Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution

Region-based segmental swapping of homologous enzymes for higher cadaverine production

BACKGROUND

Cadaverine, displaying potential in medicine, agriculture and polyamide production, is biologically produced through L-lysine decarboxylation. Considering the potential of the polyamide market, its biological production has been focused on with following diverse efforts to improve the production. In Escherichia coli, lysine decarboxylase exists in two forms: CadA and LdcC, and it is known that CadA exhibits superior catalytic activity compared to LdcC. Despite its potential, cadaverine production is limited due to increased intracellular pH, which destabilizes the decameric structure of CadA and inhibits its activity.

RESULTS

In this study, based on the structural analysis, a chimeric CadA enzyme, CL2, was engineered by replacing its pH-sensitive region with a structurally stable counterpart derived from LdcC. The resulting BLCL2 strain with CL2 produced 1.12 g/L of cadaverine-1.96 times higher than BLC strain with the wild type CadA in flask culture. Compared to the wild type CadA, structural modifications enhanced pH stability and improved the affinity of CadA toward pyridoxal 5-phosphate (PLP), its cofactor.

CONCLUSIONS

This study developed the improved strains for cadaverine production by creating the new enzyme, which is validated by enhanced amount of cadaverine. In addition, the segmental swapping guided by structure analysis was exhibited as the one of effective method in protein engineering strategies. These advancements offer a promising approach to optimizing cadaverine biosynthesis for industrial applications.

Hydrogen-Rich Water Can Restrict the Formation of Biogenic Amines in Red Beet Pickles

Fermented foods are considered the main sources of biogenic amines (BAs) in the human diet while lactic acid bacteria (LAB) are the main producers of BAs. Normal water (NW) and hydrogen-rich water (HRW) were used for preparing red beet pickles, i.e., NWP and HRWP, respectively. The formation of BAs, i.e., aromatic amines (tyramine, 2-phenylethylamine), heterocyclic amines (histamine, tryptamine), and aliphatic di-amines (putrescine), was analyzed in both beet slices and brine of NWPs and HRWPs throughout the fermentation stages. Significant differences in redox value (Eh7) between NWP and HRWP brine samples were noticed during the first and last fermentation stages with lower values found for HRWPs. Total mesophilic aerobic bacteria (TMAB), yeast–mold, and LAB counts were higher for HRWPs than NWPs for all fermentation stages. Throughout fermentation stages, the levels of all BAs were lower in HRWPs than those of NWPs, and their levels in brines were higher than those of beets. At the end of fermentation, the levels (mg/kg) of BAs in NWPs and HRWPs were, respectively: tyramine, 72.76 and 61.74 (beet) and 113.49 and 92.67 (brine), 2-phenylethylamine, 48.00 and 40.00 (beet) and 58.01 and 50.19 (brine), histamine, 67.89 and 49.12 (beet) and 91.74 and 70.92 (brine), tryptamine, 93.14 and 77.23 (beet) and 119.00 and 93.11 (brine), putrescine, 81.11 and 63.56 (beet) and 106.75 and 85.93 (brine). Levels of BAs decreased by (%): 15.15 and 18.35 (tyramine), 16.67 and 13.44 (2-phenylethylamine), 27.65 and 22.7 (histamine), 17.09 and 21.76 (tryptamine), and 21.64 and 19.5 (putrescine) for beet and brine, respectively, when HRW was used in pickle preparation instead of NW. The results of this study suggest that the best method for limiting the formation of BAs in pickles is to use HRW in the fermentation phase then replace the fermentation medium with a new acidified and brined HRW followed by a pasteurization process.

The Effect of Visible Light on the Catalytic Activity of PLP-Dependent Enzymes

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive and can cause inactivation of enzymes in certain light conditions. As most of the PLP-dependent enzymes are usually not handled in dark conditions, we evaluated the effect of visible light on the activity of PLP-dependent enzymes during production as well as transformation. We tested four amine transaminases, from Chromobacterium violaceum, Bacillus megaterium, Vibrio fluvialis and a variant from Arthrobacter species as well as two lysine decarboxylases, from Selenomonas ruminantium and the LDCc from Escherichia coli. It appeared that five of these six enzymes suffered from a significant decrease in activity by up to 90 % when handled in laboratory light conditions. Surprisingly, only the amine transaminase variant from Arthrobacter species appeared to be unaffected by light exposure and even showed an activation to 150 % relative activity over the course of 6 h regardless of the light conditions.

Improvement of cadaverine production in whole cell system with baker's yeast for cofactor regeneration

Cadaverine, 1,5-diaminopentane, is one of the most promising chemicals for biobased-polyamide production and it has been successfully produced up to molar concentration. Pyridoxal 5'-phosphate (PLP) is a critical cofactor for inducible lysine decarboxylase (CadA) and is required up to micromolar concentration level. Previously the regeneration of PLP in cadaverine bioconversion has been studied and salvage pathway pyridoxal kinase (PdxY) was successfully introduced; however, this system also required a continuous supply of adenosine 5'-triphosphate (ATP) for PLP regeneration from pyridoxal (PL) which add in cost. Herein, to improve the process further a method of ATP regeneration was established by applying baker's yeast with jhAY strain harboring CadA and PdxY, and demonstrated that providing a moderate amount of adenosine 5'-triphosphate (ATP) with the simple addition of baker's yeast could increase cadaverine production dramatically. After optimization of reaction conditions, such as PL, adenosine 5'-diphosphate, MgCl₂, and phosphate buffer, we able to achieve high production (1740 mM, 87% yield) from 2 M L-lysine. Moreover, this approach could give averaged 80.4% of cadaverine yield after three times reactions with baker's yeast and jhAY strain. It is expected that baker's yeast could be applied to other reactions requiring an ATP regeneration system.

Construction and Application of PLP Self-sufficient Biocatalysis System for Threonine Aldolase

A number of organic synthesis involve threonine aldolase (TA), a pyridoxal phosphate (PLP)-dependent enzyme. Although the addition of exogenous PLP is necessary for the reactions, it increases the cost and complicates the purification of the product. This work constructed a PLP self-sufficient biocatalysis system for TA, which included an improvement of the intracellular PLP level and co-immobilization of TA with PLP. Engineered strain BL-ST was constructed by introducing PLP synthase PdxS/T to Escherichia coli BL21(ED3). The intracellular PLP concentration of the strain increased approximately fivefold to 48.5 μmol/g_DCW. l-TA, from Bacillus nealsonii (BnLTA), was co-expressed in the strain BL-ST with PdxS/T, resulting in the engineered strain BL-BnLTA-ST. Compared with the control strain BL-BnLTA (254.1 U/L), the enzyme activity of the strain BL-BnLTA-ST reached 1518.4 U/L without the addition of exogenous PLP. An efficient co-immobilization system was then designed. The epoxy resin LX-1000HFA wrapped by polyethyleneimine (PEI) acted as a carrier to immobilize the crude enzyme solution of the strain BL-BnLTA-ST mixed with an extra 100 μM of exogenous PLP, resulting in the catalyst HFA^PEI-BnLTA-STPLP 100. HFA^PEI-BnLTA-STPLP 100 exhibited a half-life of approximately 450 h, and the application of the catalyst in the continuous biosynthesis of 3-[4-(methylsulfonyl) phenyl] serine had more than 180 batch reactions (>60%_conv) without the extra addition of exogenous PLP. The excellent compatibility and stability of the system were further confirmed by other TAs. This work introduced a PLP self-sufficient biocatalysis system that can reduce the cost of PLP and contribute to the industrial application of TA. In addition, the system may also be applied in other PLP-dependent enzymes.

Enhancing PLP-Binding Capacity of Class-III ω-Transaminase by Single Residue Substitution

Transaminases are pyridoxal-5′-phosphate (PLP) binding enzymes, broadly studied for their potential industrial application. Their affinity for PLP has been related to their performance and operational stability and while significant differences in PLP requirements have been reported, the environment of the PLP-binding pocket is highly conserved. In this study, thorough analysis of the residue interaction network of three homologous transaminases Halomonas elongata (HeTA), Chromobacterium violaceum (CvTA), and Pseudomonas fluorescens (PfTA) revealed a single residue difference in their PLP binding pocket: an asparagine at position 120 in HeTA. N120 is suitably positioned to interact with an aspartic acid known to protonate the PLP pyridinium nitrogen, while the equivalent position is occupied by a valine in the other two enzymes. Three different mutants were constructed (HeTA-N120V, CvTA-V124N, and PfTA-V129N) and functionally analyzed. Notably, in HeTA and CvTA, the asparagine variants, consistently exhibited a higher thermal stability and a significant decrease in the dissociation constant (K_d) for PLP, confirming the important role of N120 in PLP binding. Moreover, the reaction intermediate pyridoxamine-5′-phosphate (PMP) was released more slowly into the bulk, indicating that the mutation also enhances their PMP binding capacity. The crystal structure of PfTA, elucidated in this work, revealed a tetrameric arrangement with the PLP binding sites near the subunit interface. In this case, the V129N mutation had a negligible effect on PLP-binding, but it reduced its temperature stability possibly destabilizing the quaternary structure.

Protein-Rich Biomass Waste as a Resource for Future Biorefineries: State of the Art, Challenges, and Opportunities

Protein-rich biomass provides a valuable feedstock for the chemical industry. This Review describes every process step in the value chain from protein waste to chemicals. The first part deals with the physicochemical extraction of proteins from biomass, hydrolytic degradation to peptides and amino acids, and separation of amino acid mixtures. The second part provides an overview of physical and (bio)chemical technologies for the production of polymers, commodity chemicals, pharmaceuticals, and other fine chemicals. This can be achieved by incorporation of oligopeptides into polymers, or by modification and defunctionalization of amino acids, for example, their reduction to amino alcohols, decarboxylation to amines, (cyclic) amides and nitriles, deamination to (di)carboxylic acids, and synthesis of fine chemicals and ionic liquids. Bio- and chemocatalytic approaches are compared in terms of scope, efficiency, and sustainability.

Cysteine 180 Is a Redox Sensor Modulating the Activity of Human Pyridoxal 5'-Phosphate Histidine Decarboxylase

Histidine decarboxylase is a pyridoxal 5'-phosphate enzyme catalyzing the conversion of histidine to histamine, a bioactive molecule exerting its role in many modulatory processes. The human enzyme is involved in many physiological functions, such as neurotransmission, gastrointestinal track function, cell growth, and differentiation. Here, we studied the functional properties of the human enzyme and, in particular, the effects exerted at the protein level by two cysteine residues: Cys-180 and Cys-418. Surprisingly, the enzyme exists in an equilibrium between a reduced and an oxidized form whose extent depends on the redox state of Cys-180. Moreover, we determined that (i) the two enzymatic redox species exhibit modest structural changes in the coenzyme microenvironment and (ii) the oxidized form is slightly more active and stable than the reduced one. These data are consistent with the model proposed by bioinformatics analyses and molecular dynamics simulations in which the Cys-180 redox state could be responsible for a structural transition affecting the C-terminal domain reorientation leading to active site alterations. Furthermore, the biochemical properties of the purified C180S and C418S variants reveal that C180S behaves like the reduced form of the wild-type enzyme, while C418S is sensitive to reductants like the wild-type enzyme, thus allowing the identification of Cys-180 as the redox sensitive switch. On the other hand, Cys-418 appears to be a residue involved in aggregation propensity. A possible role for Cys-180 as a regulatory switch in response to different cellular redox conditions could be suggested.