Artículo

Gil, M.; Lima, A.; Rivera, B.; Rossello, J.; Urdániz, E.; Cascioferro, A.; Carrión, F.; Wehenkel, A.; Bellinzoni, M.; Batthyány, C.; Pritsch, O.; Denicola, A.; Alvarez, M.N.; Carvalho, P.C.; Lisa, M.-N.; Brosch, R.; Piuri, M.; Alzari, P.M.; Durán, R. "New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach" (2019) Journal of Proteomics. 192:321-333
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Abstract:

PknG from Mycobacterium tuberculosis is a multidomain Serine/Threonine protein kinase that regulates bacterial metabolism as well as the pathogen's ability to survive inside the host by still uncertain mechanisms. To uncover PknG interactome we developed an affinity purification-mass spectrometry strategy to stepwise recover PknG substrates and interactors; and to identify those involving PknG autophosphorylated docking sites. We report a confident list of 7 new putative substrates and 66 direct or indirect partners indicating that PknG regulates many physiological processes, such as nitrogen and energy metabolism, cell wall synthesis and protein translation. GarA and the 50S ribosomal protein L13, two previously reported substrates of PknG, were recovered in our interactome. Comparative proteome analyses of wild type and pknG null mutant M. tuberculosis strains provided evidence that two kinase interactors, the FHA-domain containing protein GarA and the enzyme glutamine synthetase, are indeed endogenous substrates of PknG, stressing the role of this kinase in the regulation of nitrogen metabolism. Interestingly, a second FHA protein was identified as a PknG substrate. Our results show that PknG phosphorylates specific residues in both glutamine synthetase and FhaA in vitro, and suggest that these proteins are phosphorylated by PknG in living mycobacteria. © 2018 Elsevier B.V.

Registro:

Documento: Artículo
Título:New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach
Autor:Gil, M.; Lima, A.; Rivera, B.; Rossello, J.; Urdániz, E.; Cascioferro, A.; Carrión, F.; Wehenkel, A.; Bellinzoni, M.; Batthyány, C.; Pritsch, O.; Denicola, A.; Alvarez, M.N.; Carvalho, P.C.; Lisa, M.-N.; Brosch, R.; Piuri, M.; Alzari, P.M.; Durán, R.
Filiación:Unidad de Bioquímica y Proteómica Analíticas Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo, 11400, Uruguay
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
Institut Pasteur de Montevideo, Unidad de Biofísica de Proteínas, Uruguay
Unité de Microbiologie Structurale, Institut Pasteur, CNRS URA 2185, Paris, France
Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
Departamento de Bioquímica, Facultad de Medicina, CEINBIO, Universidad de la República, Uruguay
Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Paraná, Brazil
Unit of Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK, Rosario, Argentina
Palabras clave:Affinity purification-mass spectrometry; FhaA; glutamine synthetase; Mycobacterium tuberculosis; PknG; Serine/Threonine protein kinase; 50s ribosomal protein L13; 60 kda chaperonin 1; acetyl propionyl coenzyme A carboxylase alpha chain; alcohol dehydrogenase iron containing protein; bacterial enzyme; fhaa protein; gara protein; glutamate ammonia ligase; inorganic pyrophosphatase; pkng protein; protein DnaK; protein serine threonine kinase; unclassified drug; affinity chromatography; Article; autophosphorylation; bacterial cell wall; bacterial strain; controlled study; enzyme analysis; enzyme phosphorylation; enzyme purification; enzyme substrate; ferredoxin iron sulfur binding protein; in vitro study; mass spectrometry; molecular docking; Mycobacterium tuberculosis; nitrogen fixation; nonhuman; priority journal; translation regulation
Año:2019
Volumen:192
Página de inicio:321
Página de fin:333
DOI: http://dx.doi.org/10.1016/j.jprot.2018.09.013
Título revista:Journal of Proteomics
Título revista abreviado:J. Proteomics
ISSN:18743919
CAS:glutamate ammonia ligase, 9023-70-5; inorganic pyrophosphatase, 9024-82-2, 9033-44-7; protein serine threonine kinase
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_18743919_v192_n_p321_Gil

Referencias:

  • World Health Organization, Annual TB Report (2017), http://www.searo.who.int/tb/documents/annual_tb_repot_2017/en/; Gengenbacher, M., Kaufmann, S.H.E., Mycobacterium tuberculosis: success through dormancy (2012) FEMS Microbiol. Rev., 36, pp. 514-532
  • Russell, D.G., Cardona, P.-J., Kim, M.-J., Allain, S., Altare, F., Foamy macrophages and the progression of the human tuberculosis granuloma (2009) Nat. Immunol., 10, pp. 943-948
  • Ortega, C., Liao, R., Anderson, L.N., Rustad, T., Ollodart, A.R., Wright, A.T., Sherman, D.R., Grundner, C., Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch (2014) PLoS Biol, 12
  • Prisic, S., Dankwa, S., Schwartz, D., Chou, M.F., Locasale, J.W., Kang, C.-M., Bemis, G., Husson, R.N., Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases (2010) Proc. Natl. Acad. Sci. U. S. A., 107, pp. 7521-7526
  • Fortuin, S., Tomazella, G.G., Nagaraj, N., Sampson, S.L., Gey van Pittius, N.C., Soares, N.C., Wiker, H.G., Warren, R.M., Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: Expanding the mycobacterial phosphoproteome catalog (2015) Front. Microbiol., 6, pp. 1-12
  • Kusebauch, U., Ortega, C., Ollodart, A., Rogers, R.S., Sherman, D.R., Moritz, R.L., Grundner, C., Mycobacterium tuberculosis supports protein tyrosine phosphorylation (2014) Proc. Natl. Acad. Sci., 111, pp. 9265-9270
  • Prisic, S., Husson, R.N., Mycobacterium tuberculosis Serine/Threonine protein kinases (2014) Microbiol. Spectr, 2
  • Sherman, D.R., Grundner, C., Agents of change - concepts in Mycobacterium tuberculosis Ser/Thr/Tyr phosphosignalling (2014) Mol. Microbiol., 94, pp. 231-241
  • Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Barrell, B.G., Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence (1998) Nature, 393, pp. 537-544
  • Av-Gay, Y., Everett, M., The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis (2000) Trends Microbiol., 8, pp. 238-244
  • Cowley, S., Ko, M., Pick, N., Chow, R., Downing, K.J., Gordhan, B.G., Betts, J.C., Av-Gay, Y., The Mycobacterium tuberculosis protein serine/threonine kinase PknG is linked to cellular glutamate/glutamine levels and is important for growth in vivo (2004) Mol. Microbiol., 52, pp. 1691-1702
  • Kruh, N.A., Troudt, J., Izzo, A., Prenni, J., Dobos, K.M., Portrait of a pathogen: the Mycobacterium tuberculosis proteome in vivo (2010) PLoS One., 5
  • Wehenkel, A., Bellinzoni, M., Graña, M., Duran, R., Villarino, A., Fernandez, P., Andre-Leroux, G., Alzari, P.M., Mycobacterial Ser/Thr protein kinases and phosphatases: physiological roles and therapeutic potential (2008) Biochim. Biophys. Acta, 1784, pp. 193-202
  • Rieck, B., Degiacomi, G., Zimmermann, M., Cascioferro, A., Boldrin, F., Lazar-Adler, N.R., Bottrill, A.R., O'Hare, H.M., PknG Senses Amino Acid Availability to Control Metabolism and Virulence of Mycobacterium tuberculosis (2017); Walburger, J., Koul, A., Nguyen, L., Prescianotto-Baschong, C., Huygen, K., Klebl, B., Thompson, C., Bacher, C., Protein kinase G from pathogenic mycobacteria promotes survival within macrophages (2004) Science, 80, pp. 1800-1804
  • Khan, M.Z., Bhaskar, A., Upadhyay, S., Kumari, P., Rajmani, R.S., Jain, P., Singh, A., Nandicoori, V.K., Protein kinase G confers survival advantage to Mycobacterium tuberculosis during latency-like conditions (2017) J. Biol. Chem., 292, pp. 16093-16108
  • Paroha, R., Chourasia, R., Mondal, R., Chaurasiya, S.K., PknG supports mycobacterial adaptation in acidic environment (2017) Mol. Cell. Biochem., pp. 1-12
  • Wolff, K.A., Nguyen, H.T., Cartabuke, R.H., Singh, A., Ogwang, S., Nguyen, L., Protein kinase G is required for intrinsic antibiotic resistance in mycobacteria (2009) Antimicrob. Agents Chemother., 53, pp. 3515-3519
  • O'Hare, H.M., Durán, R., Cerveñansky, C., Bellinzoni, M., Wehenkel, A.M., Pritsch, O., Obal, G., Alzari, P.M., Regulation of glutamate metabolism by protein kinases in mycobacteria (2008) Mol. Microbiol., 70, pp. 1408-1423
  • Wolff, K.A., de la Peña, A.H., Nguyen, H.T., Pham, T.H., Amzel, L.M., Gabelli, S.B., Nguyen, L., A redox regulatory system critical for mycobacterial survival in macrophages and biofilm development (2015) PLoS Pathog., 11, pp. 1-20
  • Deng, J., Bi, L., Zhou, L., Guo, S., Fleming, J., Jiang, H., Zhou, Y., Zhang, X., Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity (2014) Cell Rep., 9, pp. 2317-2329
  • Nakedi, K.C., Calder, B., Barnejee, M., Giddey, A., Nel, A.J., Garnett, S., Blackburn, J.M., Da Cruz Soares, N.A., Identification of novel physiological substrates of Mycobacterium Bovis BCG Protein Kinase G (PknG) by label-free quantitative phosphoproteomics (2018) Mol. Cell. Proteomics, 17, pp. 1365-1377
  • Wu, F.-L., Liu, Y., Jiang, H.-W., Luan, Y., Zhang, H., He, X., Xu, Z.-W., Tao, S.-C., The Ser/Thr protein kinase protein-protein interaction Map of M. tuberculosis (2017) Mol. Cell. Proteomics, 16, pp. 1-42
  • Gil, M., Graña, M., Schopfer, F.J., Wagner, T., Denicola, A., Freeman, B.A., Alzari, P.M., Batthyány, C., Inhibition of Mycobacterium tuberculosis PknG by non-catalytic rubredoxin domain specific modification: reaction of an electrophilic nitro-fatty acid with the Fe-S center (2013) Free Radic. Biol. Med., 65, pp. 150-161
  • Lisa, M.N., Gil, M., André-Leroux, G., Barilone, N., Durán, R., Biondi, R.M., Alzari, P.M., Molecular basis of the activity and the regulation of the eukaryotic-like S/T protein kinase PknG from Mycobacterium tuberculosis (2015) Structure., 23, pp. 1039-1048
  • Scherr, N., Honnappa, S., Kunz, G., Mueller, P., Jayachandran, R., Winkler, F., Pieters, J., Steinmetz, M.O., Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis (2007) Proc. Natl. Acad. Sci. U. S. A., 104, pp. 12151-12156
  • Durocher, D., Jackson, S.P., The FHA domain (2002) FEBS Lett., 513, pp. 58-66
  • England, P., Wehenkel, A., Martins, S., Hoos, S., André-Leroux, G., Villarino, A., Alzari, P.M., The FHA-containing protein GarA acts as a phosphorylation-dependent molecular switch in mycobacterial signaling (2009) FEBS Lett., 583, pp. 301-307
  • Villarino, A., Duran, R., Wehenkel, A., Fernandez, P., England, P., Brodin, P., Cole, S.T., Alzari, P.M., Proteomic identification of M. tuberculosis protein kinase substrates: PknB recruits GarA, a FHA domain-containing protein, through activation loop-mediated interactions (2005) J. Mol. Biol., 350, pp. 953-963
  • Nott, T.J., Kelly, G., Stach, L., Li, J., Westcott, S., Patel, D., Hunt, D.M., Smerdon, S.J., An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis (2009) Sci. Signal, 2, pp. 1-9
  • van Kessel, J.C., Marinelli, L.J., Hatfull, G.F., Recombineering mycobacteria and their phages (2008) Nat. Rev. Microbiol., 6, pp. 851-857
  • Krajewski, W.W., Jones, T.A., Mowbray, S.L., Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights (2005) Proc. Natl. Acad. Sci., 102, pp. 10499-10504
  • Shevchenko, A., Wilm, M., Vorm, O., Mann, M., Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels (1996) Anal. Chem., 68, pp. 850-858
  • Carvalho, P.C., Fischer, J.S.G., Xu, T., Yates, J.R., Barbosa, V.C., PatternLab: From mass spectra to label-free differential shotgun proteomics (2012) Curr. Protoc. Bioinforma., pp. 1-18
  • Carvalho, P.C., Lima, D.B., Leprevost, F.V., Santos, M.D.M., Fischer, J.S.G., Aquino, P.F., Moresco, J.J., Barbosa, V.C., Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 (2016) Nat. Protoc, 11, pp. 102-117
  • Carvalho, P.C., Fischer, J.S.G., Perales, J., Yates, J.R., Barbosa, V.C., Bareinboim, E., Analyzing marginal cases in differential shotgun proteomics (2011) Bioinformatics., 27, pp. 275-276
  • Kapopoulou, A., Lew, J.M., Cole, S.T., The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes (2011) Tuberculosis., 91, pp. 8-13
  • Gish, W., States, D.J., Identification of protein coding regions by database similarity search (1993) Nat Genet., 3, pp. 266-272
  • Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Von Mering, C., STRING v10: Protein-protein interaction networks, integrated over the tree of life (2015) Nucleic Acids Res., 43, pp. D447-D452
  • Mi, H., Poudel, S., Muruganujan, A., Casagrande, J.T., Thomas, P.D., PANTHER version 10: Expanded protein families and functions, and analysis tools (2016) Nucleic Acids Res., 44, pp. D336-D342
  • Vizcaino, J.A., Csordas, A., Del-Toro, N., Dianes, J.A., Griss, J., Lavidas, I., Mayer, G., Hermjakob, H., 2016 update of the PRIDE database and its related tools (2016) Nucleic Acids Res., 44, pp. D447-D456
  • Mehta, R., Pearson, J.T., Mahajan, S., Nath, A., Hickey, M.J., Sherman, D.R., Atkins, W.M., Adenylylation and catalytic properties of Mycobacterium tuberculosis glutamine synthetase expressed in Escherichia coli versus mycobacteria (2004) J. Biol. Chem., 279, pp. 22477-22482
  • Shapiro, B.M., Kingdon, H.S., Stadtman, E.R., Regulation of glutamine synthetase. VII. Adenylyl glutamine synthetase: a new form of the enzyme with altered regulatory and kinetic properties (1967) Proc. Natl. Acad. Sci. U. S. A, 58, pp. 642-649
  • Grundner, C., Gay, L.M., Alber, T., Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains (2005) Protein Sci., 14, pp. 1918-1921
  • Gupta, M., Sajid, A., Arora, G., Tandon, V., Singh, Y., Forkhead-associated domain-containing protein Rv0019c and polyketide-associated protein PapA5, from substrates of serine/threonine protein kinase PknB to interacting proteins of Mycobacterium tuberculosis (2009) J. Biol. Chem., 284, pp. 34723-34734
  • Molle, V., Soulat, D., Jault, J.M., Grangeasse, C., Cozzone, A.J., Prost, J.F., Two FHA domains on an ABC transporter, Rv1747, mediate its phosphorylation by PknF, a Ser/Thr protein kinase from Mycobacterium tuberculosis (2004) FEMS Microbiol. Lett., 234, pp. 215-223
  • Sharma, K., Gupta, M., Krupa, A., Srinivasan, N., Singh, Y., EmbR, a regulatory protein with ATPase activity, is a substrate of multiple serine/threonine kinases and phosphatase in Mycobacterium tuberculosis (2006) FEBS J., 273, pp. 2711-2721
  • Calder, B., Albeldas, C., Blackburn, J.M., Soares, N.C., Mass spectrometry offers insight into the role of ser/thr/tyr phosphorylation in the mycobacteria (2016) Front. Microbiol., 7, pp. 1-8
  • Roumestand, C., Leiba, J., Galophe, N., Margeat, E., Padilla, A., Bessin, Y., Barthe, P., Cohen-Gonsaud, M., Structural insight into the Mycobacterium tuberculosis Rv0020c protein and its interaction with the PknB kinase (2011) Structure., 19, pp. 1525-1534
  • Dahl, J.L., Kraus, C.N., Boshoff, H.I.M., Doan, B., Foley, K., Avarbock, D., Kaplan, G., Barry, C.E., The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice (2003) Proc. Natl. Acad. Sci. U. S. A., 100, pp. 10026-10031
  • Verma, R., Pinto, S.M., Patil, A.H., Advani, J., Subba, P., Kumar, M., Sharma, J., Prasad, T.S.K., Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis (2017) J. Proteome Res., 16, pp. 1632-1645
  • Rees, J.S., Lowe, N., Armean, I.M., Roote, J., Johnson, G., Drummond, E., Spriggs, H., Lilley, K.S., In vivo analysis of proteomes and interactomes using parallel affinity capture (iPAC) coupled to mass spectrometry (2011) Mol. Cell. Proteomics., 10
  • Dephoure, N., Gould, K.L., Gygi, S.P., Kellogg, D.R., Mapping and analysis of phosphorylation sites: a quick guide for cell biologists (2013) Mol. Biol. Cell., 24, pp. 535-542
  • Mann, M., Ong, S., Gr, M., Steen, H., Jensen, O.N., Pandey, A., Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome (2002) Trends Biotechnol., 20, pp. 261-268
  • Canova, M.J., Veyron-Churlet, R., Zanella-Cleon, I., Cohen-Gonsaud, M., Cozzone, A.J., Becchi, M., Kremer, L., Molle, V., The Mycobacterium tuberculosis serine/threonine kinase PknL phosphorylates Rv2175c: Mass spectrometric profiling of the activation loop phosphorylation sites and their role in the recruitment of Rv2175c (2008) Proteomics., 8, pp. 521-533
  • Gouzy, A., Poquet, Y., Neyrolles, O., Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence (2014) Nat. Rev. Microbiol., 12, pp. 729-737
  • 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 glutamine synthetase GlnA1 is essential for growth of Mycobacterium tuberculosis in human THP-1 macrophages and Guinea Pigs (2003) Infect. Immun., 71, pp. 3927-3936
  • Carette, X., Platig, J., Young, D.C., Helmel, M., Young, A.T., Wang, Z., Potluri, L.-P., Husson, R.N., Multisystem analysis of Mycobacterium tuberculosis reveals kinase-dependent remodeling of the pathogen-environment interface (2018) MBio, 9, p. e02333
  • Harth, G., Horwitz, M., An inhibitor of exported Mycobacterium tuberculosis glutamine synthetase selectively blocks the growth of pathogenic mycobacteria in axenic culture and in human monocytes: extracellular proteins as potential novel drug targets (1999) J. Exp. Med., 189, pp. 1425-1436
  • Carroll, P., Pashley, C.A., Parish, T., Functional analysis of GlnE, an essential adenylyl transferase in Mycobacterium tuberculosis (2008) J. Bacteriol., 190, pp. 4894-4902
  • Leigh, J.A., Dodsworth, J.A., Nitrogen regulation in bacteria and archaea (2007) Annu. Rev. Microbiol., 61, pp. 349-377
  • Stadtman, E.R., The story of glutamine synthetase regulation (2001) J. Biol. Chem., 276, pp. 44357-44364
  • Gee, C.C.L., Papavinasasundaram, K.G.K., Blair, S.R., Baer, C.E., Falick, A.M., King, D.S., Griffin, J.E., Alber, T., A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria (2012) Sci. Signal., 5, pp. 1-24
  • Roumestand, C., Leiba, J., Galophe, N., Margeat, E., Padilla, A., Bessin, Y., Barthe, P., Cohen-Gonsaud, M., Structural insight into the Mycobacterium tuberculosis Rv0020c protein and its interaction with the PknB kinase (2011) Structure., 19, pp. 1525-1534

Citas:

---------- APA ----------
Gil, M., Lima, A., Rivera, B., Rossello, J., Urdániz, E., Cascioferro, A., Carrión, F.,..., Durán, R. (2019) . New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach. Journal of Proteomics, 192, 321-333.
http://dx.doi.org/10.1016/j.jprot.2018.09.013
---------- CHICAGO ----------
Gil, M., Lima, A., Rivera, B., Rossello, J., Urdániz, E., Cascioferro, A., et al. "New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach" . Journal of Proteomics 192 (2019) : 321-333.
http://dx.doi.org/10.1016/j.jprot.2018.09.013
---------- MLA ----------
Gil, M., Lima, A., Rivera, B., Rossello, J., Urdániz, E., Cascioferro, A., et al. "New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach" . Journal of Proteomics, vol. 192, 2019, pp. 321-333.
http://dx.doi.org/10.1016/j.jprot.2018.09.013
---------- VANCOUVER ----------
Gil, M., Lima, A., Rivera, B., Rossello, J., Urdániz, E., Cascioferro, A., et al. New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach. J. Proteomics. 2019;192:321-333.
http://dx.doi.org/10.1016/j.jprot.2018.09.013