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Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical d-amino acid

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Abstract

Bacteria produce various d-amino acids, including non-canonical d-amino acids, to adapt to environmental changes and overcome a variety of threats. These d-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical d-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized d-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing d-Asn, d-His, or d-Trp. These d-amino acids slowed the growth of dacA- or dacB-deficient E. coli (∆dacA or ∆dacB) relative to the wild-type strain. Additionally, these d-amino acids affected biofilm formation by the ∆dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical d-amino acids, and these properties affect growth and biofilm formation.

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Abbreviations

PBPs:

Penicillin-binding proteins

GlcNAc:

N-Acetylglucosamine

MurNAc:

N-Acetylmuramic acid

Dpm:

Diaminopimelate

PLP:

Pyridoxal 5′-phosphate

HMM:

High molecular mass

LMM:

Low molecular mass

OPA:

o-Phthalaldehyde

Ac:

Acetyl

Ac2 :

Diacetyl

pNA:

p-Nitroaniline

Boc-l-Cys:

N-tert-Butoxycarbonyl-l-cysteine

WT:

Wild type

References

  • Aliashkevich A, Alvarez L, Cava F (2018) New insights into the mechanisms and biological roles of d-amino acids in complex eco-systems. Front Microbiol 9:683

    PubMed  PubMed Central  Google Scholar 

  • Arias CA, Weisner J, Blackburn JM, Reynolds PE (2000) Serine and alanine racemase activities of VanT: a protein necessary for vancomycin resistance in Enterococcus gallinarum BM4174. Microbiology 146:1727–1734

    CAS  PubMed  Google Scholar 

  • Bellais S, Arthur M, Dubost L, Hugonnet JE, Gutmann L, van Heijenoort J, Legrand R, Brouard JP, Rice L, Mainardi JL (2006) Aslfm, the d-aspartate ligase responsible for the addition of d-aspartic acid onto the peptidoglycan precursor of Enterococcus faecium. J Biol Chem 281:11586–11594

    CAS  PubMed  Google Scholar 

  • Boniface A, Parquet C, Arthur M, Mengin-Lecreulx D, Blanot D (2009) The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link. J Biol Chem 284:21856–21862

    CAS  PubMed  PubMed Central  Google Scholar 

  • Caparrós M, Pisabarro AG, de Pedro MA (1992) Effect of d-amino acids on structure and synthesis of peptidoglycan in Escherichia coli. J Bacteriol 174:5549–5559

    PubMed  PubMed Central  Google Scholar 

  • Cava F, de Pedro MA, Lam H, Davis BM, Waldor MK (2011a) Distinct pathways for modification of the bacterial cell wall by non-canonical d-amino acids. EMBO J 30:3442–3453

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cava F, Lam H, de Pedro MA, Waldor MK (2011b) Emerging knowledge of regulatory roles of d-amino acids in bacteria. Cell Mol Life Sci 68:817–831

    CAS  PubMed  Google Scholar 

  • Clarke TB, Kawai F, Park SY, Tame JR, Dowson CG, Roper DI (2009) Mutational analysis of the substrate specificity of Escherichia coli penicillin binding protein 4. Biochemistry 48:2675–2683

    CAS  PubMed  Google Scholar 

  • de Pedro MA, Quintela JC, Höltje JV, Schwarz H (1997) Murein segregation in Escherichia coli. J Bacteriol 179:2823–2834

    PubMed  PubMed Central  Google Scholar 

  • Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F (2014) Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Crystallogr D Biol Crystallogr 70:79–90

    CAS  PubMed  Google Scholar 

  • González-Leiza SM, de Pedro MA, Ayala JA (2011) AmpH, a bifunctional dd-endopeptidase and dd-carboxypeptidase of Escherichia coli. J Bacteriol 193:6887–6894

    PubMed  PubMed Central  Google Scholar 

  • Grohs P, Gutmann L, Legrand R, Schoot B, Mainardi JL (2000) Vancomycin resistance is associated with serine-containing peptidoglycan in Enterococcus gallinarum. J Bacteriol 182:6228–6232

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hernández SB, Cava F (2016) Environmental roles of microbial amino acid racemases. Environ Microbiol 18:1673–1685

    PubMed  Google Scholar 

  • Hochbaum AI, Kolodkin-Gal I, Foulston L, Kolter R, Aizenberg J, Losick R (2011) Inhibitory effects of d-amino acids on Staphylococcus aureus biofilm development. J Bacteriol 193:5616–5622

    CAS  PubMed  PubMed Central  Google Scholar 

  • Höltje JV (1998) Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol Mol Biol Rev 62:181–203

    PubMed  PubMed Central  Google Scholar 

  • Jia R, Li Y, Al-Mahamedh HH, Gu T (2017a) Enhanced biocide treatments with d-amino acid mixtures against a biofilm consortium from a water cooling tower. Front Microbiol 8:1538

    PubMed  PubMed Central  Google Scholar 

  • Jia R, Yang D, Xu D, Gu T (2017b) Mitigation of a nitrate reducing Pseudomonas aeruginosa biofilm and anaerobic biocorrosion using ciprofloxacin enhanced by d-tyrosine. Sci Rep 7:6946

    PubMed  PubMed Central  Google Scholar 

  • Kato S, Oikawa T (2018) A novel bifunctional amino acid racemase with multiple substrate specificity, MalY from Lactobacillus sakei LT-13: genome-based identification and enzymological characterization. Front Microbiol 9:403

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kawarai T, Furukawa S, Narisawa N, Hagiwara C, Ogihara H, Yamasaki M (2009) Biofilm formation by Escherichia coli in hypertonic sucrose media. J Biosci Bioeng 107:630–635

    CAS  PubMed  Google Scholar 

  • Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R (2010) d-Amino acids trigger biofilm disassembly. Science 328:627–629

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lam H, Oh DC, Cava F, Takacs CN, Clardy J, de Pedro MA, Waldor MK (2009) d-Amino acids govern stationary phase cell wall remodeling in bacteria. Science 325:1552–1555

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leiman SA, May JM, Lebar MD, Kahne D, Kolter R, Losick R (2013) d-Amino acids indirectly inhibit biofilm formation in Bacillus subtilis by interfering with protein synthesis. J Bacteriol 195:5391–5395

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li E, Wang P, Zhang D (2016) D-Phenylalanine inhibits biofilm development of a marine microbe, Pseudoalteromonas sp. SC2014. FEMS Microbiol Lett 363:fnw98

    Google Scholar 

  • Meberg BM, Paulson AL, Priyadarshini R, Young KD (2004) Endopeptidase penicillin-binding proteins 4 and 7 play auxiliary roles in determining uniform morphology of Escherichia coli. J Bacteriol 186:8326–8336

    CAS  PubMed  PubMed Central  Google Scholar 

  • Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H (2017) Identification and characterization of novel broad-spectrum amino acid racemases from Escherichia coli and Bacillus subtilis. Amino Acids 49:1885–1894

    CAS  PubMed  Google Scholar 

  • Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H (2018) Cystathionine β-lyase is involved in d-amino acid metabolism. Biochem J 475:1397–1410

    CAS  PubMed  Google Scholar 

  • Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H (2019) Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima. FEBS J 286:601–614

    CAS  PubMed  Google Scholar 

  • Mosteller RD, Goldstein RV (1975) Unusual sensitivity of Escherichia coli to adenine or adenine plus histidine. J Bacteriol 123:750–751

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mutaguchi Y, Ohmori T, Wakamatsu T, Doi K, Ohshima T (2013) Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species. J Bacteriol 195:5207–5215

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nelson DE, Young KD (2001) Contributions of PBP 5 and dd-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli. J Bacteriol 183:3055–3064

    CAS  PubMed  PubMed Central  Google Scholar 

  • Priyadarshini R, Popham DL, Young KD (2006) Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli. J Bacteriol 188:5345–5355

    CAS  PubMed  PubMed Central  Google Scholar 

  • Radkov AD, Moe LA (2013) Amino acid racemization in Pseudomonas putida KT2440. J Bacteriol 195:5016–5024

    CAS  PubMed  PubMed Central  Google Scholar 

  • Radkov AD, Moe LA (2014) Bacterial synthesis of d-amino acids. Appl Microbiol Biotechnol 98:5363–5374

    CAS  PubMed  Google Scholar 

  • Ramón-Peréz ML, Diaz-Cedillo F, Ibarra JA, Torales-Cardeña A, Rodríguez-Martínez S, Jan-Roblero J, Cancino-Diaz ME, Cancino-Diaz JC (2014) d-Amino acids inhibit biofilm formation in Staphylococcus epidermidis strains from ocular infections. J Med Microbiol 63:1369–1376

    PubMed  Google Scholar 

  • Rosen E, Tsesis I, Elbahary S, Storzi N, Kolodkin-Gal I (2016) Eradication of Enterococcus faecalis biofilms on human dentin. Front Microbiol 7:2055

    PubMed  PubMed Central  Google Scholar 

  • Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P (2008) The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev 32:234–258

    CAS  PubMed  Google Scholar 

  • She P, Chen L, Liu H, Zou Y, Luo Z, Koronfel A, Wu Y (2015) The effects of d-tyrosine combined with amikacin on the biofilms of Pseudomonas aeruginosa. Microb Pathog 86:38–44

    CAS  PubMed  Google Scholar 

  • Shimazaki J, Furukawa S, Ogihara H, Morinaga Y (2012) l-Tryptophan prevents Escherichia coli biofilm formation and triggers biofilm degradation. Biochem Biophys Res Commun 419:715–718

    CAS  PubMed  Google Scholar 

  • Soutourina J, Plateau P, Blanquet S (2000) Metabolism of d-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells. J Biol Chem 275:32535–32542

    CAS  PubMed  Google Scholar 

  • Soutourina O, Soutourina J, Blanquet S, Plateau P (2004) Formation of d-tyrosyl-tRNATyr accounts for the toxicity of d-tyrosine toward Escherichia coli. J Biol Chem 279:42560–42565

    CAS  PubMed  Google Scholar 

  • Typas A, Banzhaf M, Gross CA, Vollmer W (2012) From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol 10:123–136

    CAS  Google Scholar 

  • Vollmer W, Blanot D, de Pedro MA (2008) Peptidoglycan structure and architecture. FEMS Microbiol Rev 32:149–167

    CAS  PubMed  Google Scholar 

  • Yamashita T, Ashiuchi M, Ohnishi K, Kato S, Nagata S, Misono H (2004) Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum. Eur J Biochem 271:4798–4803

    CAS  PubMed  Google Scholar 

  • Yamauchi T, Choi SY, Okada H, Yohda M, Kumagai H, Esaki N, Soda K (1992) Properties of aspartate racemase, a pyridoxal 5'-phosphate-independent amino acid racemase. J Biol Chem 267:18361–18364

    CAS  PubMed  Google Scholar 

  • Yu C, Li X, Zhang N, Wen D, Liu C, Li Q (2016) Inhibition of biofilm formation by d-tyrosine: effect of bacterial type and d-tyrosine concentration. Water Res 92:173–179

    CAS  PubMed  Google Scholar 

  • Zilm PS, Butnejski V, Rossi-Fedele G, Kidd SP, Edwards S, Vasilev K (2017) d-Amino acids reduce Enterococcus faecalis biofilms in vitro and in the presence of antimicrobials used for root canal treatment. PLoS ONE 12:e0170670

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank S. Kitamoto and R. Takasaki (School of Pharmacy, Kitasato University) for assistance with the experiments. This work was supported in part by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant number 17K18082 (to T.M.).

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Authors and Affiliations

  1. Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan

    Tetsuya Miyamoto, Masumi Katane, Yasuaki Saitoh, Masae Sekine & Hiroshi Homma

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  1. Tetsuya Miyamoto
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  2. Masumi Katane
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  3. Yasuaki Saitoh
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  4. Masae Sekine
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  5. Hiroshi Homma
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Contributions

TM designed the study, performed most of the experiments, and analyzed the data. HH supervised the study. TM and HH wrote the manuscript. All the authors contributed to the interpretation of the results throughout the study.

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Correspondence to Hiroshi Homma.

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Miyamoto, T., Katane, M., Saitoh, Y. et al. Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical d-amino acid. Amino Acids 52, 487–497 (2020). https://doi.org/10.1007/s00726-020-02830-7

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  • DOI: https://doi.org/10.1007/s00726-020-02830-7

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