1887

Abstract

Among the nucleoid-associated proteins (NAPs), HU is the most conserved in eubacteria, engaged in overall chromosome organization and regulation of gene expression. Unlike other bacteria, HU from (MtHU), has a long carboxyl terminal domain enriched in basic amino acids, resembling eukaryotic histone N-terminal tails. As with histones, MtHU undergoes post-translational modifications and we have previously identified interacting kinases, methyltransferases, an acetyltransferase and a deacetylase. Here we show that Rv0802c interacts and succinylates MtHU. Although categorized as a succinyltransferase, we show that this GNAT superfamily member can catalyse both succinylation and acetylation of MtHU with comparable kinetic parameters. Like acetylation of MtHU, succinylation of MtHU caused reduced interaction of the NAP with DNA, determined by electrophoretic mobility shift assay and surface plasmon resonance. However, expression of Rv0802c did not significantly alter the nucleoid architecture. Although such succinylation of NAPs is rare, these modifications of the archetypal NAP may provide avenues to the organism to compensate for the underrepresentation of NAPs in its genome to control the dynamics of nucleoid architecture and cellular functions.

Funding
This study was supported by the:
  • Department of Science and Technology, Government of India (Award JC Bose)
    • Principle Award Recipient: ValakunjaNagaraja
  • Department of Biotechnology, Government of India (Award BT/PR13522/COE/34/37/2015)
    • Principle Award Recipient: ValakunjaNagaraja
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/content/journal/micro/10.1099/mic.0.001058
2021-07-05
2021-07-29
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References

  1. World Health Organization 2020; Global tuberculosis report. https://www.who.int/tb/publications/global_report/en/
  2. Datta C, Jha RK, Ganguly S, Nagaraja V. NapA (Rv0430), a novel nucleoid-associated protein that regulates a virulence operon in Mycobacterium tuberculosis in a supercoiling-dependent manner. J Mol Biol 2019; 431:1576–1591 [View Article] [PubMed]
    [Google Scholar]
  3. Datta C, Jha RK, Ahmed W, Ganguly S, Ghosh S et al. Physical and functional interaction between nucleoid-associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation. Mol Microbiol 2019; 111:981–994 [View Article] [PubMed]
    [Google Scholar]
  4. Dorman CJ. Nucleoid-Associated proteins and bacterial physiology. Adv Appl Microbiol 2009; 67:47–64 [View Article] [PubMed]
    [Google Scholar]
  5. Gordon BRG, Li Y, Wang L, Sintsova A, van Bakel H et al. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010; 107:5154–5159 [View Article] [PubMed]
    [Google Scholar]
  6. Odermatt NT, Sala C, Benjak A, Cole ST. Essential nucleoid associated protein mIHF (Rv1388) controls virulence and housekeeping genes in Mycobacterium tuberculosis. Sci Rep 2018; 8:1–14
    [Google Scholar]
  7. Pettijohn DE. Histone-like proteins and bacterial chromosome structure. J Biol Chem 1988; 263:12793–12796 [PubMed]
    [Google Scholar]
  8. Ryan VT, Grimwade JE, Nievera CJ, Leonard AC. IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms. Mol Microbiol 2002; 46:113–124 [View Article] [PubMed]
    [Google Scholar]
  9. Tarashi S, Badi SA, Moshiri A, Ebrahimzadeh N, Fateh A et al. The inter-talk between Mycobacterium tuberculosis and the epigenetic mechanisms. Epigenomics 2020; 12:455–469 [View Article] [PubMed]
    [Google Scholar]
  10. Trojanowski D, Feddersen H. Lsr2 is a nucleoid-associated protein that exerts pleiotropic effects on mycobacterial cellular processes; 2020
  11. Chen JM, Ren H, Shaw JE, Wang YJ, Li M et al. Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein. Nucleic Acids Res 2008; 36:2123–2135 [View Article] [PubMed]
    [Google Scholar]
  12. Dame RT, Wyman C, Goosen N. H-Ns mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 2000; 28:3504–3510 [View Article] [PubMed]
    [Google Scholar]
  13. Madrid C, Balsalobre C, García J, Juárez A. The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins. Mol Microbiol 2007; 63:7–14 [View Article] [PubMed]
    [Google Scholar]
  14. van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci U S A 2004; 101:6969–6974 [View Article] [PubMed]
    [Google Scholar]
  15. Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 1999; 181:6361–6370 [View Article] [PubMed]
    [Google Scholar]
  16. Hołówka J, Trojanowski D, Ginda K, Wojtaś B, Gielniewski B et al. Hupb is a bacterial nucleoid-associated protein with an indispensable eukaryotic-like tail. mBio 2017; 8:1–17 [View Article] [PubMed]
    [Google Scholar]
  17. Rouvière-Yaniv J, Gros F, Josette Rouviere-Yaniv FG. Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli. Proc Natl Acad Sci U S A 1975; 72:3428–3432 [View Article] [PubMed]
    [Google Scholar]
  18. Macvanin M, Adhya S. Architectural organization in E. coli nucleoid. Biochim Biophys Acta 2012; 1819:830–835 [View Article] [PubMed]
    [Google Scholar]
  19. Oberto J, Nabti S, Jooste V, Mignot H, Rouviere-Yaniv J. The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS One 2009; 4:e4367 [View Article] [PubMed]
    [Google Scholar]
  20. Jaffé A, Vinella D, D'Ari R, D’Ari R. The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via MinCDE. J Bacteriol 1997; 179:3494–3499 [View Article] [PubMed]
    [Google Scholar]
  21. Aki T, Adhya S. Repressor induced site-specific binding of HU for transcriptional regulation. Embo J 1997; 16:3666–3674 [View Article] [PubMed]
    [Google Scholar]
  22. Kar S, Edgar R, Adhya S. Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci U S A 2005; 102:16397–16402 [View Article] [PubMed]
    [Google Scholar]
  23. Kamashev D, Rouviere-Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. Embo J 2000; 19:6527–6535 [View Article] [PubMed]
    [Google Scholar]
  24. Shires K, Steyn L. The cold-shock stress response in Mycobacterium smegmatis induces the expression of a histone-like protein. Mol Microbiol 2001; 39:994–1009 [View Article] [PubMed]
    [Google Scholar]
  25. Wang G, RJM LFL. A histone-like protein of Helicobacter pylori protects DNA from stress damage and aids host colonization. DNA Repair 2014; 23:1–7
    [Google Scholar]
  26. Mangan MW, Lucchini S, Ó Cróinín T, Fitzgerald S, Hinton JCD et al. Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium. Microbiology 2011; 157:1075–1087 [View Article] [PubMed]
    [Google Scholar]
  27. Bhowmick T, Ghosh S, Dixit K, Ganesan V, Ramagopal UA et al. Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors. Nat Commun 2014; 5:1–13 [View Article] [PubMed]
    [Google Scholar]
  28. Mukherjee A, Bhattacharyya G, Grove A. The C-terminal domain of HU-related histone-like protein Hlp from Mycobacterium smegmatis mediates DNA end-joining. Biochemistry 2008; 47:8744–8753 [View Article] [PubMed]
    [Google Scholar]
  29. Kasinsky HE, Lewis JD, Dacks JB, Ausió J. Origin of H1 linker histones. Faseb J 2001; 15:34–42 [View Article] [PubMed]
    [Google Scholar]
  30. Grove A. Functional evolution of bacterial histone-like HU proteins. Curr Issues Mol Biol 2011; 13:1–12 [PubMed]
    [Google Scholar]
  31. Macek B, Forchhammer K, Hardouin J, Weber-Ban E, Grangeasse C et al. Protein post-translational modifications in bacteria. Nat Rev Microbiol 2019; 17:651–664 [View Article] [PubMed]
    [Google Scholar]
  32. Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2014; 97:265–286 [View Article] [PubMed]
    [Google Scholar]
  33. Liu F, Yang M, Wang X, Yang S, Gu J et al. Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. Mol Cell Proteomics 2014; 13:3352–3366
    [Google Scholar]
  34. Xie L, Wang X, Zeng J, Zhou M, Duan X et al. Proteome-wide lysine acetylation profiling of the human pathogen Mycobacterium tuberculosis. Int J Biochem Cell Biol 2015; 59:193–202 [View Article] [PubMed]
    [Google Scholar]
  35. Bonds AC, Yuan T, Werman JM, Jang J, Lu R et al. Post-translational succinylation of Mycobacterium tuberculosis enoyl-CoA hydratase EchA19 slows catalytic hydration of cholesterol catabolite 3-Oxo-chol-4,22-diene-24-oyl-CoA. ACS Infect Dis 2020; 6:2214–2224 [View Article] [PubMed]
    [Google Scholar]
  36. Bi J, Gou Z, Zhou F, Chen Y, Gan J et al. Acetylation of lysine 182 inhibits the ability of Mycobacterium tuberculosis DosR to bind DNA and regulate gene expression during hypoxia article. Emerg Microbes Infect 2018; 7:
    [Google Scholar]
  37. Yang M, Wang Y, Chen Y, Cheng Z, Gu J et al. Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis. Mol Cell Proteomics 2015; 14:796–811 [View Article] [PubMed]
    [Google Scholar]
  38. Bhusal RP, Jiao W, Kwai BXC, Reynisson J, Collins AJ et al. Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2. Nat Commun 2019; 10:1–7
    [Google Scholar]
  39. Bi J, Wang Y, Yu H, Qian X, Wang H et al. Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis. Sci Rep 2017; 7:1–11
    [Google Scholar]
  40. Noy T, Hua X, Blanchard JS. Acetylation of Acetyl-CoA Synthetase from Mycobacterium tuberculosis Leads to Specific Inactivation of the Adenylation Reaction. Arch Biochem Biophys 2008; 23:1–7
    [Google Scholar]
  41. Xu H, Hegde SS, Blanchard JS. Reversible acetylation and inactivation of Mycobacterium tuberculosis acetyl-CoA synthetase is dependent on cAMP. Biochemistry 2011; 50:5883–5892 [View Article] [PubMed]
    [Google Scholar]
  42. Gupta RK, Chauhan S, Tyagi JS. K182G substitution in DevR or C₈G mutation in the DEV box impairs protein-DNA interaction and abrogates DevR-mediated gene induction in Mycobacterium tuberculosis. Febs J 2011; 278:2131–2139 [View Article] [PubMed]
    [Google Scholar]
  43. Arora G, Bothra A, Prosser G, Arora K, Sajid A. Role of post-translational modifications in the acquisition of drug resistance in Mycobacterium tuberculosis. Febs J 20201–19 [View Article] [PubMed]
    [Google Scholar]
  44. Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE et al. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife 2020; 9:1–30 [View Article] [PubMed]
    [Google Scholar]
  45. Gupta M, Sajid A, Sharma K, Ghosh S, Arora G et al. HupB, a nucleoid-associated protein of Mycobacterium tuberculosis, is modified by serine/threonine protein kinases in vivo. J Bacteriol 2014; 196:2646–2657 [View Article] [PubMed]
    [Google Scholar]
  46. Ghosh S, Padmanabhan B, Anand C, Nagaraja V. Lysine acetylation of the Mycobacterium tuberculosis HU protein modulates its DNA binding and genome organization. Mol Microbiol 2016; 100:577–588 [View Article] [PubMed]
    [Google Scholar]
  47. Parikh A, Kumar D, Chawla Y, Kurthkoti K, Khan S et al. Development of a new generation of vectors for gene expression, gene replacement, and protein-protein interaction studies in mycobacteria. Appl Environ Microbiol 2013; 79:1718–1729 [View Article] [PubMed]
    [Google Scholar]
  48. Madeira F, Park YM, Lee J, Buso N, Gur T et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 2019; 47:W636–641 [View Article] [PubMed]
    [Google Scholar]
  49. Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 2014; 42:320–324 [View Article] [PubMed]
    [Google Scholar]
  50. Gu J, Deng J-Y, Li R, Wei H, Zhang Z et al. Cloning and characterization of NAD-dependent protein deacetylase (Rv1151c) from Mycobacterium tuberculosis. Biochemistry 2009; 74:743–748 [View Article] [PubMed]
    [Google Scholar]
  51. Anand C, Garg R, Ghosh S, Nagaraja V. A Sir2 family protein Rv1151c deacetylates HU to alter its DNA binding mode in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2017; 493:1204–1209 [View Article] [PubMed]
    [Google Scholar]
  52. Houghton JL, Green KD, Pricer RE, Mayhoub AS, Garneau-Tsodikova S. Unexpected N-acetylation of capreomycin by mycobacterial EIS enzymes. J Antimicrob Chemother 2013; 68:800–805 [View Article] [PubMed]
    [Google Scholar]
  53. Xie L, Yang W, Fan X, Xie J. Comprehensive analysis of protein acetyltransferases of human pathogen Mycobacterium tuberculosis. Biosci Rep 2019; 39:1–11 [View Article] [PubMed]
    [Google Scholar]
  54. Vetting MW, Errey JC, Blanchard JS. Rv0802c from Mycobacterium tuberculosis: the first structure of a succinyltransferase with the GNAT fold. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:978–985 [View Article] [PubMed]
    [Google Scholar]
  55. Ud-Din A, Tikhomirova A, Roujeinikova A. Structure and functional diversity of GCN5-related N-acetyltransferases (GNAT). Int J Mol Sci. 2016; 17:
    [Google Scholar]
  56. Burckhardt RM, Escalante-Semerena JC. Small-Molecule acetylation by GCN5-related N -Acetyltransferases in bacteria. Microbiol Mol Biol Rev 2020; 84:1–33
    [Google Scholar]
  57. Pan Q, Zhao FL, Eis YBC. A novel family of arylalkylamine N-acetyltransferase (EC 2.3.1.87). Sci Rep 2018; 8:1–8
    [Google Scholar]
  58. Kim KH, An DR, Song J, Yoon JY, Kim HS et al. Mycobacterium tuberculosis Eis protein initiates suppression of host immune responses by acetylation of DUSP16/MKP-7. Proc Natl Acad Sci U S A 2012; 109:7729–7734 [View Article] [PubMed]
    [Google Scholar]
  59. Duan L, Yi M, Chen J, Li S, Chen W. Mycobacterium tuberculosis EIS gene inhibits macrophage autophagy through up-regulation of IL-10 by increasing the acetylation of histone H3. Biochem Biophys Res Commun 2016; 473:1229–1234 [View Article] [PubMed]
    [Google Scholar]
  60. Chen W, Green KD, Garneau-Tsodikova S. Cosubstrate tolerance of the aminoglycoside resistance enzyme EIS from Mycobacterium tuberculosis. Antimicrob Agents Chemother 2012; 56:5831–5838 [View Article] [PubMed]
    [Google Scholar]
  61. Green KD, Biswas T, Pang AH, Willby MJ, Reed MS et al. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781–790 [View Article] [PubMed]
    [Google Scholar]
  62. Wang Y, Guo YR, Liu K, Yin Z, Liu R et al. KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase; 2018; 552273–277
  63. Guo F, Adhya S. Spiral structure of Escherichia coli HUαβ provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A 2007; 104:4309–4314 [View Article] [PubMed]
    [Google Scholar]
  64. Swinger KK, Lemberg KM, Zhang Y, Rice PA. Flexible DNA bending in HU-DNA cocrystal structures. Embo J 2003; 22:3749–3760 [View Article] [PubMed]
    [Google Scholar]
  65. Dilweg IW, Dame RT. Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria?. Biochem Soc Trans 2018; 46:1381–1392 [View Article] [PubMed]
    [Google Scholar]
  66. Roth SY, Denu JM, Allis CD, John M, John M, Denu CDA. Histone acetyltransferases. Annu Rev Biochem 2001; 70:81–120 [View Article] [PubMed]
    [Google Scholar]
  67. Dey D, Nagaraja V, Ramakumar S. Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF. Mol Phylogenet Evol 2017; 107:356–366 [View Article] [PubMed]
    [Google Scholar]
  68. Dillon SC, Dorman CJ. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 2010; 8:185–195 [View Article] [PubMed]
    [Google Scholar]
  69. Yaseen I, Choudhury M, Sritharan M, Khosla S. Histone methyltransferase SUV 39H1 participates in host defense by methylating mycobacterial histone-like protein hupB. Embo J 2018; 37:183–200 [View Article] [PubMed]
    [Google Scholar]
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