| Topic | Key finding | Specific gene/locus (if given) | Evidence type (genomic, transcriptomic, physiology, review) | Source (first author year, journal) | URL | Notes/limitations |
|---|---|---|---|---|---|---|
| Verified urease operon in *N. viennensis* EN76 | A urease alpha-subunit gene annotated as **ureC (NVIE_014740)** occurs in a **ut–ure operon**; transcript levels of **ut** and **ureC** increase strongly after urea addition and decrease after ammonia addition, indicating nitrogen-source-responsive regulation. | **ureC = NVIE_014740**; **ut = NVIE_014780** | Genomic + transcriptomic | Qin 2024, *Nature Microbiology* | https://doi.org/10.1038/s41564-023-01593-7 | This is the clearest organism-specific evidence for EN76 urease expression, but it refers to **NVIE_014740**, not the UniProt target **A0A060HQC5 / NVIE_015020 (ureC2)**; therefore these should not be conflated. Operon schematic also shown in figure context. (pqac-00000000, pqac-00000022, pqac-00000023) |
| Potential second urease copy in *N. viennensis* EN76 | Comparative genomics reported that *N. viennensis* EN76 **harbors two copies of ureABC**. | Strain-level duplication reported; specific second-copy locus not given in excerpt | Genomic | Liu 2023, *Frontiers in Microbiology* | https://doi.org/10.3389/fmicb.2023.1273211 | Supports the possibility of a second urease alpha-subunit paralog, consistent with a **ureC2-like** annotation, but the excerpt does **not** explicitly map this to **NVIE_015020/A0A060HQC5**. (pqac-00000024) |
| Broader *Ca. Nitrososphaera* duplication pattern | In *Ca. Nitrososphaera evergladensis*, all urease subunits were reported in **two copies**, and this duplication was described as characteristic of *Ca. Nitrososphaera* genomes compared with other AOA examined. | **ureA, ureB, ureC** duplicated in *Ca. N. evergladensis* | Genomic | Zhalnina 2014, *PLoS ONE* | https://doi.org/10.1371/journal.pone.0101648 | This supports lineage-level precedent for duplicated urease genes in Nitrososphaerales/related *Nitrososphaera*, but is not direct proof for the exact EN76 locus **NVIE_015020**. (pqac-00000009, pqac-00000025) |
| Earliest EN76 urease evidence | The original EN76 draft genome contained a contig with a **potential urease operon**. | Not specified in excerpt | Genomic | Tourna 2011, *PNAS* | https://doi.org/10.1073/pnas.1013488108 | Establishes early genome-based evidence for urease in EN76, but without locus IDs, operon order, or direct physiological proof of growth on urea in the cited excerpt. (pqac-00000013) |
| Urease localization in AOA | No extracellular urease activity was observed in tested AOA, and urease genes lacked secretion signals; this supports **cytoplasmic localization** of urease in *N. viennensis* and related AOA. | Urease operon genes in AOA; no secretory signal reported | Physiology + genomic inference | Qin 2023, *bioRxiv*; Qin 2024, *Nature Microbiology* | https://doi.org/10.1101/2023.08.04.551995 ; https://doi.org/10.1038/s41564-023-01593-7 | Strong functional inference for subcellular localization, but not direct microscopy/protein-localization assay. (pqac-00000010, pqac-00000019) |
| Urea utilization physiology in AOA including EN76 | Tested AOA, including *N. viennensis*, generally **prefer ammonia over urea** and repress urea-use functions when ammonia is available; after ammonia exhaustion, EN76 transitions to urea use. | EN76 urease pathway; specific loci not all listed in excerpt | Physiology + transcriptomic | Qin 2023, *bioRxiv*; Qin 2024, *Nature Microbiology* | https://doi.org/10.1101/2023.08.04.551995 ; https://doi.org/10.1038/s41564-023-01593-7 | Important for functional interpretation: urease contributes to alternative N acquisition rather than constitutive preferred substrate use under ammonia-replete conditions. (pqac-00000010, pqac-00000021) |
| Urease catalytic function | Urease (EC 3.5.1.5) hydrolyzes **urea → ammonia + carbamate**, and carbamate then decomposes to a second ammonia plus bicarbonate/CO2. The catalytic active site resides in the **UreC/α subunit**. | **UreC = alpha/large catalytic subunit** | Review/mechanistic | Hausinger 2017, *Encyclopedia of Inorganic and Bioinorganic Chemistry*; Nim 2019, *Inorganics* | https://doi.org/10.1002/9781119951438.eibc2483 ; https://doi.org/10.3390/inorganics7070085 | This is the best-supported molecular function to infer for **A0A060HQC5** if it is a true urease alpha-subunit paralog. Substrate specificity is overwhelmingly urea in conventional ureases. (pqac-00000001, pqac-00000002, pqac-00000003, pqac-00000004) |
| Metal cofactor and maturation | Conventional ureases contain a **dinuclear Ni2+ active site** bridged by a carbamylated lysine; activation requires accessory proteins **UreD/UreH, UreE, UreF, UreG**, with Ni transfer along **UreE → UreG → UreF/UreD → urease**. | Accessory genes **ureD/ureH, ureE, ureF, ureG** | Review/mechanistic | Hausinger 2017, *Encyclopedia*; Nim 2019, *Inorganics* | https://doi.org/10.1002/9781119951438.eibc2483 ; https://doi.org/10.3390/inorganics7070085 | Strongly supports annotation of a urease alpha-subunit-like protein, but does not distinguish which EN76 paralog is catalytically active. (pqac-00000002, pqac-00000005, pqac-00000006, pqac-00000007, pqac-00000008) |
| Operon organization in AOA | Most AOA genomes contain **ureABC + ureDEFG**; in many AOA, urea transporter genes (**dur3** and/or **utp/ut**) occur near urease genes. | **ureABC, ureDEFG, dur3, ut/utp** | Comparative genomics | Liu 2023, *Frontiers in Microbiology* | https://doi.org/10.3389/fmicb.2023.1273211 | Provides comparative context for EN76 operon architecture and helps explain why transporter and urease genes are often co-regulated. (pqac-00000011, pqac-00000020, pqac-00000024) |
| Soil AOA prevalence of ureC | In upland soils, an estimated **85.7–89.8% of AOA** encoded **urease (ureC)** on average; ureC was detected across all Nitrososphaerales lineages sampled. | **ureC** | Metagenomic/statistical | Zhao 2023, *The ISME Journal* | https://doi.org/10.1038/s41396-023-01493-y | Supports ecological importance of urease in soil Nitrososphaeria, relevant because EN76 is a soil AOA. This is lineage/community-level, not EN76-specific. (pqac-00000017) |
| Soil AOA ureC expression versus EN76 culture reference | In soil metatranscriptomes, most Nitrososphaerales families showed **ureC transcripts 13–22× higher** and **urea transporter transcripts 41–177× higher** than ammonium-replete *N. viennensis* reference cultures. | **ureC**, **ut** | Metatranscriptomic/statistical | Zhao 2023, *The ISME Journal* | https://doi.org/10.1038/s41396-023-01493-y | Suggests that field AOA often upregulate urea acquisition more strongly than EN76 grown under ammonium-replete lab conditions. (pqac-00000018) |
| Deep-ocean ureC prevalence and activity | In a 2024 deep-ocean study, **39% of deep-sea cells** in the sampled region contained **ureC**; globally, **~10–46%** of deep-sea cells were estimated to contain ureC. On average, **25% of deep-sea cells** assimilated urea-derived N, representing **60% of detectably active cells**. | **ureC** | Metagenomic + single-cell activity/statistical | Arandia-Gorostidi 2024, *The ISME Journal* | https://doi.org/10.1093/ismejo/wrae230 | Not EN76-specific, but demonstrates contemporary ecological importance of urease-bearing nitrifiers including Nitrososphaeria. (pqac-00000014, pqac-00000016) |
| Quantitative comparison of ureC vs amoA in the deep ocean | **ureC was ~2× more abundant than amoA** on average (**0.45 ureC/recA vs 0.23 amoA/recA**), implying substantial urea-cleaving potential outside strict ammonia oxidizers; ureC-containing MAGs were more abundant in the bathypelagic (**2.56%**) than epipelagic (**0.76%**). | **ureC, amoA** | Metagenomic/statistical | Arandia-Gorostidi 2024, *bioRxiv* | https://doi.org/10.1101/2024.07.26.605319 | Preprint values; useful recent quantitative context for environmental importance of urease/ureC. (pqac-00000014, pqac-00000015) |


*Table: This table compiles organism-specific and comparative evidence about urease genes, operon context, regulation, localization, and ecological relevance for *Nitrososphaera viennensis* EN76. It is especially useful for distinguishing the experimentally supported EN76 urease locus NVIE_014740 from the less directly documented putative paralog ureC2/NVIE_015020.*