Enzymatical and microbial degradation of cyclic dipeptides (diketopiperazines)

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.

Coagulant Plus Bacillus nitratireducens Fermentation Broth Technique Provides a Rapid Algicidal Effect of Toxic Red Tide Dinoflagellate

“…In terms of their biological safety, anti-compounds are biodegradable. Moreover, when used to control blooms, they appear to be harmless to the environment [26]. These results strongly bolster the claim that Ba3 has potential applications in controlling algae outbreaks.…”

Organic geochemistry and mineralogy suggest anthropogenic impact in speleothem chemistry from volcanic show caves of the Galapagos

“…Diketopiperazine compounds (i.e. cycled amino acids) were also detected in Bella-C coralloids, which may be used as markers (biosignatures) of microbial communities ( Borgman et al., 2019 ; Perzborn et al., 2013 ).…”

Allelopathic Inhibition by the Bacteria Bacillus cereus BE23 on Growth and Photosynthesis of the Macroalga Ulva prolifera

“…In the present study, the diketopiperazine derivatives decreased the gene expression of PsbA [54,87], directly impacting the PSII electron acceptor sides, resulting in the failure of the photosynthetic process. Given that cyclo (L-Pro-L-Pro) is easily biodegradable [88], it may be a good candidate as an environmentally friendly algicide for green algae bloom control.…”