1887

Abstract

Biopolymers on the cell surface are very important for protecting microorganisms from environmental stresses, as well as storing nutrients and minerals. Synthesis of biopolymers is well studied, while studies on the modification and degradation processes of biopolymers are limited. One of these biopolymers, poly-γ-glutamic acid (γ-PGA), is produced by Bacillus species. Bacillus subtilis PgdS, possessing three NlpC/P60 domains, hydrolyses γ-PGA. Here, we have demonstrated that several dl-endopeptidases with an NlpC/P60 domain (LytE, LytF, CwlS, CwlO, and CwlT) in B. subtilis digest not only an amide bond of d-γ-glutamyl-diaminopimelic acid in peptidoglycans but also linkages of γ-PGA produced by B. subtilis. The hydrolase activity of dl-endopeptidases towards γ-PGA was inhibited by IseA, which also inhibits their hydrolase activity towards peptidoglycans, while the hydrolysis of PgdS towards γ-PGA was not inhibited. PgdS hydrolysed only the d-/l-Glu‒d-Glu linkages of d-Glu-rich γ-PGA (d-Glu:l-Glu=7 : 3) and l-Glu-rich γ-PGA (d-Glu:l-Glu=1 : 9), indicating that PgdS can hydrolyse only restricted substrates. On the other hand, the dl-endopeptidases in B. subtilis cleaved d-/l-Glu‒d-/l-Glu linkages of d-Glu-rich γ-PGA (d-Glu:l-Glu=7 : 3), indicating that these enzymes show different substrate specificities. Thus, the dl-endopeptidases digest γ-PGA more flexibly than PgdS, even though they are annotated as “dl-endopeptidase, digesting the d-γ-glutamyl-diaminopimelic acid linkage (dl amino acid bond)”.

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2018-01-30
2019-10-18
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References

  1. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36: 407– 477 [PubMed]
    [Google Scholar]
  2. Kimura K, Itoh Y. Characterization of poly-γ-glutamate hydrolase encoded by a bacteriophage genome: possible role in phage infection of Bacillus subtilis encapsulated with poly-γ-glutamate. Appl Environ Microbiol 2003; 69: 2491– 2497 [CrossRef] [PubMed]
    [Google Scholar]
  3. Luo Z, Guo Y, Liu J, Qiu H, Zhao M et al. Microbial synthesis of poly-γ-glutamic acid: current progress, challenges, and future perspectives. Biotechnol Biofuels 2016; 9: 134 [CrossRef] [PubMed]
    [Google Scholar]
  4. Kawai Y, Marles-Wright J, Cleverley RM, Emmins R, Ishikawa S et al. A widespread family of bacterial cell wall assembly proteins. Embo J 2011; 30: 4931– 4941 [CrossRef] [PubMed]
    [Google Scholar]
  5. Myers CL, Li FK, Koo BM, El-Halfawy OM, French S et al. Identification of two phosphate starvation-induced wall teichoic acid hydrolases provides first insights into the degradative pathway of a key bacterial cell wall component. J Biol Chem 2016; 291: 26066– 26082 [CrossRef] [PubMed]
    [Google Scholar]
  6. Kimura K, Fujimoto Z. Enzymatic degradation of poly-gamma-glutamic acid. In Hamano Y. (editor) Amino-Acid Homopolymers Occurring in Nature Berlin Heidelberg: Springer-Verlag; 2010; pp. 95– 116 [Crossref]
    [Google Scholar]
  7. Dubrac S, Bisicchia P, Devine KM, Msadek T. A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway. Mol Microbiol 2008; 70: 1307– 1322 [CrossRef] [PubMed]
    [Google Scholar]
  8. Fukushima T, Szurmant H, Kim EJ, Perego M, Hoch JA. A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis. Mol Microbiol 2008; 69: 621– 632 [CrossRef] [PubMed]
    [Google Scholar]
  9. Fukushima T, Furihata I, Emmins R, Daniel RA, Hoch JA et al. A role for the essential YycG sensor histidine kinase in sensing cell division. Mol Microbiol 2011; 79: 503– 522 [CrossRef] [PubMed]
    [Google Scholar]
  10. Bisicchia P, Noone D, Lioliou E, Howell A, Quigley S et al. The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis. Mol Microbiol 2007; 65: 180– 200 [CrossRef] [PubMed]
    [Google Scholar]
  11. Ashiuchi M, Shimanouchi K, Nakamura H, Kamei T, Soda K et al. Enzymatic synthesis of high-molecular-mass poly-gamma-glutamate and regulation of its stereochemistry. Appl Environ Microbiol 2004; 70: 4249– 4255 [CrossRef] [PubMed]
    [Google Scholar]
  12. Hanby WE, Rydon HN. The capsular substance of Bacillus anthracis. Biochem J 1946; 40: 297– 309 [CrossRef] [PubMed]
    [Google Scholar]
  13. Hezayen FF, Rehm BH, Tindall BJ, Steinbüchel A. Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly(glutamic acid). Int J Syst Evol Microbiol 2001; 51: 1133– 1142 [CrossRef] [PubMed]
    [Google Scholar]
  14. Thorne CB, Leonard CG. Isolation of d- and l-glutamyl polypeptides from culture filtrates of Bacillus subtilis. J Biol Chem 1958; 233: 1109– 1112 [PubMed]
    [Google Scholar]
  15. Nagai T, Koguchi K, Itoh Y. Chemical analysis of poly-gamma-glutamic acid produced by plasmid-free Bacillus subtilis (natto): evidence that plasmids are not involved in poly-gamma-glutamic acid production. J Gen Appl Microbiol 1997; 43: 139– 143 [CrossRef] [PubMed]
    [Google Scholar]
  16. Kocianova S, Vuong C, Yao Y, Voyich JM, Fischer ER et al. Key role of poly-γ-dl-glutamic acid in immune evasion and virulence of Staphylococcus epidermidis. J Clin Invest 2005; 115: 688– 694 [CrossRef] [PubMed]
    [Google Scholar]
  17. Cromwick AM, Gross RA. Effects of manganese (II) on Bacillus licheniformis ATCC 9945A physiology and γ-poly(glutamic acid) formation. Int J Biol Macromol 1995; 17: 259– 267 [CrossRef] [PubMed]
    [Google Scholar]
  18. Candela T, Fouet A. Bacillus anthracis CapD, belonging to the γ-glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan. Mol Microbiol 2005; 57: 717– 726 [CrossRef] [PubMed]
    [Google Scholar]
  19. Wu SJ, Eiben CB, Carra JH, Huang I, Zong D et al. Improvement of a potential anthrax therapeutic by computational protein design. J Biol Chem 2011; 286: 32586– 32592 [CrossRef] [PubMed]
    [Google Scholar]
  20. Ashiuchi M, Nakamura H, Yamamoto M, Misono H. Novel poly-γ-glutamate-processing enzyme catalyzing gamma-glutamyl DD-amidohydrolysis. J Biosci Bioeng 2006; 102: 60– 65 [CrossRef] [PubMed]
    [Google Scholar]
  21. Yamaguchi H, Furuhata K, Fukushima T, Yamamoto H, Sekiguchi J. Characterization of a new Bacillus subtilis peptidoglycan hydrolase gene, yvcE (named cwlO), and the enzymatic properties of its encoded protein. J Biosci Bioeng 2004; 98: 174– 181 [CrossRef] [PubMed]
    [Google Scholar]
  22. Mitsui N, Murasawa H, Sekiguchi J. Disruption of the cell wall lytic enzyme CwlO affects the amount and molecular size of poly-γ-glutamic acid produced by Bacillus subtilis (natto). J Gen Appl Microbiol 2011; 57: 35– 43 [CrossRef] [PubMed]
    [Google Scholar]
  23. Feng J, Gao W, Gu Y, Zhang W, Cao M et al. Functions of poly-gamma-glutamic acid (γ-PGA) degradation genes in γ-PGA synthesis and cell morphology maintenance. Appl Microbiol Biotechnol 2014; 98: 6397– 6407 [CrossRef] [PubMed]
    [Google Scholar]
  24. Ishikawa S, Hara Y, Ohnishi R, Sekiguchi J. Regulation of a new cell wall hydrolase gene, cwlF, which affects cell separation in Bacillus subtilis. J Bacteriol 1998; 180: 2549– 2555 [PubMed]
    [Google Scholar]
  25. Ohnishi R, Ishikawa S, Sekiguchi J. Peptidoglycan hydrolase LytF plays a role in cell separation with CwlF during vegetative growth of Bacillus subtilis. J Bacteriol 1999; 181: 3178– 3184 [PubMed]
    [Google Scholar]
  26. Fukushima T, Afkham A, Kurosawa S, Tanabe T, Yamamoto H et al. A new d,l-endopeptidase gene product, YojL (renamed CwlS), plays a role in cell separation with LytE and LytF in Bacillus subtilis. J Bacteriol 2006; 188: 5541– 5550 [CrossRef] [PubMed]
    [Google Scholar]
  27. Hashimoto M, Ooiwa S, Sekiguchi J. Synthetic lethality of the lytE cwlO genotype in Bacillus subtilis is caused by lack of d,l-endopeptidase activity at the lateral cell wall. J Bacteriol 2012; 194: 796– 803 [CrossRef] [PubMed]
    [Google Scholar]
  28. Fukushima T, Kitajima T, Yamaguchi H, Ouyang Q, Furuhata K et al. Identification and characterization of novel cell wall hydrolase CwlT: a two-domain autolysin exhibiting n-acetylmuramidase and dl-endopeptidase activities. J Biol Chem 2008; 283: 11117– 11125 [CrossRef] [PubMed]
    [Google Scholar]
  29. DeWitt T, Grossman AD. The bifunctional cell wall hydrolase CwlT is needed for conjugation of the integrative and conjugative element ICEBs1 in Bacillus subtilis and B. anthracis. J Bacteriol 2014; 196: 1588– 1596 [CrossRef] [PubMed]
    [Google Scholar]
  30. Arai R, Fukui S, Kobayashi N, Sekiguchi J. Solution structure of IseA, an inhibitor protein of dl-endopeptidases from Bacillus subtilis, reveals a novel fold with a characteristic inhibitory loop. J Biol Chem 2012; 287: 44736– 44748 [CrossRef] [PubMed]
    [Google Scholar]
  31. Fukushima T, Sekiguchi J. Zymographic Techniques for the analysis of bacterial cell wall in Bacillus. Methods Mol Biol 2016; 1440: 87– 98 [CrossRef] [PubMed]
    [Google Scholar]
  32. Fukushima T, Yao Y, Kitajima T, Yamamoto H, Sekiguchi J. Characterization of new l,d-endopeptidase gene product CwlK (previous YcdD) that hydrolyzes peptidoglycan in Bacillus subtilis. Mol Genet Genomics 2007; 278: 371– 383 [CrossRef] [PubMed]
    [Google Scholar]
  33. Sudiarta IP, Fukushima T, Sekiguchi J. Bacillus subtilis CwlP of the SP-β prophage has two novel peptidoglycan hydrolase domains, muramidase and cross-linkage digesting dd-endopeptidase. J Biol Chem 2010; 285: 41232– 41243 [CrossRef] [PubMed]
    [Google Scholar]
  34. Stanley NR, Lazazzera BA. Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-γ-dl-glutamic acid production and biofilm formation. Mol Microbiol 2005; 57: 1143– 1158 [CrossRef] [PubMed]
    [Google Scholar]
  35. Ohsawa T, Tsukahara K, Ogura M. Bacillus subtilis response regulator DegU is a direct activator of pgsB transcription involved in gamma-poly-glutamic acid synthesis. Biosci Biotechnol Biochem 2009; 73: 2096– 2102 [CrossRef] [PubMed]
    [Google Scholar]
  36. Shida T, Mukaijo K, Ishikawa S, Yamamoto H, Sekiguchi J. Production of long-chain levan by a sacC insertional mutant from Bacillus subtilis 327UH. Biosci Biotechnol Biochem 2002; 66: 1555– 1558 [CrossRef] [PubMed]
    [Google Scholar]
  37. Xu Q, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW et al. Structures of a bifunctional cell wall hydrolase CwlT containing a novel bacterial lysozyme and an NlpC/P60 dl-endopeptidase. J Mol Biol 2014; 426: 169– 184 [CrossRef] [PubMed]
    [Google Scholar]
  38. Yamamoto H, Hashimoto M, Higashitsuji Y, Harada H, Hariyama N et al. Post-translational control of vegetative cell separation enzymes through a direct interaction with specific inhibitor IseA in Bacillus subtilis. Mol Microbiol 2008; 70: 168– 182 [CrossRef] [PubMed]
    [Google Scholar]
  39. Xu Q, Sudek S, McMullan D, Miller MD, Geierstanger B et al. Structural basis of murein peptide specificity of a γ-d-glutamyl-l-diamino acid endopeptidase. Structure 2009; 17: 303– 313 [CrossRef] [PubMed]
    [Google Scholar]
  40. Tjalsma H, Antelmann H, Jongbloed JD, Braun PG, Darmon E et al. Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome. Microbiol Mol Biol Rev 2004; 68: 207– 233 [CrossRef] [PubMed]
    [Google Scholar]
  41. Yamamoto H, Miyake Y, Hisaoka M, Kurosawa S, Sekiguchi J. The major and minor wall teichoic acids prevent the sidewall localization of vegetative dl-endopeptidase LytF in Bacillus subtilis. Mol Microbiol 2008; 70: 297– 310 [CrossRef] [PubMed]
    [Google Scholar]
  42. Osera C, Amati G, Calvio C, Galizzi A. SwrAA activates poly-γ-glutamate synthesis in addition to swarming in Bacillus subtilis. Microbiology 2009; 155: 2282– 2287 [CrossRef] [PubMed]
    [Google Scholar]
  43. Kearns DB, Chu F, Rudner R, Losick R. Genes governing swarming in Bacillus subtilis and evidence for a phase variation mechanism controlling surface motility. Mol Microbiol 2004; 52: 357– 369 [CrossRef] [PubMed]
    [Google Scholar]
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