014780) transcripts changed by ~10-fold within 24 h after switching between urea and ammonia; apparent substrate affinities showed Km(app) ammonia = 0.68 ± 0.16 µM versus Km(app) urea = 8.97 ± 1.27 µM, with ~10-fold lower specific affinity for urea; ammonia-grown cells given 10 µM urea showed no immediate O2 uptake until ammonia depletion, indicating repression of urea use during ammonia growth (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2024ammoniaoxidizingbacteriaand pages 55-58, qin2024ammoniaoxidizingbacteriaand media 2caafcb9)	Shows that urease-linked urea oxidation in soil AOA is inducible but typically secondary to ammonia use; useful for modeling nitrogen-source competition in soils and bioreactors and for interpreting ureC expression as a condition-dependent, not constitutive, marker	Jan 2024	https://doi.org/10.1038/s41564-023-01593-7
Zhao et al. 2023 — soil Nitrososphaeria resource acquisition	Across 12 major soil Nitrososphaeria lineages, 85.7–89.8% of AOA in surveyed soils were estimated to encode urease based on ureC relative to amoA/rpoB reads (liu2023genomicinsightinto pages 1-2)	Indicates that urea use is a widespread niche-defining trait in soil archaeal nitrifiers, supporting application of ureC-based analyses in predicting nitrogen acquisition strategies and coexistence patterns in agricultural and natural soils	Aug 2023	https://doi.org/10.1038/s41396-023-01493-y
Arandia-Gorostidi et al. 2024 — dark ocean urea assimilation and nitrification	Regional deep-sea metagenomes estimated ureC in 39% of cells; global datasets estimated 10–46% of deep-sea cells carry ureC (median ~36%); on average 25% of deep-sea cells assimilated urea-derived N, or 60% of detectably active cells; urea concentrations ranged 21 nM–1.1 µM; peak nitrification at 150 m reached 16.1 nmol N L^-1 from ammonium and 11.8 nmol N L^-1 from urea; urea-based nitrification rates were statistically indistinguishable from ammonia-based rates at sampled depths; urea-supported chemoautotrophic C fixation was estimated at 1.4–8.8 mg C m^-2 d^-1, ~5–7% of sinking POC at study sites (arandiagorostidi2024ureaassimilationanda pages 13-17, arandiagorostidi2024ureaassimilationand pages 1-2, arandiagorostidi2024ureaassimilationanda pages 17-20, arandiagorostidi2024ureaassimilationanda pages 8-13)	Demonstrates that ureC-bearing archaeal and bacterial communities substantially support deep-ocean N cycling and some chemoautotrophic production; relevant to ocean biogeochemical models and to interpreting ureC as an ecologically important marker beyond surface waters	Jan 2024	https://doi.org/10.1093/ismejo/wrae230
Hollibaugh et al. 2024 preprint / 2023 Southern Ocean study — polar nitrification	Thaumarchaeota-associated ureC abundance was variable by water mass, with highest mean 1.2 × 10^6 copies L^-1 in CDW; mean ureC/rrs ≈ 0.14 overall; ammonia oxidation averaged 10.9 nmol L^-1 d^-1 versus urea oxidation 2.6 nmol L^-1 d^-1 (or 1.5 nmol L^-1 d^-1 excluding high outliers); AO and UO differed significantly among water masses (p = 0.008) (hollibaugh2023contributionofurean pages 14-18)	Suggests urea contributes a measurable but generally smaller share of nitrification in polar waters; useful for constraining regional nitrogen-cycle budgets and for evaluating when ureC abundance does or does not predict active urea-based nitrification	Feb 2024 preprint / 2023 study	https://doi.org/10.1101/2024.02.20.581251

Table: This table summarizes key 2023–2024 quantitative findings on ureC/urease and urea-based nitrification or assimilation in archaeal nitrifiers across culture, soil, and ocean systems. It highlights the most useful recent statistics for functional interpretation and environmental application.

9) Key takeaways for functional annotation of ureC1 (A0A060HK93) in N. viennensis

Molecular function: ureC1 (NVIE_014740) encodes the urease alpha (catalytic) subunit; it supports urea utilization via an operon that includes a urea transporter (ut; NVIE_014780). (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2023differentialsubstrateaffinity pages 10-13)
Physiological role: supplies intracellular ammonia from urea; urea use is inducible and repressed by ammonia, consistent with regulated nitrogen-source prioritization. (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2024ammoniaoxidizingbacteriaand pages 55-58)
Substrate preference: much higher apparent affinity for ammonia than urea (Km(app) 0.68 µM vs 8.97 µM). (qin2024ammoniaoxidizingbacteriaand pages 8-11, qin2024ammoniaoxidizingbacteriaand media 2caafcb9)
Localization: urease is cytoplasmic/intracellular; no extracellular urease activity detected and no secretion signals in urease genes. (qin2023differentialsubstrateaffinity pages 4-7, qin2023differentialsubstrateaffinity pages 7-10)
Ecological relevance: ureC is widespread among Nitrososphaeria in soils and among deep-ocean communities; urea can make substantial contributions to assimilation and, in some settings, nitrification. (liu2023genomicinsightinto pages 1-2, arandiagorostidi2024ureaassimilationand pages 1-2, arandiagorostidi2024ureaassimilationanda pages 8-13)

References

(qin2024ammoniaoxidizingbacteriaand pages 8-11): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature microbiology, 9:524-536, Jan 2024. URL: https://doi.org/10.1038/s41564-023-01593-7, doi:10.1038/s41564-023-01593-7. This article has 122 citations and is from a highest quality peer-reviewed journal.
(qin2023differentialsubstrateaffinity pages 10-13): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria. bioRxiv, Aug 2023. URL: https://doi.org/10.1101/2023.08.04.551995, doi:10.1101/2023.08.04.551995. This article has 1 citations.
(tourna2011nitrososphaeraviennensisan pages 2-3): Maria Tourna, Michaela Stieglmeier, Anja Spang, Martin Könneke, Arno Schintlmeister, Tim Urich, Marion Engel, Michael Schloter, Michael Wagner, Andreas Richter, and Christa Schleper. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences, 108:8420-8425, Apr 2011. URL: https://doi.org/10.1073/pnas.1013488108, doi:10.1073/pnas.1013488108. This article has 1117 citations and is from a highest quality peer-reviewed journal.
(tourna2011nitrososphaeraviennensisan pages 3-4): Maria Tourna, Michaela Stieglmeier, Anja Spang, Martin Könneke, Arno Schintlmeister, Tim Urich, Marion Engel, Michael Schloter, Michael Wagner, Andreas Richter, and Christa Schleper. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences, 108:8420-8425, Apr 2011. URL: https://doi.org/10.1073/pnas.1013488108, doi:10.1073/pnas.1013488108. This article has 1117 citations and is from a highest quality peer-reviewed journal.
(qin2023differentialsubstrateaffinity pages 4-7): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria. bioRxiv, Aug 2023. URL: https://doi.org/10.1101/2023.08.04.551995, doi:10.1101/2023.08.04.551995. This article has 1 citations.
(qin2023differentialsubstrateaffinity pages 7-10): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria. bioRxiv, Aug 2023. URL: https://doi.org/10.1101/2023.08.04.551995, doi:10.1101/2023.08.04.551995. This article has 1 citations.
(qin2024ammoniaoxidizingbacteriaand media 2caafcb9): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature microbiology, 9:524-536, Jan 2024. URL: https://doi.org/10.1038/s41564-023-01593-7, doi:10.1038/s41564-023-01593-7. This article has 122 citations and is from a highest quality peer-reviewed journal.
(liu2023genomicinsightinto pages 9-11): Qian Liu, Yuhao Chen, and Xue-Wei Xu. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Frontiers in Microbiology, Dec 2023. URL: https://doi.org/10.3389/fmicb.2023.1273211, doi:10.3389/fmicb.2023.1273211. This article has 10 citations and is from a peer-reviewed journal.
(liu2023genomicinsightinto pages 1-2): Qian Liu, Yuhao Chen, and Xue-Wei Xu. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Frontiers in Microbiology, Dec 2023. URL: https://doi.org/10.3389/fmicb.2023.1273211, doi:10.3389/fmicb.2023.1273211. This article has 10 citations and is from a peer-reviewed journal.
(qin2024ammoniaoxidizingbacteriaand pages 55-58): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature microbiology, 9:524-536, Jan 2024. URL: https://doi.org/10.1038/s41564-023-01593-7, doi:10.1038/s41564-023-01593-7. This article has 122 citations and is from a highest quality peer-reviewed journal.
(qin2024ammoniaoxidizingbacteriaand pages 11-16): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature microbiology, 9:524-536, Jan 2024. URL: https://doi.org/10.1038/s41564-023-01593-7, doi:10.1038/s41564-023-01593-7. This article has 122 citations and is from a highest quality peer-reviewed journal.
(qin2024ammoniaoxidizingbacteriaand pages 58-62): Wei Qin, Stephany P. Wei, Yue Zheng, Eunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Baozhan Wang, Hanyan Li, Lei Hou, Qing Tao, Wyatt W. Chlouber, Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jizhong Zhou, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willm Martens-Habbena, and Mari-Karoliina H. Winkler. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nature microbiology, 9:524-536, Jan 2024. URL: https://doi.org/10.1038/s41564-023-01593-7, doi:10.1038/s41564-023-01593-7. This article has 122 citations and is from a highest quality peer-reviewed journal.
(arandiagorostidi2024ureaassimilationand pages 1-2): Nestor Arandia-Gorostidi, Alexander L Jaffe, Alma E Parada, Bennett J Kapili, Karen L Casciotti, Rebecca S R Salcedo, Chloé M J Baumas, and Anne E Dekas. Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean. The ISME Journal, Jan 2024. URL: https://doi.org/10.1093/ismejo/wrae230, doi:10.1093/ismejo/wrae230. This article has 10 citations.
(arandiagorostidi2024ureaassimilationanda pages 8-13): Nestor Arandia-Gorostidi, Alexander L. Jaffe, Alma E. Parada, Bennett J. Kapili, Karen L. Casciotti, Rebecca S. R. Salcedo, Chloé M. J. Baumas, and Anne E. Dekas. Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean. bioRxiv, Jul 2024. URL: https://doi.org/10.1101/2024.07.26.605319, doi:10.1101/2024.07.26.605319. This article has 1 citations.
(arandiagorostidi2024ureaassimilationanda pages 17-20): Nestor Arandia-Gorostidi, Alexander L. Jaffe, Alma E. Parada, Bennett J. Kapili, Karen L. Casciotti, Rebecca S. R. Salcedo, Chloé M. J. Baumas, and Anne E. Dekas. Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean. bioRxiv, Jul 2024. URL: https://doi.org/10.1101/2024.07.26.605319, doi:10.1101/2024.07.26.605319. This article has 1 citations.
(hollibaugh2023contributionofurean pages 14-18): JT Hollibaugh, A Okotie-Oyekan, and J Damashek. Contribution of urea-n to nitrification in the southern ocean west of the antarctic peninsula. Unknown journal, 2023.
(arandiagorostidi2024ureaassimilationanda pages 13-17): Nestor Arandia-Gorostidi, Alexander L. Jaffe, Alma E. Parada, Bennett J. Kapili, Karen L. Casciotti, Rebecca S. R. Salcedo, Chloé M. J. Baumas, and Anne E. Dekas. Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean. bioRxiv, Jul 2024. URL: https://doi.org/10.1101/2024.07.26.605319, doi:10.1101/2024.07.26.605319. This article has 1 citations.

Artifacts

Citations

qin2024ammoniaoxidizingbacteriaand pages 55-58
tourna2011nitrososphaeraviennensisan pages 3-4
qin2024ammoniaoxidizingbacteriaand pages 58-62
liu2023genomicinsightinto pages 1-2
arandiagorostidi2024ureaassimilationanda pages 8-13
hollibaugh2023contributionofurean pages 14-18
qin2023differentialsubstrateaffinity pages 4-7
qin2024ammoniaoxidizingbacteriaand pages 8-11
qin2023differentialsubstrateaffinity pages 10-13
tourna2011nitrososphaeraviennensisan pages 2-3
qin2023differentialsubstrateaffinity pages 7-10
liu2023genomicinsightinto pages 9-11
qin2024ammoniaoxidizingbacteriaand pages 11-16
arandiagorostidi2024ureaassimilationand pages 1-2
arandiagorostidi2024ureaassimilationanda pages 17-20
arandiagorostidi2024ureaassimilationanda pages 13-17
https://doi.org/10.1038/s41564-023-01593-7
https://doi.org/10.1101/2023.08.04.551995
https://doi.org/10.3389/fmicb.2023.1273211
https://doi.org/10.1073/pnas.1013488108
https://doi.org/10.1038/s41396-023-01493-y
https://doi.org/10.1093/ismejo/wrae230
https://doi.org/10.1101/2024.02.20.581251
https://doi.org/10.1038/s41564-023-01593-7,
https://doi.org/10.1101/2023.08.04.551995,
https://doi.org/10.1073/pnas.1013488108,
https://doi.org/10.3389/fmicb.2023.1273211,
https://doi.org/10.1093/ismejo/wrae230,
https://doi.org/10.1101/2024.07.26.605319,

📚 Additional Documentation

Notes

(ureC1-notes.md)

ureC1 notes

UniProt A0A060HK93 names ureC1 as urease subunit alpha, EC 3.5.1.5 [file:9ARCH/ureC1/ureC1-uniprot.txt "RecName: Full=Urease subunit alpha"; "EC=3.5.1.5"].
The UniPathway urea catabolic process annotation is accepted because urease directly hydrolyzes urea [GO_REF:0000041; file:9ARCH/ureC1/ureC1-goa.tsv].

📄 View Raw YAML

id: A0A060HK93
gene_symbol: ureC1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:926571
  label: Nitrososphaera viennensis EN76
description: >-
  ureC1 encodes the urease alpha catalytic subunit NVIE_014740 in
  Nitrososphaera viennensis EN76. It hydrolyzes imported urea intracellularly,
  supplying ammonia/ammonium for nitrogen metabolism and ammonia oxidation when
  urea is available.
existing_annotations:
- term:
    id: GO:0009039
    label: urease activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      ACCEPT. UreC is the catalytic alpha subunit of urease, EC 3.5.1.5.
    action: ACCEPT
    reason: >-
      The UniProt record names ureC1 as urease subunit alpha and assigns EC
      3.5.1.5. NCBIfam TIGR01792 and PANTHER PTHR43440 support conserved urease
      alpha-subunit function. Falcon research also found organism-specific
      literature mapping NVIE_014740 to the regulated EN76 urease locus.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: 'RecName: Full=Urease subunit alpha; EC=3.5.1.5.'
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: NCBIfam; TIGR01792; urease_alph; 1.
    - reference_id: file:9ARCH/ureC1/ureC1-deep-research-falcon.md
      supporting_text: >-
        Recent EN76 literature explicitly identifies ureC/NVIE_014740 as the
        urease alpha subunit in a urea transporter-urease operon.
- term:
    id: GO:0016151
    label: nickel cation binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      ACCEPT. Urease is a nickel metalloenzyme, so nickel binding is expected.
    action: ACCEPT
    reason: >-
      Nickel binding is part of the urease catalytic mechanism. The UniProt
      record explicitly states that the enzyme binds two nickel ions per
      subunit. Family research notes that rare iron ureases exist, so nickel
      binding should be supported by gene-specific evidence rather than
      propagated blindly from urease-family membership.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: Binds 2 nickel ions per subunit.
    - reference_id: file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md
      supporting_text: >-
        PTHR43440 family research supports nickel-dependent urease annotations
        for canonical UreC homologs with explicit Ni-binding evidence, while
        warning that iron urease paralogs make blanket nickel propagation
        unsafe.
- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      KEEP_AS_NON_CORE. Correct but less informative than urease activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Urease is a hydrolase, but this parent term is less informative than
      GO:0009039 urease activity and should not be treated as the core MF.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: 'RecName: Full=Urease subunit alpha; EC=3.5.1.5.'
- term:
    id: GO:0016810
    label: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      KEEP_AS_NON_CORE. Correct parent activity for urease, but the specific
      urease activity is the core molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      This parent C-N hydrolase term is technically consistent with urease
      chemistry, but GO:0009039 is the supported specific activity.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: 'RecName: Full=Urease subunit alpha; EC=3.5.1.5.'
- term:
    id: GO:0019627
    label: urea metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: >-
      ACCEPT. Urease directly metabolizes urea.
    action: ACCEPT
    reason: >-
      ureC1 encodes the catalytic urease subunit, so urea metabolic process is a
      direct biological-process annotation, not merely pathway context. In
      EN76, urea utilization is regulated by nitrogen source and ureC/ut
      transcripts respond to urea versus ammonia.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: 'PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1.'
    - reference_id: file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md
      supporting_text: >-
        Family research identifies canonical UreC/large-subunit ureases as the
        catalytic subunits for urea hydrolysis, supporting urea catabolism for
        conserved UreC proteins.
    - reference_id: file:9ARCH/ureC1/ureC1-deep-research-falcon.md
      supporting_text: >-
        In N. viennensis EN76, ut and ureC/NVIE_014740 transcripts change about
        tenfold after urea versus ammonia addition, supporting regulated urea
        utilization by this locus.
- term:
    id: GO:0043419
    label: urea catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: >-
      ACCEPT. The UniPathway annotation is specific and useful for this
      nitrogen-metabolism gene: ureC1 is a urease catalytic subunit that
      directly catalyzes urea degradation.
    action: ACCEPT
    reason: >-
      UniPathway adds the correct process for the catalytic reaction. Urease
      hydrolyzes urea to ammonium and hydrogencarbonate/CO2, making urea
      catabolism direct rather than regulatory or downstream context. The
      Falcon report further supports intracellular urea hydrolysis rather than
      an extracellular urease model for EN76.
    supported_by:
    - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
      supporting_text: 'PATHWAY: Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1.'
    - reference_id: file:9ARCH/ureC1/ureC1-deep-research-falcon.md
      supporting_text: >-
        Culture studies found no extracellular urease activity and no secretion
        signal context for the urease genes, supporting intracellular urea
        catabolism in ammonia-oxidizing archaea including EN76.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000104
  title: Automatic assignment of GO terms by UniProt keyword mapping
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:9ARCH/ureC1/ureC1-uniprot.txt
  title: UniProt record for ureC1
  findings:
  - statement: >-
      UniProt names A0A060HK93 as urease subunit alpha, EC 3.5.1.5.
- id: file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md
  title: Falcon family deep research for PTHR43440 urease alpha subunits
  findings:
  - statement: >-
      Family research supports urease activity and urea catabolism for
      conserved UreC catalytic subunits, but highlights rare iron-dependent
      ureases as a reason not to infer nickel binding without gene-specific
      metal evidence.
- id: file:9ARCH/ureC1/ureC1-deep-research-falcon.md
  title: Falcon deep research for ureC1
  findings:
  - statement: >-
      Falcon deep research for ureC1 identified organism-specific support for
      NVIE_014740 as ureC in a regulated urea transporter-urease operon in
      Nitrososphaera viennensis EN76. Urea oxidation has lower apparent affinity
      than ammonia oxidation, and ut/ureC transcripts change about tenfold after
      urea versus ammonia addition.
core_functions:
- description: >-
    Catalyzes urea hydrolysis as a nickel-dependent urease alpha subunit,
    contributing to urea catabolism in Nitrososphaera viennensis.
  molecular_function:
    id: GO:0009039
    label: urease activity
  directly_involved_in:
  - id: GO:0043419
    label: urea catabolic process
  supported_by:
  - reference_id: file:9ARCH/ureC1/ureC1-uniprot.txt
    supporting_text: >-
      RecName: Full=Urease subunit alpha; EC=3.5.1.5.
  - reference_id: file:interpro/panther/PTHR43440/PTHR43440-deep-research-falcon.md
    supporting_text: >-
      Canonical urease large/alpha subunits house the dinuclear active site and
      catalyze urea hydrolysis; ureC1 has explicit EC and nickel-binding
      support.
  - reference_id: file:9ARCH/ureC1/ureC1-deep-research-falcon.md
    supporting_text: >-
      Falcon deep research supports ureC1/NVIE_014740 as the EN76 urease alpha
      subunit in an intracellular urea-utilization system; culture evidence
      indicates urea is transported into the cell, hydrolyzed by urease, and
      used as an ammonia source when ammonia is limiting.

ureC1

Gene Description

Existing Annotations Review

Core Functions

Catalyzes urea hydrolysis as a nickel-dependent urease alpha subunit, contributing to urea catabolism in Nitrososphaera viennensis.

References

Deep Research

Falcon

Research Report: Functional annotation of ureC1 (UniProt A0A060HK93; locus NVIE_014740) in Nitrososphaera viennensis EN76 (9ARCH)

1) Target verification (avoid gene-symbol ambiguity)

2) Key concepts and current understanding (definitions and mechanistic role)

2.1 Urease and the meaning of ureC/ureC1

2.2 Pathway context in nitrifying archaea: urea as an ammonia precursor

3) Molecular function, substrate specificity, and operon/regulatory context (organism-specific)

3.1 Reaction and substrate specificity

3.2 Operon context and accessory functions (transport + urease)

3.3 Regulation: inducible urea utilization and repression by ammonia

4) Subcellular localization (where ureC1 functions)

5) Biological role in cellular metabolism and nitrogen cycling

5.1 Role in N. viennensis physiology

5.2 Broader ecological context (soil and ocean)

6) Recent developments (2023–2024) and expert analysis

7) Current applications and real-world implementations

7.1 Environmental monitoring and biogeochemical modeling

7.2 Interpreting ureC as an activity proxy (limitations)

8) Evidence tables

9) Key takeaways for functional annotation of ureC1 (A0A060HK93) in N. viennensis

Artifacts

Citations

📚 Additional Documentation

Notes

ureC1 notes

📄 View Raw YAML