Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms

Abstract

L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5′-phosphate. The ldc1E gene was subcloned into the pET-30a(+) vector and highly expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent Km, kcat, and kcat/Km values of 1.08±0.16 mM, 5.09±0.63 s−1, and 4.73×103 s−1 M−1, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg−1 protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.

Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

“…S3 ). The observation that this activity rate is 30 times smaller than that of E. coli LdcI at the same conditions 31 , 32 may indicate that, similarly to LdcI and related enzymes 33 , 34 , optimal LdcF activity is pH, salt, and temperature-dependent. We were able to determine the structure of F. novicida LdcF from X-ray diffraction data collected to a resolution of 3.4 Å (Supplementary Table S1 and Supplementary Fig.…”

Effective Biodegradation of Aflatoxin B1 Using the Bacillus licheniformis (BL010) Strain

“…There have also been reports of significant AFB1 reduction, but no product has been detected [38,41,42]. These results suggest that AFB1 is likely metabolized to degradation products with chemical properties that differ from those of the parent compound [43], perhaps because this process is catalyzed by multiple enzymes [42].…”

Growth Inhibition of Aflatoxigenic Molds and Biodegradation of Aflatoxin B1 by Certain Bacterial Isolates

“…There were reports of a significant reduction in AFB1 but no product was detected. These findings indicate that AFB1 is likely metabolized to degradation products with chemical properties that vary from those of the parent compound (Deng et al, 2017), probably because multiple enzymes catalyze this process (Alberts et al, 2006). While, Eshelli et al (2015) reported that the HPLC, ion-trap ESIMS, and HR-FTMS confirmed the cleavage of the lactone group of AFB1 degraded by Rhodococcus, as the peak area designated for AFB1 was decreasing over time.In contrast, the metabolization of AFB1 into other unknown substances that may be identified by HPLC and/or LC-MS was previously reported (Zheng et al, 2016;Prettl et al, 2017;Raksha et al, 2016;Wang et al, 2018).…”