1887

Abstract

Despite its genome sequencing more than two decades ago, the majority of the genes of remain functionally uncharacterized. Patatins are one such class of proteins that, despite undergoing an expansion in this pathogenic species compared to their non-pathogenic cousins, remain largely unstudied. Recent advances in protein structure prediction using machine learning tools such as AlphaFold2 have provided high-confidence predicted structures for all proteins. Here we present detailed analyses of the patatin family of using AlphaFold-predicted structures, providing insights into likely modes of regulation, membrane interaction and substrate binding. Regulatory domains within this family of proteins include cyclic nucleotide binding, lid-like domains and other helical domains. Using structural homologues, we identified the likely membrane localization mechanisms and substrate-binding sites. These analyses reveal diversity in their regulatory capacity, mechanisms of membrane binding and likely length of fatty acid substrates. Together, this analysis suggests unique roles for the eight predicted patatins of .

Funding
This study was supported by the:
  • Department of Biotechnology, Ministry of Science and Technology, India (Award BT/PR30856/Med/29/1363/2018)
    • Principle Award Recipient: SheetalGandotra
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2022-12-13
2024-12-09
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References

  1. Global health estimates: Leading causes of death. n.d https://www.who.int/data/gho/data/themes/mortality-and-global-health-estimates/ghe-leading-causes-of-death accessed 6 September 2022
  2. World Health Organization Global AIDS statistics. AIDS Care 2001; 13:688 [View Article]
    [Google Scholar]
  3. Anderson RJ. The chemistry of the lipids of the tubercle bacillus. Yale J Biol Med 1943; 15:311–345 [PubMed]
    [Google Scholar]
  4. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998; 393:537–544 [View Article] [PubMed]
    [Google Scholar]
  5. Li Y, Li W, Xie Z, Xu H, He Z-G. MpbR, an essential transcriptional factor for Mycobacterium tuberculosis survival in the host, modulates PIM biosynthesis and reduces innate immune responses. J Genet Genomics 2019; 46:575–589 [View Article] [PubMed]
    [Google Scholar]
  6. Rens C, Chao JD, Sexton DL, Tocheva EI, Av-Gay Y. Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis. Microbiology 2021; 167: [View Article]
    [Google Scholar]
  7. Hunter RL, Olsen MR, Jagannath C, Actor JK. Multiple roles of cord factor in the pathogenesis of primary, secondary, and cavitary tuberculosis, including a revised description of the pathology of secondary disease. Ann Clin Lab Sci 2006; 36:371–386 [PubMed]
    [Google Scholar]
  8. Cambier CJ, O’Leary SM, O’Sullivan MP, Keane J, Ramakrishnan L. Phenolic glycolipid facilitates mycobacterial escape from microbicidal tissue-resident macrophages. Immunity 2017; 47:552–565 [View Article] [PubMed]
    [Google Scholar]
  9. Ruhl CR, Pasko BL, Khan HS, Kindt LM, Stamm CE et al. Mycobacterium tuberculosis sulfolipid-1 activates nociceptive neurons and induces cough. Cell 2020; 181:293–305 [View Article] [PubMed]
    [Google Scholar]
  10. Johnsson K, King DS, Schultz PG. Studies on the mechanism of action of isoniazid and ethionamide in the chemotherapy of tuberculosis. J Am Chem Soc 1995; 117:5009–5010 [View Article]
    [Google Scholar]
  11. Gaspar AH, Machner MP. VipD is a Rab5-activated phospholipase A1 that protects Legionella pneumophila from endosomal fusion. Proc Natl Acad Sci U S A 2014; 111:4560–4565 [View Article] [PubMed]
    [Google Scholar]
  12. Shaver CM, Hauser AR. Relative contributions of Pseudomonas aeruginosa ExoU, ExoS, and ExoT to virulence in the lung. Infect Immun 2004; 72:6969–6977 [View Article] [PubMed]
    [Google Scholar]
  13. Borgo GM, Burke TP, Tran CJ, Lo NTN, Engström P et al. A patatin-like phospholipase mediates Rickettsia parkeri escape from host membranes. Nat Commun 2022; 13:3656 [View Article] [PubMed]
    [Google Scholar]
  14. Santucci P, Diomandé S, Poncin I, Alibaud L, Viljoen A et al. Delineating the physiological roles of the PE and catalytic domains of LipY in lipid consumption in mycobacterium-infected foamy macrophages. Infect Immun 2018; 86:e00394-18 [View Article] [PubMed]
    [Google Scholar]
  15. Raynaud C, Guilhot C, Rauzier J, Bordat Y, Pelicic V et al. Phospholipases C are involved in the virulence of Mycobacterium tuberculosis. Mol Microbiol 2002; 45:203–217 [View Article] [PubMed]
    [Google Scholar]
  16. Assis PA, Espíndola MS, Paula-Silva FWG, Rios WM, Pereira PAT et al. Mycobacterium tuberculosis expressing phospholipase C subverts PGE2 synthesis and induces necrosis in alveolar macrophages. BMC Microbiol 2014; 14:128 [View Article]
    [Google Scholar]
  17. Jaeger K-E, Ransac S, Dijkstra BW, Colson C, Heuvel M et al. Bacterial lipases. FEMS Microbiol Rev 1994; 15:29–63 [View Article] [PubMed]
    [Google Scholar]
  18. Deb C, Daniel J, Sirakova TD, Abomoelak B, Dubey VS et al. A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. J Biol Chem 2006; 281:3866–3875 [View Article]
    [Google Scholar]
  19. West NP, Chow FME, Randall EJ, Wu J, Chen J et al. Cutinase‐like proteins of Mycobacterium tuberculosis : characterization of their variable enzymatic functions and active site identification. FASEB J 2009; 23:1694–1704 [View Article] [PubMed]
    [Google Scholar]
  20. Côtes K, Bakala N’Goma JC, Dhouib R, Douchet I, Maurin D et al. Lipolytic enzymes in Mycobacterium tuberculosis. Appl Microbiol Biotechnol 2008; 78:741–749 [View Article] [PubMed]
    [Google Scholar]
  21. Martinez C, Nicolas A, van Tilbeurgh H, Egloff MP, Cudrey C et al. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry 1994; 33:83–89 [View Article] [PubMed]
    [Google Scholar]
  22. Goins CM, Schreidah CM, Dajnowicz S, Ronning DR. Structural basis for lipid binding and mechanism of the Mycobacterium tuberculosis Rv3802 phospholipase. J Biol Chem 2018; 293:1363–1372 [View Article] [PubMed]
    [Google Scholar]
  23. Flores-Díaz M, Monturiol-Gross L, Naylor C, Alape-Girón A, Flieger A. Bacterial sphingomyelinases and phospholipases as virulence factors. Microbiol Mol Biol Rev 2016; 80:597–628 [View Article] [PubMed]
    [Google Scholar]
  24. Sakurai J, Nagahama M, Oda M. Clostridium perfringens alpha-toxin: characterization and mode of action. J Biochem 2004; 136:569–574 [View Article] [PubMed]
    [Google Scholar]
  25. Terada LS, Johansen KA, Nowbar S, Vasil AI, Vasil ML. Pseudomonas aeruginosa hemolytic phospholipase C suppresses neutrophil respiratory burst activity. Infect Immun 1999; 67:2371–2376 [View Article] [PubMed]
    [Google Scholar]
  26. Smith GA, Marquis H, Jones S, Johnston NC, Portnoy DA et al. The two distinct phospholipases C of Listeria monocytogenes have overlapping roles in escape from a vacuole and cell-to-cell spread. Infect Immun 1995; 63:4231–4237 [View Article]
    [Google Scholar]
  27. Schué M, Maurin D, Dhouib R, Bakala N’Goma J-C, Delorme V et al. Two cutinase-like proteins secreted by Mycobacterium tuberculosis show very different lipolytic activities reflecting their physiological function. FASEB J 2010; 24:1893–1903 [View Article] [PubMed]
    [Google Scholar]
  28. Parker SK, Barkley RM, Rino JG, Vasil ML. Mycobacterium tuberculosis Rv3802c encodes a phospholipase/thioesterase and is inhibited by the antimycobacterial agent tetrahydrolipstatin. PLoS One 2009; 4:e4281 [View Article] [PubMed]
    [Google Scholar]
  29. Yang Y, Kulka K, Montelaro RC, Reinhart TA, Sissons J et al. A hydrolase of trehalose dimycolate induces nutrient influx and stress sensitivity to balance intracellular growth of Mycobacterium tuberculosis. Cell Host Microbe 2014; 15:153–163 [View Article] [PubMed]
    [Google Scholar]
  30. Kienesberger PC, Oberer M, Lass A, Zechner R. Mammalian patatin domain containing proteins: a family with diverse lipolytic activities involved in multiple biological functions. J Lipid Res 2009; 50 Suppl:S63–8 [View Article] [PubMed]
    [Google Scholar]
  31. Vancanneyt G, Sonnewald U, Hofgen R, Willmitzer L. Expression of a patatin-like protein in the anthers of potato and sweet pepper flowers. Plant Cell 1989; 1:533–540 [View Article] [PubMed]
    [Google Scholar]
  32. Rydel TJ, Williams JM, Krieger E, Moshiri F, Stallings WC et al. The crystal structure, mutagenesis, and activity studies reveal that patatin is a lipid acyl hydrolase with a Ser-Asp catalytic dyad. Biochemistry 2003; 42:6696–6708 [View Article] [PubMed]
    [Google Scholar]
  33. Banerji S, Flieger A. Patatin-like proteins: a new family of lipolytic enzymes present in bacteria?. Microbiology 2004; 150:522–525 [View Article]
    [Google Scholar]
  34. Sato H, Frank DW, Hillard CJ, Feix JB, Pankhaniya RR et al. The mechanism of action of the Pseudomonas aeruginosa-encoded type III cytotoxin, ExoU. EMBO J 2003; 22:2959–2969 [View Article] [PubMed]
    [Google Scholar]
  35. da Mata Madeira PV, Zouhir S, Basso P, Neves D, Laubier A et al. Structural basis of lipid targeting and destruction by the type V secretion system of Pseudomonas aeruginosa. J Mol Biol 2016; 428:1790–1803 [View Article] [PubMed]
    [Google Scholar]
  36. Severin GB, Ramliden MS, Hawver LA, Wang K, Pell ME et al. Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae. Proc Natl Acad Sci U S A 2018; 115:E6048–E6055 [View Article] [PubMed]
    [Google Scholar]
  37. Rahman MS, Gillespie JJ, Kaur SJ, Sears KT, Ceraul SM et al. Rickettsia typhi possesses phospholipase A2 enzymes that are involved in infection of host cells. PLoS Pathog 2013; 9:e1003399 [View Article]
    [Google Scholar]
  38. Ohno Y, Kamiyama N, Nakamichi S, Kihara A. PNPLA1 is a transacylase essential for the generation of the skin barrier lipid ω-O-acylceramide. Nat Commun 2017; 8:14610 [View Article] [PubMed]
    [Google Scholar]
  39. Kumari M, Schoiswohl G, Chitraju C, Paar M, Cornaciu I et al. Adiponutrin functions as a nutritionally regulated lysophosphatidic acid acyltransferase. Cell Metab 2012; 15:691–702 [View Article] [PubMed]
    [Google Scholar]
  40. Lake AC, Sun Y, Li J-L, Kim JE, Johnson JW et al. Expression, regulation, and triglyceride hydrolase activity of Adiponutrin family members. J Lipid Res 2005; 46:2477–2487 [View Article] [PubMed]
    [Google Scholar]
  41. Gao JG, Shih A, Gruber R, Schmuth M, Simon M. GS2 as a retinol transacylase and as a catalytic dyad independent regulator of retinylester accretion. Mol Genet Metab 2009; 96:253–260 [View Article] [PubMed]
    [Google Scholar]
  42. Gendrin C, Contreras-Martel C, Bouillot S, Elsen S, Lemaire D et al. Structural basis of cytotoxicity mediated by the type III secretion toxin ExoU from Pseudomonas aeruginosa. PLoS Pathog 2012; 8:e1002637 [View Article] [PubMed]
    [Google Scholar]
  43. Lucas M, Gaspar AH, Pallara C, Rojas AL, Fernández-Recio J et al. Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. Proc Natl Acad Sci U S A 2014; 111:E3514–23 [View Article] [PubMed]
    [Google Scholar]
  44. Kumari B, Saini V, Kaur J, Kaur J. Rv2037c, a stress induced conserved hypothetical protein of Mycobacterium tuberculosis, is a phospholipase: role in cell wall modulation and intracellular survival. Int J Biol Macromol 2020; 153:817–835 [View Article] [PubMed]
    [Google Scholar]
  45. Cui Z, Dang G, Song N, Cui Y, Li Z et al. Rv3091, an extracellular patatin-like phospholipase in Mycobacterium tuberculosis, prolongs intracellular survival of recombinant Mycolicibacterium smegmatis by mediating phagosomal escape. Front Microbiol 2020; 11:2204 [View Article] [PubMed]
    [Google Scholar]
  46. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000; 302:205–217 [View Article] [PubMed]
    [Google Scholar]
  47. Kemena C, Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 2009; 25:2455–2465 [View Article] [PubMed]
    [Google Scholar]
  48. Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 2014; 42:W320–4 [View Article] [PubMed]
    [Google Scholar]
  49. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
    [Google Scholar]
  50. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307–1320 [View Article] [PubMed]
    [Google Scholar]
  51. Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA et al. Pfam: the protein families database in 2021. Nucleic Acids Res 2021; 49:D412–D419 [View Article] [PubMed]
    [Google Scholar]
  52. 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] [PubMed]
    [Google Scholar]
  53. Varadi M, Anyango S, Deshpande M, Nair S, Natassia C et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 2022; 50:D439–D444 [View Article] [PubMed]
    [Google Scholar]
  54. 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]
  55. Hagemans D, van Belzen IAEM, Morán Luengo T, Rüdiger SGD. A script to highlight hydrophobicity and charge on protein surfaces. Front Mol Biosci 2015; 2:56 [View Article] [PubMed]
    [Google Scholar]
  56. Holm L. Using Dali for protein structure cDali for Protein Structure Comparison. Methods Mol Biol 2020; 2112:29–42 [View Article]
    [Google Scholar]
  57. Pavelka A, Sebestova E, Kozlikova B, Brezovsky J, Sochor J et al. CAVER: algorithms for analyzing dynamics of tunnels in macromolecules. IEEE/ACM Trans Comput Biol Bioinform 2016; 13:505–517 [View Article] [PubMed]
    [Google Scholar]
  58. Sassetti CM, Boyd DH, Rubin EJ. Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci U S A 2001; 98:12712–12717 [View Article] [PubMed]
    [Google Scholar]
  59. Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M et al. Highly accurate protein structure prediction for the human proteome. Nature 2021; 596:590–596 [View Article] [PubMed]
    [Google Scholar]
  60. Wang H, Klein MG, Snell G, Lane W, Zou H et al. Structure of Human GIVD cytosolic phospholipase A2 reveals insights into substrate recognition. J Mol Biol 2016; 428:2769–2779 [View Article] [PubMed]
    [Google Scholar]
  61. Su Y, Dostmann WRG, Herberg FW, Durick K, Xuong N et al. Regulatory subunit of protein kinase a: structure of deletion mutant with cAMP binding domains. Science 1995; 269:807–813 [View Article] [PubMed]
    [Google Scholar]
  62. Nambi S, Badireddy S, Visweswariah SS, Anand GS. Cyclic AMP-induced conformational changes in mycobacterial protein acetyltransferases. J Biol Chem 2012; 287:18115–18129 [View Article]
    [Google Scholar]
  63. Rehmann H, Wittinghofer A, Bos JL. Capturing cyclic nucleotides in action: snapshots from crystallographic studies. Nat Rev Mol Cell Biol 2007; 8:63–73 [View Article]
    [Google Scholar]
  64. Krasteva PV, Bernal-Bayard J, Travier L, Martin FA, Kaminski P-A et al. Insights into the structure and assembly of a bacterial cellulose secretion system. Nat Commun 2017; 8:2065 [View Article]
    [Google Scholar]
  65. Shabb JB, Ng L, Corbin JD. One amino acid change produces a high affinity cGMP-binding site in cAMP-dependent protein kinase. J Biol Chem 1990; 265:16031–16034 [View Article]
    [Google Scholar]
  66. Reed RB, Sandberg M, Jahnsen T, Lohmann SM, Francis SH et al. Fast and slow cyclic nucleotide-dissociation sites in cAMP-dependent protein kinase are transposed in type Ibeta cGMP-dependent protein kinase. J Biol Chem 1996; 271:17570–17575 [View Article] [PubMed]
    [Google Scholar]
  67. Chang P, Sun T, Heier C, Gao H, Xu H et al. Interaction of the lysophospholipase PNPLA7 with lipid droplets through the catalytic region. Mol Cells 2020; 43:286–297 [View Article] [PubMed]
    [Google Scholar]
  68. Ku B, Lee K-H, Park WS, Yang C-S, Ge J et al. VipD of Legionella pneumophila targets activated Rab5 and Rab22 to interfere with endosomal trafficking in macrophages. PLoS Pathog 2012; 8:e1003082 [View Article] [PubMed]
    [Google Scholar]
  69. Heng J, Zhao Y, Liu M, Liu Y, Fan J et al. Substrate-bound structure of the E. coli multidrug resistance transporter MdfA. Cell Res 2015; 25:1060–1073 [View Article] [PubMed]
    [Google Scholar]
  70. Varela MF, Sansom CE, Griffith JK. Mutational analysis and molecular modelling of an amino acid sequence motif conserved in antiporters but not symporters in a transporter superfamily. Mol Membr Biol 1995; 12:313–319 [View Article] [PubMed]
    [Google Scholar]
  71. Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N et al. Outward open conformation of a major facilitator superfamily multidrug/H+ antiporter provides insights into switching mechanism. Nat Commun 2018; 9:4005 [View Article] [PubMed]
    [Google Scholar]
  72. Kumar S, Athreya A, Gulati A, Nair RM, Mahendran I et al. Structural basis of inhibition of a transporter from Staphylococcus aureus, NorC, through a single-domain camelid antibody. Commun Biol 2021; 4:836 [View Article] [PubMed]
    [Google Scholar]
  73. Lomovskaya O, Lewis K. Emr, an Escherichia coli locus for multidrug resistance. Proc Natl Acad Sci U S A 1992; 89:8938–8942 [View Article] [PubMed]
    [Google Scholar]
  74. Lee EH, Shafer WM. The farAB-encoded efflux pump mediates resistance of gonococci to long-chained antibacterial fatty acids. Mol Microbiol 1999; 33:839–845 [View Article] [PubMed]
    [Google Scholar]
  75. Paulsen PA, Custódio TF, Pedersen BP. Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily. Nat Commun 2019; 10:407 [View Article] [PubMed]
    [Google Scholar]
  76. Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 1986; 5:3021–3027 [View Article] [PubMed]
    [Google Scholar]
  77. Malley KR, Koroleva O, Miller I, Sanishvili R, Jenkins CM et al. The structure of iPLA2β reveals dimeric active sites and suggests mechanisms of regulation and localization. Nat Commun 2018; 9:765 [View Article] [PubMed]
    [Google Scholar]
  78. Målen H, Pathak S, Søfteland T, de Souza GA, Wiker HG. Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv. BMC Microbiol 2010; 10:132 [View Article] [PubMed]
    [Google Scholar]
  79. de Souza GA, Leversen NA, Målen H, Wiker HG. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway. J Proteomics 2011; 75:502–510 [View Article] [PubMed]
    [Google Scholar]
  80. Mawuenyega KG, Forst CV, Dobos KM, Belisle JT, Chen J et al. Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol Biol Cell 2005; 16:396–404 [View Article] [PubMed]
    [Google Scholar]
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