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Enzymatical and microbial degradation of cyclic dipeptides (diketopiperazines).

Perzborn M, Syldatk C, Rudat J - AMB Express (2013)

Bottom Line: NA04-01 (DSM 24917) degraded cyclo(l-Asp-l-Phe), cyclo(l-Gly-l-Phe) and cyclo(l-Asp-l-Asp).The first enantioselective cleavage of cyclo(dl-Ala-dl-Ala) was detected with the newly isolated strains Paenibacillus sp. 32A (DSM 27214) and Microbacterium sp. 40A (DSM 27211).Altogether, five bacterial strains were newly identified for the cleavage of DKPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Karlsruhe Institute of Technology, Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany. mareike.perzborn@kit.edu.

ABSTRACT
Diketopiperazines (DKPs) are cyclic dipeptides, representing an abundant class of biologically active natural compounds. Despite their widespread occurrence in nature, little is known about their degradation. In this study, the enzymatical and microbial cleavage of DKPs was investigated. Peptidase catalyzed hydrolysis of certain DKPs was formerly reported, but could not be confirmed in this study. While testing additional peptidases and DKPs no degradation was detected, indicating peptidase stability of the peptide bond in cyclic dipeptides. Besides confirmation of the reported degradation of cyclo(l-Asp-l-Phe) by Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062), cleavage of cyclo(l-Asp-l-Asp) by DSM 329 was detected. Other DKPs were not hydrolyzed by both strains, demonstrating high substrate specificity. The degradation of cyclo(l-Asp-l-Phe) by DSM 40062 was shown to be inducible. Three strains, which are able to hydrolyze hydantoins and dihydropyrimidines, were identified for the degradation of DKPs: Leifsonia sp. K3 (DSM 27212) and Bacillus sp. A16 (DSM 25052) cleaved cyclo(dl-Ala-dl-Ala) and cyclo(l-Gly-l-Phe), and Rhizobium sp. NA04-01 (DSM 24917) degraded cyclo(l-Asp-l-Phe), cyclo(l-Gly-l-Phe) and cyclo(l-Asp-l-Asp). The first enantioselective cleavage of cyclo(dl-Ala-dl-Ala) was detected with the newly isolated strains Paenibacillus sp. 32A (DSM 27214) and Microbacterium sp. 40A (DSM 27211). Cyclo(l-Ala-d-Ala) and cyclo(l-Ala-l-Ala) were completely degraded, whereas the enantiomer cyclo(d-Ala-d-Ala) was not attacked. Altogether, five bacterial strains were newly identified for the cleavage of DKPs. These bacteria may be of value for industrial purposes, such as degradation of undesirable DKPs in food and drugs and production of (enantiopure) dipeptides and amino acids.

No MeSH data available.


Related in: MedlinePlus

Substrate spectrum for Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062). Hydrolysis of different DKPs by crude extract of (A) DSM 329 and (B) DSM 40062, and by resting cells of (C) DSM 329 and (D) DSM 40062. Each value is the mean of three replicates with error bars representing the standard deviation; pc: protein concentration, cdm: cell dry mass.
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Figure 2: Substrate spectrum for Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062). Hydrolysis of different DKPs by crude extract of (A) DSM 329 and (B) DSM 40062, and by resting cells of (C) DSM 329 and (D) DSM 40062. Each value is the mean of three replicates with error bars representing the standard deviation; pc: protein concentration, cdm: cell dry mass.

Mentions: For Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062) the substrate specificity was investigated with 11 DKPs. The reported hydrolysis of cyclo(l-Asp-l-Phe) (Yokozeki et al. 1990) was shown with crude extract (Figure 2A, B) and resting cells (Figure 2C, D). Moreover, activity towards cyclo(l-Asp-l-Asp) was measured with crude extract and resting cells of DSM 329 (Figure 2A, C). All other tested DKPs were not cleaved by both strains.


Enzymatical and microbial degradation of cyclic dipeptides (diketopiperazines).

Perzborn M, Syldatk C, Rudat J - AMB Express (2013)

Substrate spectrum for Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062). Hydrolysis of different DKPs by crude extract of (A) DSM 329 and (B) DSM 40062, and by resting cells of (C) DSM 329 and (D) DSM 40062. Each value is the mean of three replicates with error bars representing the standard deviation; pc: protein concentration, cdm: cell dry mass.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852281&req=5

Figure 2: Substrate spectrum for Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062). Hydrolysis of different DKPs by crude extract of (A) DSM 329 and (B) DSM 40062, and by resting cells of (C) DSM 329 and (D) DSM 40062. Each value is the mean of three replicates with error bars representing the standard deviation; pc: protein concentration, cdm: cell dry mass.
Mentions: For Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062) the substrate specificity was investigated with 11 DKPs. The reported hydrolysis of cyclo(l-Asp-l-Phe) (Yokozeki et al. 1990) was shown with crude extract (Figure 2A, B) and resting cells (Figure 2C, D). Moreover, activity towards cyclo(l-Asp-l-Asp) was measured with crude extract and resting cells of DSM 329 (Figure 2A, C). All other tested DKPs were not cleaved by both strains.

Bottom Line: NA04-01 (DSM 24917) degraded cyclo(l-Asp-l-Phe), cyclo(l-Gly-l-Phe) and cyclo(l-Asp-l-Asp).The first enantioselective cleavage of cyclo(dl-Ala-dl-Ala) was detected with the newly isolated strains Paenibacillus sp. 32A (DSM 27214) and Microbacterium sp. 40A (DSM 27211).Altogether, five bacterial strains were newly identified for the cleavage of DKPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Karlsruhe Institute of Technology, Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany. mareike.perzborn@kit.edu.

ABSTRACT
Diketopiperazines (DKPs) are cyclic dipeptides, representing an abundant class of biologically active natural compounds. Despite their widespread occurrence in nature, little is known about their degradation. In this study, the enzymatical and microbial cleavage of DKPs was investigated. Peptidase catalyzed hydrolysis of certain DKPs was formerly reported, but could not be confirmed in this study. While testing additional peptidases and DKPs no degradation was detected, indicating peptidase stability of the peptide bond in cyclic dipeptides. Besides confirmation of the reported degradation of cyclo(l-Asp-l-Phe) by Paenibacillus chibensis (DSM 329) and Streptomyces flavovirens (DSM 40062), cleavage of cyclo(l-Asp-l-Asp) by DSM 329 was detected. Other DKPs were not hydrolyzed by both strains, demonstrating high substrate specificity. The degradation of cyclo(l-Asp-l-Phe) by DSM 40062 was shown to be inducible. Three strains, which are able to hydrolyze hydantoins and dihydropyrimidines, were identified for the degradation of DKPs: Leifsonia sp. K3 (DSM 27212) and Bacillus sp. A16 (DSM 25052) cleaved cyclo(dl-Ala-dl-Ala) and cyclo(l-Gly-l-Phe), and Rhizobium sp. NA04-01 (DSM 24917) degraded cyclo(l-Asp-l-Phe), cyclo(l-Gly-l-Phe) and cyclo(l-Asp-l-Asp). The first enantioselective cleavage of cyclo(dl-Ala-dl-Ala) was detected with the newly isolated strains Paenibacillus sp. 32A (DSM 27214) and Microbacterium sp. 40A (DSM 27211). Cyclo(l-Ala-d-Ala) and cyclo(l-Ala-l-Ala) were completely degraded, whereas the enantiomer cyclo(d-Ala-d-Ala) was not attacked. Altogether, five bacterial strains were newly identified for the cleavage of DKPs. These bacteria may be of value for industrial purposes, such as degradation of undesirable DKPs in food and drugs and production of (enantiopure) dipeptides and amino acids.

No MeSH data available.


Related in: MedlinePlus