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Volume 12, Issue 4

Functional shifts of the dual-substrate phosphoribosyl isomerase PriA from primary to specialized metabolism in rare Actinomycetota Open Access

This article is part of the Advances in the biology of Actinomycetes collection

Abstract

Evolutionary functional innovations can occur while gene families expand and two homologous (or analogous) genes co-occur. PriA is a dual-substrate enzyme family exclusive to , with activities in -histidine and -tryptophan biosynthesis (HisA and TrpF activities) that evolved after the loss of the gene. Since this gene loss, PriA has undergone multiple functional gain and loss events in central metabolism. Here, we report further evolutionary scenarios of PriA. First, in , a rare family, PriA coexists with HisA, concomitant with the loss of its HisA but not TrpF activity, and is recruited in a physiological genome context. Second, a homologue, , is located in the biosynthetic gene cluster of the specialized metabolites adechlorin and 2′-amino-2′-deoxyadenosine. The gene is encoded in several genomes of the family and coexists with the expected and conserved . In this scenario, the PriA enzymes conserve both activities, whereas AdeK has only detectable levels of HisA activity, which might be related to specificity for a chlorinated intermediary during adechlorin biosynthesis. The gene was first identified in strain ATCC-39365, previously designated as sp., but reclassified here as sp. We further identified unprecedented adechlorin/2′-amino-2′-deoxyadenosine/pentostatin producers within the and genera. Phylogenomic analysis revealed additional recruitments of and homologues into diverse uncharacterized biosynthetic gene clusters taxonomically related to the nucleoside antibiotics adechlorin, pentostatin and pyrazomycin. These findings highlight how enzyme family expansions and recruitment drive metabolic functional innovation in , involving both gene loss and gain throughout central and specialized metabolism, and how evolutionary genome mining allows unbiased natural product discovery.

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  • Accepted:
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Keyword(s): Actinomycetota , adechlorin , biosynthetic gene cluster , enzyme evolution , gene expansion , genome mining and PriA
Funding
This study was supported by the:
  • CONACYT (Award 757173)
    • Principal Award Recipient: LuisRodrigo Rosas-Becerra
  • Institute of Biology, Leiden University
    • Principal Award Recipient: LuisRodrigo Rosas-Becerra
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2026-04-22

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References

  1. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 2010; 11:97–108 [View Article] [PubMed]
     [Google Scholar]
  2. Wagner A. Gene duplications, robustness and evolutionary innovations. BioEssays 2008; 30:367–373 [View Article]
     [Google Scholar]
  3. Firn RD, Jones CG. A Darwinian view of metabolism: molecular properties determine fitness. J Exp Bot 2009; 60:719–726 [View Article] [PubMed]
     [Google Scholar]
  4. Sélem-Mojica N, Aguilar C, Gutiérrez-García K, Martínez-Guerrero CE, Barona-Gómez F. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microb Genom 2019; 5:e000260 [View Article] [PubMed]
     [Google Scholar]
  5. Vining LC. Secondary metabolism, inventive evolution and biochemical diversity--a review. Gene 1992; 115:135–140 [View Article] [PubMed]
     [Google Scholar]
  6. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev 2016; 80:1–43 [View Article] [PubMed]
     [Google Scholar]
  7. Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol 2022; 7:726–735 [View Article] [PubMed]
     [Google Scholar]
  8. Selim MSM, Abdelhamid SA, Mohamed SS. Secondary metabolites and biodiversity of actinomycetes. J Genet Eng Biotechnol 2021; 19:72 [View Article] [PubMed]
     [Google Scholar]
  9. Schniete JK, Cruz-Morales P, Selem-Mojica N, Fernández-Martínez LT, Hunter IS et al. Expanding primary metabolism helps generate the metabolic robustness to facilitate antibiotic biosynthesis in Streptomyces. mBio 2018; 9:e02283-17 [View Article] [PubMed]
     [Google Scholar]
  10. Cruz-Morales P, Kopp JF, Martínez-Guerrero C, Yáñez-Guerra LA, Selem-Mojica N et al. Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model Streptomycetes. Genome Biol Evol 2016; 8:1906–1916 [View Article] [PubMed]
     [Google Scholar]
  11. Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB et al. Minimum information about a biosynthetic gene cluster. Nat Chem Biol 2015; 11:625–631 [View Article] [PubMed]
     [Google Scholar]
  12. Barona-Gómez F, Hodgson DA. Occurrence of a putative ancient-like isomerase involved in histidine and tryptophan biosynthesis. EMBO Rep 2003; 4:296–300 [View Article] [PubMed]
     [Google Scholar]
  13. Henn-Sax M, Thoma R, Schmidt S, Hennig M, Kirschner K et al. Two (betaalpha)(8)-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates. Biochemistry 2002; 41:12032–12042 [View Article] [PubMed]
     [Google Scholar]
  14. Jürgens C, Strom A, Wegener D, Hettwer S, Wilmanns M et al. Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc Natl Acad Sci USA 2000; 97:9925–9930 [View Article] [PubMed]
     [Google Scholar]
  15. Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion. Science 2000; 289:1546–1550 [View Article]
     [Google Scholar]
  16. Priestle JP, Grütter MG, White JL, Vincent MG, Kania M et al. Three-dimensional structure of the bifunctional enzyme N-(5’-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli. Proc Natl Acad Sci USA 1987; 84:5690–5694 [View Article]
     [Google Scholar]
  17. Gao Y, Xu G, Wu P, Liu J, Cai Y-S et al. Biosynthesis of 2′-Chloropentostatin and 2′-Amino-2′-deoxyadenosine highlights a single gene cluster responsible for two independent pathways in Actinomadura sp. strain ATCC 39365. Appl Environ Microbiol 2017; 83:e00078-17 [View Article] [PubMed]
     [Google Scholar]
  18. Zhao C, Yan S, Li Q, Zhu H, Zhong Z et al. An Fe 2+ ‐ and α‐ketoglutarate‐dependent halogenase acts on nucleotide substrates. Angew Chem Int Ed 2020; 59:9478–9484 [View Article]
     [Google Scholar]
  19. Juárez-Vázquez AL, Edirisinghe JN, Verduzco-Castro EA, Michalska K, Wu C et al. Evolution of substrate specificity in a retained enzyme driven by gene loss. Elife 2017; 6:e22679 [View Article] [PubMed]
     [Google Scholar]
  20. Noda-García L, Camacho-Zarco AR, Medina-Ruíz S, Gaytán P, Carrillo-Tripp M et al. Evolution of substrate specificity in a recipient’s enzyme following horizontal gene transfer. Mol Biol Evol 2013; 30:2024–2034 [View Article] [PubMed]
     [Google Scholar]
  21. Verduzco-Castro EA, Michalska K, Endres M, Juárez-Vazquez AL, Noda-García L et al. Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop. Biochem J 2016; 473:1141–1152 [View Article] [PubMed]
     [Google Scholar]
  22. Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2023; 51:D603–D610 [View Article]
     [Google Scholar]
  23. Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2016; 2:e000093 [View Article] [PubMed]
     [Google Scholar]
  24. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  25. Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH et al. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 2020; 16:60–68 [View Article] [PubMed]
     [Google Scholar]
  26. Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol 2015; 32:820–832 [View Article]
     [Google Scholar]
  27. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006; 2:2006.0008 [View Article] [PubMed]
     [Google Scholar]
  28. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article]
     [Google Scholar]
  29. Adams NE, Thiaville JJ, Proestos J, Juárez-Vázquez AL, McCoy AJ et al. Promiscuous and adaptable enzymes fill “holes” in the tetrahydrofolate pathway in Chlamydia species. mBio 2014; 5:e01378-14 [View Article] [PubMed]
     [Google Scholar]
  30. Noda-García L, Juárez-Vázquez AL, Ávila-Arcos MC, Verduzco-Castro EA, Montero-Morán G et al. Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome. BMC Evol Biol 2015; 15:107 [View Article] [PubMed]
     [Google Scholar]
  31. Quan J, Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 2009; 4:e6441 [View Article] [PubMed]
     [Google Scholar]
  32. Noda-García L, Camacho-Zarco AR, Verdel-Aranda K, Wright H, Soberón X et al. Identification and analysis of residues contained on beta --> alpha loops of the dual-substrate (beta alpha)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity. Protein Sci 2010; 19:535–543 [View Article] [PubMed]
     [Google Scholar]
  33. Jumper J, Evans R, Pritzel A, Green T, Figurnov M et al. Highly accurate protein structure prediction with alphafold. Nature 2021; 596:583–589 [View Article]
     [Google Scholar]
  34. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 2021; 30:70–82 [View Article] [PubMed]
     [Google Scholar]
  35. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009; 25:1189–1191 [View Article] [PubMed]
     [Google Scholar]
  36. Tunac JB, Underhill M. 2’-Chloropentostatin: discovery, fermentation and biological activity. J Antibiot 1985; 38:1344–1349 [View Article]
     [Google Scholar]
  37. Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of actinobacteria from marine sediments in valparaíso bay, Chile. Front Microbiol 2015; 6:737 [View Article] [PubMed]
     [Google Scholar]
  38. Due AV, Kuper J, Geerlof A, von Kries JP, Wilmanns M. Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis. Proc Natl Acad Sci USA 2011; 108:3554–3559 [View Article] [PubMed]
     [Google Scholar]
  39. Wright H, Noda-García L, Ochoa-Leyva A, Hodgson DA, Fülöp V et al. The structure/function relationship of a dual-substrate (betaalpha)8-isomerase. Biochem Biophys Res Commun 2008; 365:16–21 [View Article] [PubMed]
     [Google Scholar]
  40. Xie G, Keyhani NO, Bonner CA, Jensen RA. Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol Mol Biol Rev 2003; 67:303–342 [View Article]
     [Google Scholar]
  41. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  42. Chen W, Qi J, Wu P, Wan D, Liu J et al. Natural and engineered biosynthesis of nucleoside antibiotics in actinomycetes. J Ind Microbiol Biotechnol 2016; 43:401–417 [View Article] [PubMed]
     [Google Scholar]
  43. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N et al. Sharing and community curation of mass spectrometry data with global natural products social molecular networking. Nat Biotechnol 2016; 34:828–837 [View Article]
     [Google Scholar]
  44. Schmutzer M, Dasmeh P, Wagner A. Frustration can limit the adaptation of promiscuous enzymes through gene duplication and specialisation. J Mol Evol 2024; 92:104–120 [View Article] [PubMed]
     [Google Scholar]
  45. Copley SD. Evolution of new enzymes by gene duplication and divergence. FEBS J 2020; 287:1262–1283 [View Article] [PubMed]
     [Google Scholar]
  46. Suhadolnik RJ, Pornbanlualap S, Baker DC, Tiwari KN, Hebbler AK. Stereospecific 2’-amination and 2’-chlorination of adenosine by Actinomadura in the biosynthesis of 2’-amino-2’-deoxyadenosine and 2’-chloro-2’-deoxycoformycin. Arch Biochem Biophys 1989; 270:374–382 [View Article] [PubMed]
     [Google Scholar]
  47. Utagawa T, Morisawa H, Yamanaka S, Yamazaki A, Yoshinaga F et al. Microbial synthesis of purine arabinosides and their biological activity. Agric Bio Chem 1985; 49:2167–2171 [View Article]
     [Google Scholar]
  48. Hughes AL. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci 1994; 256:119–124 [View Article] [PubMed]
     [Google Scholar]
  49. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biol 2002; 3:RESEARCH0008 [View Article] [PubMed]
     [Google Scholar]
  50. Balskus EP, Walsh CT. Investigating the initial steps in the biosynthesis of cyanobacterial sunscreen scytonemin. J Am Chem Soc 2008; 130:15260–15261 [View Article] [PubMed]
     [Google Scholar]
  51. Soule T, Palmer K, Gao Q, Potrafka RM, Stout V et al. A comparative genomics approach to understanding the biosynthesis of the sunscreen scytonemin in cyanobacteria. BMC Genomics 2009; 10:336 [View Article]
     [Google Scholar]
  52. Kämpfer P, Glaeser SP, Schäfer J, Lodders N, Martin K et al. Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds. Int J Syst Evol Microbiol 2013; 63:119–123 [View Article]
     [Google Scholar]
  53. Mayilraj S, Saha P, Suresh K, Saini HS. Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 2006; 56:1657–1661 [View Article] [PubMed]
     [Google Scholar]
  54. Ramaprasad EVV, Sasikala Ch, Ramana ChV. Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva. Int J Syst Evol Microbiol 2015; 65:4627–4631 [View Article]
     [Google Scholar]
  55. Zhang L-Y, Ming H, Meng X-L, Fang B-Z, Jiao J-Y et al. Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave. Antonie van Leeuwenhoek 2019; 112:179–186 [View Article]
     [Google Scholar]
  56. Trzoss L, Fukuda T, Costa-Lotufo LV, Jimenez P, La Clair JJ et al. Seriniquinone, a selective anticancer agent, induces cell death by autophagocytosis, targeting the cancer-protective protein dermcidin. Proc Natl Acad Sci USA 2014; 111:14687–14692 [View Article]
     [Google Scholar]
  57. Yang X-W, Zhang G-Y, Ying J-X, Yang B, Zhou X-F et al. Isolation, characterization, and bioactivity evaluation of 3-((6-Methylpyrazin-2-yl)methyl)-1H-indole, a new alkaloid from a deep-sea-derived actinomycete Serinicoccus profundi sp. nov. Marine Drugs 2012; 11:33–39 [View Article]
     [Google Scholar]
  58. Díaz-Cárdenas C, Cantillo A, Rojas LY, Sandoval T, Fiorentino S et al. Microbial diversity of saline environments: searching for cytotoxic activities. AMB Express 2017; 7:223 [View Article] [PubMed]
     [Google Scholar]
  59. Quintana ET, Goodfellow M. Streptosporangium. In In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons; 2015 [View Article]
     [Google Scholar]
  60. Goodfellow M, Stanton LN, Simpson TJ, Minnikin DE. The family Streptosporangiaceae. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. eds The Prokaryotes Springer; 1990 pp 725–753 [View Article]
     [Google Scholar]
  61. Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I. et al. eds Bergey’s manual of systematic bacteriology, 2nd. edn Springer; 2012 [View Article]
     [Google Scholar]
  62. Guo X, Liu N, Li X, Ding Y, Shang F et al. Red soils harbor diverse culturable actinomycetes that are promising sources of novel secondary metabolites. Appl Environ Microbiol 2015; 81:3086–3103 [View Article] [PubMed]
     [Google Scholar]
  63. Kudo T, Itoh T, Miyadoh S, Shomura T, Seino A. Herbidospora gen. nov., a new genus of the family streptosporangiaceae Goodfellow et al. 1990. Int J Syst Bacteriol 1993; 43:319–328 [View Article] [PubMed]
     [Google Scholar]
  64. Saygin H, Ay H, Guven K, Cetin D, Sahin N. Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family streptosporangiaceae isolated from the Karakum Desert. Antonie van Leeuwenhoek 2019; 112:409–423 [View Article] [PubMed]
     [Google Scholar]
  65. Yamada Y, Inahashi Y, Goda Y, Také A, Matsumoto A. Rhizohabitans arisaemae gen. nov., sp. nov., a novel actinomycete of the family Streptosporangiaceae. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  66. Nazari B, Forneris CC, Gibson MI, Moon K, Schramma KR et al. Nonomuraea sp. ATCC 55076 harbours the largest actinomycete chromosome to date and the kistamicin biosynthetic gene cluster. Medchemcomm 2017; 8:780–788 [View Article] [PubMed]
     [Google Scholar]
  67. Yushchuk O, Vior NM, Andreo-Vidal A, Berini F, Rückert C et al. Genomic-led discovery of a novel glycopeptide antibiotic by Nonomuraea coxensis DSM 45129. ACS Chem Biol 2021; 16:915–928 [View Article] [PubMed]
     [Google Scholar]
  68. Goldstein BP, Selva E, Gastaldo L, Berti M, Pallanza R et al. A40926, a new glycopeptide antibiotic with anti-Neisseria activity. Antimicrob Agents Chemother 1987; 31:1961–1966 [View Article]
     [Google Scholar]
  69. Castiglione F, Lazzarini A, Carrano L, Corti E, Ciciliato I et al. Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens. Chem & Biol 2008; 15:22–31 [View Article]
     [Google Scholar]
  70. Covington BC, Spraggins JM, Ynigez-Gutierrez AE, Hylton ZB, Bachmann BO. Response of secondary metabolism of hypogean actinobacterial genera to chemical and biological stimuli. Appl Environ Microbiol 2018; 84:e01125-18 [View Article] [PubMed]
     [Google Scholar]
  71. Doroghazi JR, Metcalf WW. Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes. BMC Genomics 2013; 14:611 [View Article] [PubMed]
     [Google Scholar]
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Functional shifts of the dual-substrate phosphoribosyl isomerase PriA from primary to specialized metabolism in rare Actinomycetota
M Gen 12, 001634 (2026); https://doi.org/10.1099/mgen.0.001634
/content/journal/mgen/10.1099/mgen.0.001634
/content/journal/mgen/10.1099/mgen.0.001634
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