Characterization, cloning, sequencing, and expression of an aminopeptidase N from Streptomyces sp. TH-4

Substrate Characterization for Hydrolysis of Multiple Types of Aromatic Esters by Promiscuous Aminopeptidases

Synthetic aromatic esters, widely employed in agriculture, food, and chemical industries, have become emerging environmental pollutants due to their strong hydrophobicity and poor bioavailability. This study attempted to address this issue by extracellularly expressing the promiscuous aminopeptidase (Aps) from Pseudomonas aeruginosa GF31 in B. subtilis, achieving an impressive enzyme activity of 13.7 U/mg. Notably, we have demonstrated, for the first time, the Aps-mediated degradation of diverse aromatic esters, including but not limited to pyrethroids, phthalates, and parabens. A biochemical characterization of Aps reveals its esterase properties and a broader spectrum of substrate profiles. The degradation rates of p-nitrobenzene esters (p-NB) with different side chain structures vary under the action of Aps, showing a preference for substrates with relatively longer alkyl side chains. The structure-dependent degradability aligns well with the binding energies between Aps and p-NB. Molecular docking and enzyme-substrate interaction elucidate that hydrogen bonding, hydrophobic interactions, and π-π stacking collectively stabilize the enzyme-substrate conformation, promoting substrate hydrolysis. These findings provide new insights into the enzymatic degradation of aromatic ester pollutants, laying a foundation for the further development and modification of promiscuous enzymes.

Novel activity of Streptomyces aminopeptidase P

Streptomyces aminopeptidase P enzymes are proline-specific peptidases that belong to the peptidase M24 family. To evaluate the activity of a commercial Streptomyces aminopeptidase P, named ‘XPO DUET’, we performed three experiments involving degradation of tryptic casein, production of free amino acids from casein hydrolysate, and hydrolysis of synthetic peptides. Using an ion-trap liquid chromatography–mass spectrometry (LC–MS) apparatus, we demonstrate that XPO DUET could degrade FFVAPFPEVFGK, an allergic and bitter peptide, VAPFPEVFGK, and PEVFGK from tryptic casein. All amino acids, except Ala, Asp, Glu, and Tyr, were released in an XPO DUET activity-dependent manner during the hydrolysis of casein hydrolysate. LC–MS analysis also revealed the ability of XPO DUET to completely hydrolyze Phe-Phe-Phe into free Phe. Thus, we confirm that XPO DUET possesses broader specificity than its known activity toward Xaa-Pro peptides. Because XPO DUET is a food-grade peptidase, it is useful in the bioprocessing of protein hydrolysates through its combination with other food-grade peptidases.

Evaluation of the Hydrolysis Specificity of an Aminopeptidase from Bacillus licheniformis SWJS33 Using Synthetic Peptides and Soybean Protein Isolate

The substrate specificity of aminopeptidases has often been determined against aminoacyl-p-nitroanilide; thus, its specificity toward synthetic peptides and complex substrates remained unclear. The hydrolysis specificity of an aminopeptidase from Bacillus licheniformis SWJS33 (BLAM) was evaluated using a series of synthetic peptides and soybean protein isolate. The aminopeptidase showed high specificity for dipeptides with Leu, Val, Ala, Gly, and Phe at the N-terminus, and the specificity was significantly affected by the nature of the penultimate residue. In the hydrolysis of soy protein isolate, BLAM preferred peptides with Leu, Glu, Gly, and Ala at the N-terminus by free amino acid analysis and preferred peptides with Leu, Ala, Ser, Trp, and Tyr at the N-terminus by UPLC-MS/MS. The introduction of complex substrates provides a deeper understanding of the aminopeptidase's specificity, which can instruct the application of the enzyme in protein hydrolysis.

Diminished exoproteome of Frankia spp. in culture and symbiosis

Frankia species are the most geographically widespread gram-positive plant symbionts, carrying out N(2) fixation in root nodules of trees and woody shrubs called actinorhizal plants. Taking advantage of the sequencing of three Frankia genomes, proteomics techniques were used to investigate the population of extracellular proteins (the exoproteome) from Frankia, some of which potentially mediate host-microbe interactions. Initial two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of culture supernatants indicated that cytoplasmic proteins appeared in supernatants as cells aged, likely because older hyphae lyse in this slow-growing filamentous actinomycete. Using liquid chromatography coupled to tandem mass spectrometry to identify peptides, 38 proteins were identified in the culture supernatant of Frankia sp. strain CcI3, but only three had predicted export signal peptides. In symbiotic cells, 42 signal peptide-containing proteins were detected from strain CcI3 in Casuarina cunninghamiana and Casuarina glauca root nodules, while 73 and 53 putative secreted proteins containing signal peptides were identified from Frankia strains in field-collected root nodules of Alnus incana and Elaeagnus angustifolia, respectively. Solute-binding proteins were the most commonly identified secreted proteins in symbiosis, particularly those predicted to bind branched-chain amino acids and peptides. These direct proteomics results complement a previous bioinformatics study that predicted few secreted hydrolytic enzymes in the Frankia proteome and provide direct evidence that the symbiosis succeeds partly, if not largely, because of a benign relationship.