Experimental characterization of two archaeal inosine 5'-monophosphate cyclohydrolases


Autoři: Caroline A. Hunter aff001;  Nicholas I. Plymale aff001;  Kevin M. Smee aff001;  Catherine A. Sarisky aff001
Působiště autorů: Department of Chemistry, Roanoke College, Salem, Virginia, United States of America aff001
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223983

Souhrn

There is variability as to how archaea catalyze the final step of de novo purine biosynthesis to form inosine 5’-monophosphate (IMP) from 5-formamidoimidazole-4-carboxamide ribonucleotide (FAICAR). Although non-archaea almost uniformly use the bifunctional PurH protein, which has an N-terminal IMP cyclohydrolase (PurH2) fused to a C-terminal folate-dependent aminoimidazole-4-carboxamide ribonucleotide (AICAR) formyltransferase (PurH1) domain, a survey of the genomes of archaea reveals use of PurH2 (with or without fusion to PurH1), the “euryarchaeal signature protein” PurO, or an unidentified crenarchaeal IMP cyclohydrolase. In this report, we present the cloning and functional characterization of two representatives of the known IMP cyclohydrolase families. The locus TK0430 in Thermococcus kodakarensis encodes a PurO-type IMP cyclohydrolase with demonstrated activity despite its position in a cluster of apparently redundant biosynthetic genes, the first functional characterization of a PurO from a non-methanogen. Kinetic characterization reveals a Km for FAICAR of 1.56 ± 0.39 μM and a kcat of 0.48 ± 0.04 s-1. The locus AF1811 from Archaeoglobus fulgidus encodes a PurH2-type IMP cyclohydrolase. This Archaeoglobus fulgidus PurH2 has a Km of 7.8 ± 1.8 μM and kcat of 1.32 ± 0.14 s-1, representing the first characterization of an archaeal PurH2 and the first characterization of PurH2 that naturally occurs unfused to an AICAR formyltransferase domain. Each of these two characterized IMP cyclohydrolases converts FAICAR to IMP in vitro, and each cloned gene allows the growth on purine-deficient media of an E. coli purine auxotroph lacking the purH2 gene.

Klíčová slova:

Archaea – Biosynthesis – Enzyme kinetics – Genetic loci – High performance liquid chromatography – Paleogenetics – Staphylococcus – Purines


Zdroje

1. Brown AM, Hoopes SL, White RH, Sarisky CA. Purine Biosynthesis in Archaea: Variations on a Theme. Biology Direct. 2011; 6: 63. doi: 10.1186/1745-6150-6-63 22168471

2. Costa Brandão Cruz D, Lima Santana L, Siqueira Guedes A, Teodoro de Souza J, Arthur Santos Marbach P. Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes. Genome Biology and Evolution. 2019 April; 11(4): 1235–1249. doi: 10.1093/gbe/evz035 30785193

3. Kang YN, Tran A, White RH, Ealick SE. A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase. Biochemistry. 2007 May 1; 46(17): 5050–5062. doi: 10.1021/bi061637j 17407260

4. Wolan DW, Cheong CG, Greasley SE, Wilson IA. Structural Insights into the Human and Avian IMP Cyclohydrolase Mechanism via Crystal Structures with the Bound XMP Inhibitor. Biochemistry. 2004; 43(5): 1171–1183. doi: 10.1021/bi030162i 14756553

5. Graupner M, Xu H, White RH. New class of IMP cyclohydrolases in Methanococcus jannaschii. J Bacteriol. 2002 Mar; 184(5): 1471–1473. doi: 10.1128/JB.184.5.1471-1473.2002 11844782

6. Davis JJ, Olsen GJ. Characterizing the Native Codon Usages of a Genome: An axis projection approach. Mol Biol Evol. 2011 Aug 2; 28(1): 211–221. doi: 10.1093/molbev/msq185 20679093

7. Zhang Y, Morar M, Ealick SE. Structural Biology of the Purine Biosynthetic Pathway. Cellular and Molecular Life Sciences. 2008; 65(23): 3699–3724. doi: 10.1007/s00018-008-8295-8 18712276

8. Bulock KG, Beardsley GP, Anderson KS. The Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase): A Surprising Lack of Substrate Channeling. The Journal of Biological Chemistry. 2002; 277: 22168–22174. doi: 10.1074/jbc.M111964200 11948179

9. Rayl EA, Moroson BA, Beardsley GP. The Human purH Gene Product, 5-Aminoimidazole-4-carboxamide Ribonucleotide Formyltransferase/IMP Cyclohydrolase: Cloning, Sequencing, Expression, Purification, Kinetic Analysis, and Domain Mapping. The Journal of Biological Chemistry. 1996; 271: 2225–2233. doi: 10.1074/jbc.271.4.2225 8567683

10. Verma P, Kar B, Varshney R, Roy P, Sharma AK. Characterization of AICAR transformylase/IMP cyclohydrolase (ATIC) from Staphylococcus lugdunensis. FEBS Journal. 2017; 284(24): 4233–4261. doi: 10.1111/febs.14303 29063699

11. Vergis JM, Beardsley GP. Catalytic mechanism of the cyclohydrolase activity of human aminoimidazole carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase. Biochemistry. 2004; 43(5): 1184–1192. doi: 10.1021/bi035139b 14756554

12. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2001.

13. Mueller WT, Benkovic SJ. On the Purification and Mechanism of Action of 5-Aminoimidazole-4-carboxamide-Ribonucleotide Transformylase from Chicken Liver. Biochemistry. 1981; 20: 337–344. doi: 10.1021/bi00505a017 7470484

14. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2: 2006.0008.

15. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2001.

16. Kitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, Toyonaga H, et al. Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Research. 2005; 12(5): 291–299. doi: 10.1093/dnares/dsi012 16769691

17. Beeder J, Nilsen RK, Rosnes JT, Torsvik T, Lien T. Archaeoglobus fulgidus Isolated from Hot North Sea Oil Field Waters. Applied and Environmental Microbiology. 1994; 60(4): 1227–1231. 16349231

18. Atomi H, Fukui T, Kanai T, Morikawa M, Imanaka T. Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archaea. 2004; 1(4): 263–267. 15810436

19. Ownby K, Xu H, White RH. A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase. A new enzyme in purine biosynthesis. J Biol Chem. 2005 Mar 25; 280(12): 10881–10887. doi: 10.1074/jbc.M413937200 15623504


Článek vyšel v časopise

PLOS One


2019 Číslo 10