Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
23 04 2020
23 04 2020
Historique:
received:
12
09
2019
accepted:
31
03
2020
entrez:
25
4
2020
pubmed:
25
4
2020
medline:
1
8
2020
Statut:
epublish
Résumé
Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.
Identifiants
pubmed: 32327655
doi: 10.1038/s41467-020-15876-8
pii: 10.1038/s41467-020-15876-8
pmc: PMC7181641
doi:
Substances chimiques
Bacterial Proteins
0
Aspartic Acid
30KYC7MIAI
Aspartate Aminotransferases
EC 2.6.1.1
Nitrogen
N762921K75
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1960Subventions
Organisme : NIAID NIH HHS
ID : U19 AI107774
Pays : United States
Références
Ellens, K. W. et al. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Res. 45, 11495–11514 (2017).
pubmed: 29059321
pmcid: 5714238
doi: 10.1093/nar/gkx937
Chen, L. & Vitkup, D. Distribution of orphan metabolic activities. Trends Biotechnol. 25, 343–348 (2007).
pubmed: 17580095
doi: 10.1016/j.tibtech.2007.06.001
WHO. Global tuberculosis report 2018. 1–231. https://reliefweb.int/report/world/global-tuberculosis-report-2018 (2018).
Griffin, J. E. et al. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog. 7, e1002251 (2011).
pubmed: 21980284
pmcid: 3182942
doi: 10.1371/journal.ppat.1002251
Grishin, N. V., Phillips, M. A. & Goldsmith, E. J. Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci. Publ. Protein Soc. 4, 1291–1304 (1995).
doi: 10.1002/pro.5560040705
Bramucci, E., Milano, T. & Pascarella, S. Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5’-phosphate dependent enzymes of fold type I. Biochem. Biophys. Res. Commun. 415, 88–93 (2011).
pubmed: 22020104
doi: 10.1016/j.bbrc.2011.10.017
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
pubmed: 30357350
doi: 10.1093/nar/gky995
Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47, D351–D360 (2019).
pubmed: 30398656
doi: 10.1093/nar/gky1100
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016).
pubmed: 26582926
doi: 10.1093/nar/gkv1248
Yang, Z., Zeng, X. & Tsui, S. K.-W. Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. BMC Genomics 20, 394 (2019).
pubmed: 31113361
pmcid: 6528289
doi: 10.1186/s12864-019-5746-6
Ortega, C. et al. Systematic survey of serine hydrolase activity in Mycobacterium tuberculosis defines changes associated with persistence. Cell Chem. Biol. 23, 290–298 (2016).
pubmed: 26853625
pmcid: 4803444
doi: 10.1016/j.chembiol.2016.01.003
Penn, B. H. et al. An Mtb-human protein-protein interaction map identifies a switch between host antiviral and antibacterial responses. Mol. Cell 71, 637–648.e5 (2018).
pubmed: 30118682
pmcid: 6329589
doi: 10.1016/j.molcel.2018.07.010
Wang, M., Herrmann, C. J., Simonovic, M., Szklarczyk, D. & von Mering, C. Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics 15, 3163–3168 (2015).
pubmed: 25656970
pmcid: 6680238
doi: 10.1002/pmic.201400441
Ehrt, S., Schnappinger, D. & Rhee, K. Y. Metabolic principles of persistence and pathogenicity in Mycobacterium tuberculosis. Nat. Rev. Microbiol. 16, 496–507 (2018).
pubmed: 29691481
pmcid: 6045436
doi: 10.1038/s41579-018-0013-4
Gouzy, A. et al. Mycobacterium tuberculosis nitrogen assimilation and host colonization require aspartate. Nat. Chem. Biol. 9, 674–676 (2013).
pubmed: 24077180
doi: 10.1038/nchembio.1355
Gouzy, A., Poquet, Y. & Neyrolles, O. Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence. Nat. Rev. Microbiol. 12, 729–737 (2014).
pubmed: 25244084
doi: 10.1038/nrmicro3349
Johnson, E. O. et al. Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes. Nature 571, 72–78 (2019).
pubmed: 31217586
doi: 10.1038/s41586-019-1315-z
de Carvalho, L. P. S. et al. Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase. Chem. Biol. 17, 323–332 (2010).
pubmed: 20416504
pmcid: 2878197
doi: 10.1016/j.chembiol.2010.03.009
Shen, H. et al. The human knockout gene CLYBL connects itaconate to vitamin B12. Cell 171, 771–782.e11 (2017).
pubmed: 29056341
pmcid: 5827971
doi: 10.1016/j.cell.2017.09.051
Cooper, A. J. L. & Kuhara, T. α-Ketoglutaramate: an overlooked metabolite of glutamine and a biomarker for hepatic encephalopathy and inborn errors of the urea cycle. Metab. Brain Dis. 29, 991–1006 (2014).
pubmed: 24234505
doi: 10.1007/s11011-013-9444-9
Nobe, Y. et al. The novel substrate recognition mechanism utilized by aspartate aminotransferase of the extreme thermophile Thermus thermophilus HB8. J. Biol. Chem. 273, 29554–29564 (1998).
pubmed: 9792664
doi: 10.1074/jbc.273.45.29554
Yagi, T., Kagamiyama, H., Nozaki, M. & Soda, K. [17] Glutamate-aspartate transaminase from microorganisms. in Methods in Enzymology, Vol. 113 83–89 (ed. Meister, A.) (Academic Press, 1985).
Han, Q., Fang, J. & Li, J. Kynurenine aminotransferase and glutamine transaminase K of Escherichia coli: identity with aspartate aminotransferase. Biochem. J. 360, 617–623 (2001).
pubmed: 11736651
pmcid: 1222264
doi: 10.1042/bj3600617
Sigrist, C. J. A. et al. New and continuing developments at PROSITE. Nucleic Acids Res. 41, D344–D347 (2013).
pubmed: 23161676
doi: 10.1093/nar/gks1067
Son, H. F. & Kim, K.-J. Structural insights into a novel class of aspartate aminotransferase from Corynebacterium glutamicum. PloS ONE 11, e0158402 (2016).
pubmed: 27355211
pmcid: 4927141
doi: 10.1371/journal.pone.0158402
Dolzan, M. et al. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett. 571, 141–146 (2004).
pubmed: 15280032
doi: 10.1016/j.febslet.2004.06.075
Mehta, P. K., Hale, T. I. & Christen, P. Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 214, 549–561 (1993).
pubmed: 8513804
doi: 10.1111/j.1432-1033.1993.tb17953.x
Malashkevich, V. N., Onuffer, J. J., Kirsch, J. F. & Jansonius, J. N. Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase. Nat. Struct. Biol. 2, 548–553 (1995).
pubmed: 7664122
doi: 10.1038/nsb0795-548
Wrenger, C. et al. Specific inhibition of the aspartate aminotransferase of Plasmodium falciparum. J. Mol. Biol. 405, 956–971 (2011).
pubmed: 21087616
doi: 10.1016/j.jmb.2010.11.018
Guidetti, P., Amori, L., Sapko, M. T., Okuno, E. & Schwarcz, R. Mitochondrial aspartate aminotransferase: a third kynurenate-producing enzyme in the mammalian brain. J. Neurochem. 102, 103–111 (2007).
pubmed: 17442055
doi: 10.1111/j.1471-4159.2007.04556.x
Duff, S. M. G. et al. The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure. Arch. Biochem. Biophys. 528, 90–101 (2012).
pubmed: 22750542
doi: 10.1016/j.abb.2012.06.006
Carroll, P., Pashley, C. A. & Parish, T. Functional analysis of GlnE, an essential adenylyl transferase in Mycobacterium tuberculosis. J. Bacteriol. 190, 4894–4902 (2008).
pubmed: 18469098
pmcid: 2446997
doi: 10.1128/JB.00166-08
Yuan, J. et al. Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol. Syst. Biol. 5, 302 (2009).
pubmed: 19690571
pmcid: 2736657
doi: 10.1038/msb.2009.60
Tullius, M. V., Harth, G. & Horwitz, M. A. Glutamine synthetase GlnA1 is essential for growth of Mycobacterium tuberculosis in human THP-1 macrophages and guinea pigs. Infect. Immun. 71, 3927–3936 (2003).
pubmed: 12819079
pmcid: 162033
doi: 10.1128/IAI.71.7.3927-3936.2003
Catazaro, J., Caprez, A., Guru, A., Swanson, D. & Powers, R. Functional evolution of PLP-dependent enzymes based on active-site structural similarities. Proteins Struct. Funct. Bioinforma. 82, 2597–2608 (2014).
doi: 10.1002/prot.24624
Onuffer, J. J. & Kirsch, J. F. Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis. Protein Sci. 4, 1750–1757 (1995).
pubmed: 8528073
pmcid: 2143225
doi: 10.1002/pro.5560040910
Cole, S. T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998).
pubmed: 9634230
doi: 10.1038/31159
Amorim Franco, T. M., Hegde, S. & Blanchard, J. S. Chemical mechanism of the branched-chain aminotransferase IlvE from Mycobacterium tuberculosis. Biochemistry 55, 6295–6303 (2016).
pubmed: 27780341
pmcid: 5443349
doi: 10.1021/acs.biochem.6b00928
Bhor, V. M., Dev, S., Vasanthakumar, G. R. & Surolia, A. Spectral and kinetic characterization of 7,8-diaminopelargonic acid synthase from Mycobacterium tuberculosis. IUBMB Life 58, 225–233 (2006).
pubmed: 16754301
doi: 10.1080/15216540600746997
Nasir, N., Anant, A., Vyas, R. & Biswal, B. K. Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities. Sci. Rep. 6, 18880 (2016).
pubmed: 26738801
pmcid: 4703992
doi: 10.1038/srep18880
Holt, M. C. et al. Biochemical characterization and structure-based mutational analysis provide insight into the binding and mechanism of action of novel aspartate aminotransferase inhibitors. Biochemistry 57, 6604–6614 (2018).
pubmed: 30365304
pmcid: 6487875
doi: 10.1021/acs.biochem.8b00914
Gouzy, A. et al. Mycobacterium tuberculosis exploits asparagine to assimilate nitrogen and resist acid stress during infection. PLoS Pathog. 10, e1003928 (2014).
pubmed: 24586151
pmcid: 3930563
doi: 10.1371/journal.ppat.1003928
Agapova, A. et al. Flexible nitrogen utilisation by the metabolic generalist pathogen Mycobacterium tuberculosis. eLife 8, e41129 (2019).
Lal, P. B., Schneider, B. L., Vu, K. & Reitzer, L. The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in Escherichia coli. Mol. Microbiol. 94, 843–856 (2014).
pubmed: 25243376
doi: 10.1111/mmi.12801
Gelfand, D. H. & Steinberg, R. A. Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases. J. Bacteriol. 130, 429–440 (1977).
pubmed: 15983
pmcid: 235221
doi: 10.1128/JB.130.1.429-440.1977
Bennett, B. D. et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593–599 (2009).
pubmed: 19561621
pmcid: 2754216
doi: 10.1038/nchembio.186
Soga, T. et al. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J. Proteome Res. 2, 488–494 (2003).
pubmed: 14582645
doi: 10.1021/pr034020m
Sugimoto, M. et al. MMMDB: mouse multiple tissue metabolome database. Nucleic Acids Res. 40, D809–D814 (2012).
pubmed: 22139941
doi: 10.1093/nar/gkr1170
Reitzer, L. Nitrogen assimilation and global regulation in Escherichia coli. Annu. Rev. Microbiol. 57, 155–176 (2003).
pubmed: 12730324
doi: 10.1146/annurev.micro.57.030502.090820
Reitzer, L. Biosynthesis of glutamate, aspartate, asparagine, L-alanine, and D-alanine. EcoSal Plus 1, 1–18 (2004).
doi: 10.1128/ecosalplus.3.6.1.3
Somashekar, B. S. et al. Metabolic profiling of lung granuloma in Mycobacterium tuberculosis infected guinea pigs: ex vivo 1H magic angle spinning NMR studies. J. Proteome Res. 10, 4186–4195 (2011).
pubmed: 21732701
doi: 10.1021/pr2003352
Borah, K. et al. Intracellular Mycobacterium tuberculosis exploits multiple host nitrogen sources during growth in human macrophages. Cell Rep. 29, 3580–3591.e4 (2019).
pubmed: 31825837
pmcid: 6915324
doi: 10.1016/j.celrep.2019.11.037
Bhattacharyya, N. et al. An aspartate-specific solute-binding protein regulates protein kinase G activity to control glutamate metabolism in Mycobacteria. mBio 9, e00931–18 (2018).
pubmed: 30065086
pmcid: 6069109
Rieck, B. et al. PknG senses amino acid availability to control metabolism and virulence of Mycobacterium tuberculosis. PLoS Pathog. 13, e1006399 (2017).
pubmed: 28545104
pmcid: 5448819
doi: 10.1371/journal.ppat.1006399
Murphy, K. C., Papavinasasundaram, K. & Sassetti, C. M. Mycobacterial recombineering. Methods Mol. Biol. 1285, 177–199 (2015).
pubmed: 25779316
doi: 10.1007/978-1-4939-2450-9_10
Tautenhahn, R., Patti, G. J., Rinehart, D. & Siuzdak, G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal. Chem. 84, 5035–5039 (2012).
pubmed: 22533540
pmcid: 3703953
doi: 10.1021/ac300698c
Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinforma. Oxf. Engl. 24, 2534–2536 (2008).
doi: 10.1093/bioinformatics/btn323
Pashley, C. A., Brown, A. C., Robertson, D. & Parish, T. Identification of the Mycobacterium tuberculosis GlnE promoter and its response to nitrogen availability. Microbiology 152, 2727–2734 (2006).
pubmed: 16946267
doi: 10.1099/mic.0.28942-0
Weischenfeldt, J. & Porse, B. Bone marrow-derived macrophages (BMM): isolation and applications. Cold Spring Harb. Protoc. 2008, pdb.prot5080 (2008).
Rial, D. V. & Ceccarelli, E. A. Removal of DnaK contamination during fusion protein purifications. Protein Expr. Purif. 25, 503–507 (2002).
pubmed: 12182832
doi: 10.1016/S1046-5928(02)00024-4
Jaisson, S., Veiga-da-Cunha, M. & Van Schaftingen, E. Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2. Biochimie 91, 1066–1071 (2009).
pubmed: 19596042
doi: 10.1016/j.biochi.2009.07.002
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D. Biol. Crystallogr. 67, 235–242 (2011).
pubmed: 21460441
pmcid: 21460441
doi: 10.1107/S0907444910045749
Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D. Biol. Crystallogr. 66, 22–25 (2010).
pubmed: 20057045
doi: 10.1107/S0907444909042589
Kabsch, W. XDS. Acta Crystallogr. D. Biol. Crystallogr. 66, 125–132 (2010).
pubmed: 20124692
pmcid: 20124692
doi: 10.1107/S0907444909047337
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D. Biol. Crystallogr. 58, 1948–1954 (2002).
pubmed: 12393927
doi: 10.1107/S0907444902016657
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 20383002
doi: 10.1107/S0907444910007493
Liebschner, D. et al. Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallogr. Sect. Struct. Biol. 73, 148–157 (2017).
doi: 10.1107/S2059798316018210
Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254
doi: 10.1002/jcc.20084
Mendler, K. et al. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res. 47, 4442–4448 (2019).
pubmed: 31081040
pmcid: 6511854
doi: 10.1093/nar/gkz246
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
pubmed: 6602468
pmcid: 6602468
doi: 10.1093/nar/gkz239