Protein & Cell

, Volume 3, Issue 3, pp 163–170 | Cite as

A phylum level analysis reveals lipoprotein biosynthesis to be a fundamental property of bacteria

  • Iain C. Sutcliffe
  • Dean J. Harrington
  • Matthew I. Hutchings
Perspective

Abstract

Bacterial lipoproteins are proteins that are post-translationally modified with a diacylglyceride at an N-terminal cysteine, which serves to tether these proteins to the outer face of the plasma membrane or to the outer membrane. This paper reviews recent insights into the enzymology of bacterial lipoprotein biosynthesis and localization. Moreover, we use bioinformatic analyses of bacterial lipoprotein signal peptide features and of the key biosynthetic enzymes to consider the distribution of lipoprotein biosynthesis at the phylum level. These analyses support the important conclusion that lipoprotein biosynthesis is a fundamental pathway utilized across the domain bacteria. Moreover, with the exception of a small number of sequences likely to derive from endosymbiont genomes, the enzymes of bacterial lipoprotein biosynthesis appear unique to bacteria, making this pathway an attractive target for the development of novel antimicrobials. Whilst lipoproteins with comparable signal peptide features are encoded in the genomes of Archaea, it is clear that these lipoproteins have a distinctive biosynthetic pathway that has yet to be characterized.

References

  1. Asanuma, M., Kurokawa, K., Ichikawa, R., Ryu, K.-H., Chae, J.-H., Dohmae, N., Lee, B.L., and Nakayama, H. (2011). Structural evidence of α-aminoacylated lipoproteins of Staphylococcus aureus. FEBS J 278, 716–728.CrossRefGoogle Scholar
  2. Babu, M.M., Priya, M.L., Selvan, A.T., Madera, M., Gough, J., Aravind, L., and Sankaran, K. (2006). A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol 188, 2761–2773.CrossRefGoogle Scholar
  3. Bagos, P.G., Tsirigos, K.D., Liakopoulos, T.D., and Hamodrakas, S.J. (2008). Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res 7, 5082–5093.CrossRefGoogle Scholar
  4. Bardy, S.L., Eichler, J., and Jarrell, K.F. (2003). Archaeal signal peptides—a comparative survey at the genome level. Protein Sci 12, 1833–1843.CrossRefGoogle Scholar
  5. Bendtsen, J.D., Binnewies, T.T., Hallin, P.F., Sicheritz-Pontén, T., and Ussery, D.W. (2005). Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology 151, 1725–1727.CrossRefGoogle Scholar
  6. Braun, V., and Wu, H.C. (1994). Lipoproteins: structure function, biosynthesis and model for protein export. New Comp. Biochem. 27, 319–341.CrossRefGoogle Scholar
  7. Bubeck Wardenburg, J., Williams, W.A., and Missiakas, D. (2006). Host defenses against Staphylococcus aureus infection require recognition of bacterial lipoproteins. Proc Natl Acad Sci U S A 103, 13831–13836.CrossRefGoogle Scholar
  8. Buddelmeijer, N., and Young, R. (2010). The essential Escherichia coli apolipoprotein N-acyltransferase (Lnt) exists as an extracytoplasmic thioester acyl-enzyme intermediate. Biochemistry 49, 341–346.CrossRefGoogle Scholar
  9. Celebi, N., Dalbey, R.E., and Yuan, J. (2008). Mechanism and hydrophobic forces driving membrane protein insertion of subunit II of cytochrome bo3 oxidase. J Mol Biol 375, 1282–1292.CrossRefGoogle Scholar
  10. Chandler, J.R., and Dunny, G.M. (2004). Enterococcal peptide sex pheromones: synthesis and control of biological activity. Peptides 25, 1377–1388.CrossRefGoogle Scholar
  11. Daley, D.O., Rapp, M., Granseth, E., Melén, K., Drew, D., and von Heijne, G. (2005). Global topology analysis of the Escherichia coli inner membrane proteome. Science 308, 1321–1323.CrossRefGoogle Scholar
  12. Denham, E.L., Ward, P.N., and Leigh, J.A. (2008). Lipoprotein signal peptides are processed by Lsp and Eep of Streptococcus uberis. J Bacteriol 190, 4641–4647.CrossRefGoogle Scholar
  13. Fernández Robledo, J.A., Caler, E., Matsuzaki, M., Keeling, P.J., Shanmugam, D., Roos, D.S., and Vasta, G.R. (2011). The search for the missing link: a relic plastid in Perkinsus? Int J Parasitol 41, 1217–1229.CrossRefGoogle Scholar
  14. Fukuda, A., Matsuyama, S., Hara, T., Nakayama, J., Nagasawa, H., and Tokuda, H. (2002). Aminoacylation of the N-terminal cysteine is essential for Lol-dependent release of lipoproteins from membranes but does not depend on lipoprotein sorting signals. J Biol Chem 277, 43512–43518.CrossRefGoogle Scholar
  15. Giménez, M.I., Dilks, K., and Pohlschröder, M. (2007). Haloferax volcanii twin-arginine translocation substates include secreted soluble, C-terminally anchored and lipoproteins. Mol Microbiol 66, 1597–1606.CrossRefGoogle Scholar
  16. Gupta, S.D., and Wu, H.C. (1991). Identification and subcellular localization of apolipoprotein N-acyltransferase in Escherichia coli. FEMS Microbiol Lett 62, 37–41.CrossRefGoogle Scholar
  17. Henneke, P., Dramsi, S., Mancuso, G., Chraibi, K., Pellegrini, E., Theilacker, C., Hübner, J., Santos-Sierra, S., Teti, G., Golenbock, D.T., et al. (2008). Lipoproteins are critical TLR2 activating toxins in group B streptococcal sepsis. J Immunol 180, 6149–6158.CrossRefGoogle Scholar
  18. Hillmann, F., Argentini, M., and Buddelmeijer, N. (2011). Kinetics and phospholipid specificity of apolipoprotein N-acyltransferase. J Biol Chem 286, 27936–27946.CrossRefGoogle Scholar
  19. Hutchings, M.I., Hong, H.-J., Leibovitz, E., Sutcliffe, I.C., and Buttner, M.J. (2006). The CseBC-σE cell envelope stress signal transduction system of Streptomyces coelicolor is modulated by a novel lipoprotein. CseA. J. Bacteriol. 188, 7222–7229.CrossRefGoogle Scholar
  20. Hutchings, M.I., Palmer, T., Harrington, D.J., and Sutcliffe, I.C. (2009). Lipoprotein biogenesis in Gram-positive bacteria: knowing when to hold’ em, knowing when to fold’ em. Trends Microbiol 17, 13–21.CrossRefGoogle Scholar
  21. Ito, H., Ura, A., Oyamada, Y., Yoshida, H., Yamagishi, J., Narita, S., Matsuyama, S., and Tokuda, H. (2007). A new screening method to identify inhibitors of the Lol (localization of lipoproteins) system, a novel antibacterial target. Microbiol Immunol 51, 263–270.CrossRefGoogle Scholar
  22. Johnston, K.L., Wu, B., Guimarães, A., Ford, L., Slatko, B.E., and Taylor, M.J. (2010). Lipoprotein biosynthesis as a target for anti-Wolbachia treatment of filarial nematodes. Parasit Vectors 3, 99.CrossRefGoogle Scholar
  23. Joseph, S.J., Fernández-Robledo, J.A., Gardner, M.J., El-Sayed, N.M., Kuo, C.-H., Schott, E.J., Wang, H., Kissinger, J.C., and Vasta, G.R. (2010). The Alveolate Perkinsus marinus: biological insights from EST gene discovery. BMC Genomics 11, 228.CrossRefGoogle Scholar
  24. Juncker, A.S., Willenbrock, H., Von Heijne, G., Brunak, S., Nielsen, H., and Krogh, A. (2003). Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12, 1652–1662.CrossRefGoogle Scholar
  25. Kiho, T., Nakayama, M., Yasuda, K., Miyakoshi, S., Inukai, M., and Kogen, H. (2004). Structure-activity relationships of globomycin analogues as antibiotics. Bioorg Med Chem 12, 337–361.CrossRefGoogle Scholar
  26. Kumru, O.S., Schulze, R.J., Rodnin, M.V., Ladokhin, A.S., and Zückert, W.R. (2011). Surface localization determinants of Borrelia OspC/Vsp family lipoproteins. J Bacteriol 193, 2814–2825.CrossRefGoogle Scholar
  27. Le Hénaff, M., Crémet, J.Y., and Fontenelle, C. (2002). Purification and characterization of the major lipoprotein (P28) of Spiroplasma apis. Protein Expr Purif 24, 489–496.CrossRefGoogle Scholar
  28. Lewenza, S., Mhlanga, M.M., and Pugsley, A.P. (2008). Novel inner membrane retention signals in Pseudomonas aeruginosa lipoproteins. J Bacteriol 190, 6119–6125.CrossRefGoogle Scholar
  29. Lewenza, S., Vidal-Ingigliardi, D., and Pugsley, A.P. (2006). Direct visualization of red fluorescent lipoproteins indicates conservation of the membrane sorting rules in the family Enterobacteriaceae. J Bacteriol 188, 3516–3524.CrossRefGoogle Scholar
  30. Mattar, S., Scharf, B., Kent, S.B.H., Rodewald, K., Oesterhelt, D., and Engelhard, M. (1994). The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation. J Biol Chem 269, 14939–14945.Google Scholar
  31. Narita, S.-I. (2011). ABC transporters involved in the biogenesis of the outer membrane in gram-negative bacteria. Biosci Biotechnol Biochem 75, 1044–1054.CrossRefGoogle Scholar
  32. Narita, S.-I., and Tokuda, H. (2006). An ABC transporter mediating the membrane detachment of bacterial lipoproteins depending on their sorting signals. FEBS Lett 580, 1164–1170.CrossRefGoogle Scholar
  33. Narita, S.-I., and Tokuda, H. (2007). Amino acids at positions 3 and 4 determine the membrane specificity of Pseudomonas aeruginosa lipoproteins. J Biol Chem 282, 13372–13378.CrossRefGoogle Scholar
  34. Narita, S.-I., and Tokuda, H. (2011). Overexpression of LolCDE allows deletion of the Escherichia coli gene encoding apolipoprotein N-acyltransferase. J Bacteriol 193, 4832–4840.CrossRefGoogle Scholar
  35. Nowack, E.C.M., Melkonian, M., and Glöckner, G. (2008). Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr Biol 18, 410–418.CrossRefGoogle Scholar
  36. Okuda, S., and Tokuda, H. (2009). Model of mouth-to-mouth transfer of bacterial lipoproteins through inner membrane LolC, periplasmic LolA, and outer membrane LolB. Proc Natl Acad Sci U S A 106, 5877–5882.CrossRefGoogle Scholar
  37. Pailler, J., Aucher, W., Pires, M., and Buddelmeijer, N. (2012). Phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) of E. coli has seven transmembrane segments and its essential residues are embedded in the membrane. J Bacteriol. doi:10.1128/JB.06641-11.Google Scholar
  38. Pathania, R., Zlitni, S., Barker, C., Das, R., Gerritsma, D.A., Lebert, J., Awuah, E., Melacini, G., Capretta, F.A., and Brown, E.D. (2009). Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. Nat Chem Biol 5, 849–856.CrossRefGoogle Scholar
  39. Qi, H.-Y., Sankaran, K., Gan, K., and Wu, H.C. (1995). Structure-function relationship of bacterial prolipoprotein diacylglyceryl transferase: functionally significant conserved regions. J Bacteriol 177, 6820–6824.Google Scholar
  40. Rahman, O., Cummings, S.P., Harrington, D.J., and Sutcliffe, I.C. (2008). Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria. World J Microbiol Biotechnol 24, 2377–2382.CrossRefGoogle Scholar
  41. Reffuveille, F., Leneveu, C., Chevalier, S., Auffray, Y., and Rincé, A. (2011). Lipoproteins of Enterococcus faecalis: bioinformatic identification, expression analysis and relation to virulence. Microbiology 157, 3001–3013.CrossRefGoogle Scholar
  42. Réglier-Poupet, H., Frehel, C., Dubail, I., Beretti, J.-L., Berche, P., Charbit, A., and Raynaud, C. (2003). Maturation of lipoproteins by type II signal peptidase is required for phagosomal escape of Listeria monocytogenes. J Biol Chem 278, 49469–49477.CrossRefGoogle Scholar
  43. Remans, K., Vercammen, K., Bodilis, J., and Cornelis, P. (2010). Genome-wide analysis and literature-based survey of lipoproteins in Pseudomonas aeruginosa. Microbiology 156, 2597–2607.CrossRefGoogle Scholar
  44. Rhodes, R.G., Samarasam, M.N., Van Groll, E.J., and McBride, M.J. (2011). Mutations in Flavobacterium johnsoniae sprE result in defects in gliding motility and protein secretion. J Bacteriol 193, 5322–5327.CrossRefGoogle Scholar
  45. Robichon, C., Vidal-Ingigliardi, D., and Pugsley, A.P. (2005). Depletion of apolipoprotein N-acyltransferase causes mislocalization of outer membrane lipoproteins in Escherichia coli. J Biol Chem 280, 974–983.CrossRefGoogle Scholar
  46. Saleh, M., Song, C., Nasserulla, S., and Leduc, L.G. (2010). Indicators from archaeal secretomes. Microbiol Res 165, 1–10.CrossRefGoogle Scholar
  47. Sankaran, K., Gan, K., Rash, B., Qi, H.-Y., Wu, H.C., and Rick, P.D. (1997). Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli. J Bacteriol 179, 2944–2948.Google Scholar
  48. Sankaran, K., Gupta, S.D., and Wu, H.C. (1995). Modification of bacterial lipoproteins. Methods Enzymol 250, 683–697.CrossRefGoogle Scholar
  49. Sankaran, K., and Wu, H.C. (1995). Bacterial prolipoprotein signal peptidase. Methods Enzymol 248, 169–180.CrossRefGoogle Scholar
  50. Schenk, M., Belisle, J.T., and Modlin, R.L. (2009). TLR2 looks at lipoproteins. Immunity 31, 847–849.CrossRefGoogle Scholar
  51. Schulze, R.J., Chen, S.Y., Kumru, O.S., and Zückert, W.R. (2010). Translocation of Borrelia burgdorferi surface lipoprotein OspA through the outer membrane requires an unfolded conformation and can initiate at the C-terminus. Mol Microbiol 76, 1266–1278.CrossRefGoogle Scholar
  52. Schulze, R.J., and Zückert, W.R. (2006). Borrelia burgdorferi lipoproteins are secreted to the outer surface by default. Mol Microbiol 59, 1473–1484.CrossRefGoogle Scholar
  53. Selvan, A.T., and Sankaran, K. (2008). Localization and characterization of prolipoprotein diacylglyceryl transferase (Lgt) critical in bacterial lipoprotein biosynthesis. Biochimie 90, 1647–1655.CrossRefGoogle Scholar
  54. Serebryakova, M.V., Demina, I.A., Galyamina, M.A., Kondratov, I.G., Ladygina, V.G., and Govorun, V.M. (2011). The acylation state of surface lipoproteins of mollicute Acholeplasma laidlawii. J Biol Chem 286, 22769–22776.CrossRefGoogle Scholar
  55. Setubal, J.C., Reis, M., Matsunaga, J., and Haake, D.A. (2006). Lipoprotein computational prediction in spirochaetal genomes. Microbiology 152, 113–121.CrossRefGoogle Scholar
  56. Shruthi, H., Babu, M.M., and Sankaran, K. (2010). TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. J Mol Evol 70, 359–370.CrossRefGoogle Scholar
  57. Storf, S., Pfeiffer, F., Dilks, K., Chen, Z.Q., Imam, S., and Pohlschröder, M. (2010). Mutational and bioinformatic analysis of haloarchaeal lipobox-containing proteins. Archaea 2010, 410975.CrossRefGoogle Scholar
  58. Sutcliffe, I.C. (2010). A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18, 464–470.CrossRefGoogle Scholar
  59. Sutcliffe, I.C., and Harrington, D.J. (2002). Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes. Microbiology 148, 2065–2077.CrossRefGoogle Scholar
  60. Suzuki, T., Itoh, A., Ichihara, S., and Mizushima, S. (1987). Characterization of the sppA gene coding for protease IV, a signal peptide peptidase of Escherichia coli. J Bacteriol 169, 2523–2528.Google Scholar
  61. Thompson, B.J., Widdick, D.A., Hicks, M.G., Chandra, G., Sutcliffe, I.C., Palmer, T., and Hutchings, M.I. (2010). Investigating lipoprotein biogenesis and function in the model Gram-positive bacterium Streptomyces coelicolor. Mol Microbiol 77, 943–957.CrossRefGoogle Scholar
  62. Tjalsma, H., Zanen, G., Venema, G., Bron, S., and van Dijl, J.M. (1999). The potential active site of the lipoprotein-specific (type II) signal peptidase of Bacillus subtilis. J Biol Chem 274, 28191–28197.CrossRefGoogle Scholar
  63. Tokuda, H. (2009). Biogenesis of outer membranes in Gram-negative bacteria. Biosci Biotechnol Biochem 73, 465–473.CrossRefGoogle Scholar
  64. Tschumi, A., Nai, C., Auchli, Y., Hunziker, P., Gehrig, P., Keller, P., Grau, T., and Sander, P. (2009). Identification of apolipoprotein N-acyltransferase (Lnt) in mycobacteria. J Biol Chem 284, 27146–27156.CrossRefGoogle Scholar
  65. Tsukahara, J., Mukaiyama, K., Okuda, S., Narita, S.-I., and Tokuda, H. (2009). Dissection of LolB function—lipoprotein binding, membrane targeting and incorporation of lipoproteins into lipid bilayers. FEBS J 276, 4496–4504.CrossRefGoogle Scholar
  66. van Bloois, E., Haan, G.-J., de Gier, J.-W., Oudega, B., and Luirink, J. (2006). Distinct requirements for translocation of the N-tail and C-tail of the Escherichia coli inner membrane protein CyoA. J Biol Chem 281, 10002–10009.CrossRefGoogle Scholar
  67. Vidal-Ingigliardi, D., Lewenza, S., and Buddelmeijer, N. (2007). Identification of essential residues in apolipoprotein N-acyl transferase, a member of the CN hydrolase family. J Bacteriol 189, 4456–4464.CrossRefGoogle Scholar
  68. Widdick, D.A., Hicks, M.G., Thompson, B.J., Tschumi, A., Chandra, G., Sutcliffe, I.C., Brülle, J.K., Sander, P., Palmer, T., and Hutchings, M.I. (2011). Dissecting the complete lipoprotein biogenesis pathway in Streptomyces scabies. Mol Microbiol 80, 1395–1412.CrossRefGoogle Scholar
  69. Yu, Z., Lavèn, M., Klepsch, M., de Gier, J.-W., Bitter, W., van Ulsen, P., and Luirink, J. (2011). Role for Escherichia coli YidD in membrane protein insertion. J Bacteriol 193, 5242–5251.CrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Iain C. Sutcliffe
    • 1
  • Dean J. Harrington
    • 2
  • Matthew I. Hutchings
    • 3
  1. 1.School of Life SciencesUniversity of Northumbria at NewcastleNewcastle upon TyneUK
  2. 2.Division of Biomedical Science, School of Life SciencesUniversity of BradfordWest YorkshireUK
  3. 3.School of Biological SciencesUniversity of East AngliaNorwichUK

Personalised recommendations