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Comparative phylogenomics of bacterial urease systems reveals architectural conservation, lineage-specific specialization, and candidate horizontal transfer.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Comparative phylogenomics of bacterial urease systems reveals architectural conservation, lineage-specific specialization, and candidate horizontal transfer.
Συγγραφείς: Sarkar MP; Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, 733134, West Bengal, India., Pal A; Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, 733134, West Bengal, India. ayonpal.ruc@gmail.com.
Πηγή: Molecular genetics and genomics : MGG [Mol Genet Genomics] 2026 Aug 29; Vol. 301 (1). Date of Electronic Publication: 2026 Aug 29.
Τύπος έκδοσης: Journal Article; Comparative Study
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101093320 Publication Model: Electronic Cited Medium: Internet ISSN: 1617-4623 (Electronic) Linking ISSN: 16174623 NLM ISO Abbreviation: Mol Genet Genomics Subsets: MEDLINE
Imprint Name(s): Original Publication: Berlin : Springer-Verlag, c2001-
Ιατρικοί όροι (MeSH): Urease*/genetics , Bacteria*/genetics , Bacteria*/enzymology , Bacteria*/classification , Gene Transfer, Horizontal*, Genome, Bacterial/genetics ; Genomics/methods ; Bacterial Proteins/genetics ; Helicobacter/genetics ; Helicobacter/enzymology ; Phylogeny ; Evolution, Molecular
Περίληψη: Urease is a nickel-dependent, multi-gene bacterial system that contributes to nitrogen acquisition, pH homeostasis, and ecological adaptation, yet most comparative studies rely on single-gene markers such as ureC. Here, we analyzed 237 complete genomes from a stratified bacterial panel integrating ecological and genome-level metadata, annotation-guided screening, profile-HMM detection, locus reconstruction, and species-tree comparison. Within this panel, 149 genomes encoded at least one complete urease locus, 11 contained candidate but incomplete neighborhoods, and 77 lacked any supported urease locus. At the locus level, we recovered 173 urease-associated neighborhoods, including 150 canonical ureABC loci, 7 Helicobacter AB fusion loci, and 16 partial or split loci. The canonical three-subunit architecture therefore dominated the dataset, whereas the Helicobacter-type configuration persisted as a small but stable lineage-restricted alternative. Eight genomes encoded duplicated complete canonical systems, and in each case, both loci mapped to the same top-level assembly sequence record. Their paired loci differed in gene order and typically shared only about 62-63% concatenated ureABC identity, consistent with older divergence or secondary acquisition rather than recent exact duplication. Comparison of the concatenated ureABC gene tree with the species tree identified 12 candidate incongruent loci, all involving complete canonical systems. A manual review of the strongest examples highlighted ecologically coherent modules in nitrifiers and marine cyanobacteria, as well as nickel- and hydrogenase-associated urease neighborhoods in enteric bacteria. Together, these results establish bacterial urease as a broadly conserved but evolutionarily flexible genomic component shaped by architectural conservation, lineage-specific specialization, duplication, and occasional intergeneric transfer.
(© 2026. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests. Ethical approval: Not applicable. Copyright statement: The authors certify that no copyrighted material from other sources was used or included in this study or reproduced in this manuscript.
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PLoS One. 2010 Nov 29;5(11):e15042. (PMID: 21124783)
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Science. 2000 Jan 21;287(5452):482-5. (PMID: 10642549)
Infect Immun. 1987 Sep;55(9):2198-203. (PMID: 3623698)
Microbiol Mol Biol Rev. 2009 Jun;73(2):249-99. (PMID: 19487728)
J Biol Chem. 2013 May 10;288(19):13178-85. (PMID: 23539618)
J Adv Res. 2018 Feb 26;13:39-50. (PMID: 30094081)
Nat Rev Microbiol. 2012 Nov;10(11):743-54. (PMID: 23042564)
PLoS Pathog. 2014 Dec 11;10(12):e1004472. (PMID: 25501953)
J Bacteriol. 1990 Oct;172(10):5837-43. (PMID: 2211515)
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J Bacteriol. 2004 Nov;186(22):7645-52. (PMID: 15516578)
Mol Biol Evol. 2016 Jun;33(6):1635-8. (PMID: 26921390)
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BMC Microbiol. 2010 Apr 10;10:107. (PMID: 20380737)
Mol Microbiol. 2002 Feb;43(3):703-15. (PMID: 11929526)
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Mol Biol Evol. 2009 Jul;26(7):1641-50. (PMID: 19377059)
Contributed Indexing: Keywords: Helicobacter pylori; ureABCDEFG; urtABCDE; Phylogenomics; Urease
Substance Nomenclature: EC 3.5.1.5 (Urease)
0 (Bacterial Proteins)
Entry Date(s): Date Created: 20260829 Date Completed: 20260829 Latest Revision: 20261008
Update Code: 20261008
DOI: 10.1007/s00438-026-02507-y
PMID: 42667423
Βάση Δεδομένων: MEDLINE
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  Data: Comparative phylogenomics of bacterial urease systems reveals architectural conservation, lineage-specific specialization, and candidate horizontal transfer.
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  Data: <searchLink fieldCode="AU" term="%22Sarkar+MP%22">Sarkar MP</searchLink>; Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, 733134, West Bengal, India.<br /><searchLink fieldCode="AU" term="%22Pal+A%22">Pal A</searchLink>; Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, 733134, West Bengal, India. ayonpal.ruc@gmail.com.
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  Data: <searchLink fieldCode="MM" term="%22Urease%22">Urease*</searchLink>/<searchLink fieldCode="MM" term="%22Urease+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+enzymology%22">enzymology</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Gene+Transfer%2C+Horizontal%22">Gene Transfer, Horizontal*</searchLink><br /><searchLink fieldCode="MH" term="%22Genome%2C+Bacterial%22">Genome, Bacterial</searchLink>/<searchLink fieldCode="MH" term="%22Genome%2C+Bacterial+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Genomics%22">Genomics</searchLink>/<searchLink fieldCode="MH" term="%22Genomics+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Bacterial+Proteins%22">Bacterial Proteins</searchLink>/<searchLink fieldCode="MH" term="%22Bacterial+Proteins+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Helicobacter%22">Helicobacter</searchLink>/<searchLink fieldCode="MH" term="%22Helicobacter+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Helicobacter%22">Helicobacter</searchLink>/<searchLink fieldCode="MH" term="%22Helicobacter+enzymology%22">enzymology</searchLink> ; <searchLink fieldCode="MH" term="%22Phylogeny%22">Phylogeny</searchLink> ; <searchLink fieldCode="MH" term="%22Evolution%2C+Molecular%22">Evolution, Molecular</searchLink>
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  Data: Urease is a nickel-dependent, multi-gene bacterial system that contributes to nitrogen acquisition, pH homeostasis, and ecological adaptation, yet most comparative studies rely on single-gene markers such as ureC. Here, we analyzed 237 complete genomes from a stratified bacterial panel integrating ecological and genome-level metadata, annotation-guided screening, profile-HMM detection, locus reconstruction, and species-tree comparison. Within this panel, 149 genomes encoded at least one complete urease locus, 11 contained candidate but incomplete neighborhoods, and 77 lacked any supported urease locus. At the locus level, we recovered 173 urease-associated neighborhoods, including 150 canonical ureABC loci, 7 Helicobacter AB fusion loci, and 16 partial or split loci. The canonical three-subunit architecture therefore dominated the dataset, whereas the Helicobacter-type configuration persisted as a small but stable lineage-restricted alternative. Eight genomes encoded duplicated complete canonical systems, and in each case, both loci mapped to the same top-level assembly sequence record. Their paired loci differed in gene order and typically shared only about 62-63% concatenated ureABC identity, consistent with older divergence or secondary acquisition rather than recent exact duplication. Comparison of the concatenated ureABC gene tree with the species tree identified 12 candidate incongruent loci, all involving complete canonical systems. A manual review of the strongest examples highlighted ecologically coherent modules in nitrifiers and marine cyanobacteria, as well as nickel- and hydrogenase-associated urease neighborhoods in enteric bacteria. Together, these results establish bacterial urease as a broadly conserved but evolutionarily flexible genomic component shaped by architectural conservation, lineage-specific specialization, duplication, and occasional intergeneric transfer.<br /> (© 2026. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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  Group: Ab
  Data: Declarations. Conflict of interest: The authors declare no competing interests. Ethical approval: Not applicable. Copyright statement: The authors certify that no copyrighted material from other sources was used or included in this study or reproduced in this manuscript.
– Name: Ref
  Label: References
  Group: RefInfo
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(PMID: <searchLink fieldCode="PM" term="%2215066830%22">15066830)</searchLink><br />Microbiome. 2023 Apr 15;11(1):76. (PMID: <searchLink fieldCode="PM" term="%2237060083%22">37060083)</searchLink><br />Science. 2000 Jan 21;287(5452):482-5. (PMID: <searchLink fieldCode="PM" term="%2210642549%22">10642549)</searchLink><br />Infect Immun. 1987 Sep;55(9):2198-203. (PMID: <searchLink fieldCode="PM" term="%223623698%22">3623698)</searchLink><br />Microbiol Mol Biol Rev. 2009 Jun;73(2):249-99. (PMID: <searchLink fieldCode="PM" term="%2219487728%22">19487728)</searchLink><br />J Biol Chem. 2013 May 10;288(19):13178-85. (PMID: <searchLink fieldCode="PM" term="%2223539618%22">23539618)</searchLink><br />J Adv Res. 2018 Feb 26;13:39-50. (PMID: <searchLink fieldCode="PM" term="%2230094081%22">30094081)</searchLink><br />Nat Rev Microbiol. 2012 Nov;10(11):743-54. (PMID: <searchLink fieldCode="PM" term="%2223042564%22">23042564)</searchLink><br />PLoS Pathog. 2014 Dec 11;10(12):e1004472. 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(PMID: <searchLink fieldCode="PM" term="%2237380083%22">37380083)</searchLink><br />Infect Immun. 2000 Feb;68(2):470-7. (PMID: <searchLink fieldCode="PM" term="%2210639406%22">10639406)</searchLink><br />Nat Commun. 2025 Dec 6;16(1):10946. (PMID: <searchLink fieldCode="PM" term="%2241353279%22">41353279)</searchLink><br />Mol Microbiol. 2000 Jun;36(5):1071-84. (PMID: <searchLink fieldCode="PM" term="%2210844692%22">10844692)</searchLink><br />Genome Biol. 2015 Aug 06;16:157. (PMID: <searchLink fieldCode="PM" term="%2226243257%22">26243257)</searchLink><br />PLoS Pathog. 2017 Jun 23;13(6):e1006464. (PMID: <searchLink fieldCode="PM" term="%2228644872%22">28644872)</searchLink><br />Arch Biochem Biophys. 2014 Feb 15;544:142-52. (PMID: <searchLink fieldCode="PM" term="%2224036122%22">24036122)</searchLink><br />Mol Biol Evol. 2009 Jul;26(7):1641-50. (PMID: <searchLink fieldCode="PM" term="%2219377059%22">19377059)</searchLink>
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