Purification and characterization of vanillin dehydrogenases from alkaliphile Micrococcus sp. TA1 and neutrophile Burkholderia cepacia TM1

Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

Molecular cloning and characterization of vanillin dehydrogenase from Streptomyces sp. NL15-2K

Background

Streptomyces sp. NL15-2K, previously isolated from the forest soil, features an extensive catabolic network for lignin-derived aromatic compounds, including pathways transforming ferulic acid to vanillin, vanillic acid, and protocatechuic acid. To successfully use Streptomyces sp. NL15-2K as a biocatalyst for vanillin production, it is necessary to characterize the vanillin dehydrogenase (VDH) that degrades the produced vanillin to vanillic acid, as well as the gene encoding this enzyme. Here, we cloned the VDH-encoding gene (vdh) from strain NL15-2K and comprehensively characterized its gene product.

Results

The vdh open reading frame contains 1488 bp and encodes a 496-amino-acid protein with a calculated molecular mass of 51,705 Da. Whereas the apparent native molecular mass of recombinant VDH was estimated to be 214 kDa by gel filtration analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a subunit molecular mass of ca. 56 kDa, indicating that VDH is a homotetramer. The recombinant enzyme showed optimal activity at 45 °C and pH 9.5. The VDH substrate specificity followed this order: vanillin (100%) > protocatechualdehyde (91%) > benzaldehyde (79%) > p-hydroxybenzaldehyde (56%) > isovanillin (49%) ≈ salicylaldehyde (48%) > anisaldehyde (15%) ≈ veratraldehyde (12%). Although peptide mass fingerprinting and BLAST searches indicated that this enzyme is a salicylaldehyde dehydrogenase (SALDH), the determined kinetic parameters clearly demonstrated that the enzyme is a vanillin dehydrogenase. Lastly, phylogenetic analysis revealed that VDH from Streptomyces sp. NL15-2K forms an independent branch in the phylogenetic tree and, hence, is evolutionarily distinct from other VDHs and SALDHs whose activities have been confirmed experimentally.

Conclusions

Our findings not only enhance the understanding of the enzymatic properties of VDH and the characteristics of its amino acid sequence, but also contribute to the development of Streptomyces sp. NL15-2K into a biocatalyst for the biotransformation of ferulic acid to vanillin.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1309-2) contains supplementary material, which is available to authorized users.

Agrowaste to vanillin conversion by a natural Pediococcus acidilactici strain BD16

Owing to its flavoring, antimicrobial, antioxidant and anticarcinogenic nature, vanillin is widely used in foods, beverages, perfumes and pharmaceutical products. Ferulic acid (FA) is an important precursor of vanillin which is abundant in cereals like maize, rice and wheat and sugar beet. A major drawback of microbial vanillin production from FA is the degradation and biotransformation of toxic vanillin to other phenolic derivatives. The present study is undertaken to explore microbial vanillin production from FA precursor rice bran by employing vanillin-resistant Pediococcus acidilactici BD16, a natural lactic acid bacteria isolate. Extracellular, intracellular and cellular vanillin dehydrogenase activity was found least, which was minimized vanillin degradation, and the strain resists more than 5 g L^-1 vanillin in the medium. A metabolomics approach was followed for the detection of FA, vanillin and other metabolites generated during fermentation of rice bran medium. A metabolic pathway was also predicted for vanillin biosynthesis. Approximately 1.06 g L^-1 of crude vanillin was recovered from rice-bran-containing medium and this further offers scope for the industrial utilization of the organism and its genetic manipulation to enhance production of biovanillin.

A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde

Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed similar k_cat/K_m values for syringaldehyde (2100 s⁻¹·mM⁻¹) and vanillin (1700 s⁻¹·mM⁻¹), whereas LigV substantially preferred vanillin (8800 s⁻¹·mM⁻¹) over syringaldehyde (1.4 s⁻¹·mM⁻¹). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster.

Characterization of Cd36_03230p, a putative vanillin dehydrogenase from Candida dubliniensis

Despite its annotation as such, Cd36_03230p is not a vanillin dehydrogenase.

Functional characterization of a vanillin dehydrogenase in Corynebacterium glutamicum

Vanillin dehydrogenase (VDH) is a crucial enzyme involved in the degradation of lignin-derived aromatic compounds. Herein, the VDH from Corynebacterium glutamicum was characterized. The relative molecular mass (Mr) determined by SDS-PAGE was ~51 kDa, whereas the apparent native Mr values revealed by gel filtration chromatography were 49.5, 92.3, 159.0 and 199.2 kDa, indicating the presence of dimeric, trimeric and tetrameric forms. Moreover, the enzyme showed its highest level of activity toward vanillin at pH 7.0 and 30°C, and interestingly, it could utilize NAD(+) and NADP(+) as coenzymes with similar efficiency and showed no obvious difference toward NAD(+) and NADP(+). In addition to vanillin, this enzyme exhibited catalytic activity toward a broad range of substrates, including p-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, o-phthaldialdehyde, cinnamaldehyde, syringaldehyde and benzaldehyde. Conserved catalytic residues or putative cofactor interactive sites were identified based on sequence alignment and comparison with previous studies, and the function of selected residues were verified by site-directed mutagenesis analysis. Finally, the vdh deletion mutant partially lost its ability to grow on vanillin, indicating the presence of alternative VDH(s) in Corynebacterium glutamicum. Taken together, this study contributes to understanding the VDH diversity from bacteria and the aromatic metabolism pathways in C. glutamicum.

Estimation of inhibitory effects of hemicellulosic wood hydrolysate inhibitors on PHA production by Burkholderia cepacia ATCC 17759 using response surface methodology

Sugar maple hemicellulosic hydrolysate was utilized as a renewable feedstock for polyhydroxyalkanoates production by Burkholderia cepacia ATCC 17759. To estimate inhibitory effects of the hydrolysate, response surface methodology was utilized to analyze cell growth and PHA accumulation in the presence of multiple inhibitors. Mixture design was employed to study the correlation between the proportion of phenolics and total inhibition. The resultant models (R(2) as 92.42% and 93.14% for cell growth and PHA production, respectively) indicated syringic acid was the most inhibitory among three phenolics and synergistic inhibition was observed for the combinations of vanillin/syringic acid and vanillic acid/syringic acid. When furfural, levulinic acid, and acetate were also present during the fermentation, central composite design was employed. The regression model using 48 h cell growth as the response surface (R(2)=87.82%) showed acetate was the most inhibitory. Additionally, strong synergistic effects were observed for the combinations of acetate/phenolics and levulinic acid/furfural.

Production of polyhydroxyalkanoates by Burkholderia cepacia ATCC 17759 using a detoxified sugar maple hemicellulosic hydrolysate

Sugar maple hemicellulosic hydrolysate containing 71.9 g/l of xylose was used as an inexpensive feedstock to produce polyhydroxyalkanoates (PHAs) by Burkholderia cepacia ATCC 17759. Several inhibitory compounds present in wood hydrolysate were analyzed for effects on cell growth and PHA production with strong inhibition observed at concentrations of 1 g/l furfural, 2 g/l vanillin, 7 g/l levulinic acid, and 1 M acetic acid. Gradual catabolism of lower concentrations of these inhibitors was observed in this study. To increase the fermentability of wood hydrolysate, several detoxification methods were tested. Overliming combined with low-temperature sterilization resulted in the highest removal of total inhibitory phenolics (65%). A fed-batch fermentation exhibited maximum PHA production after 96 h (8.72 g PHA/L broth and 51.4% of dry cell weight). Compositional analysis by NMR and physical–chemical characterization showed that PHA produced from wood hydrolysate was composed of polyhydroxybutyrate (PHB) with a molecular mass (M  N) of 450.8 kDa, a melting temperature (T  m) of 174.4°C, a glass transition temperature (T  g) of 7.31°C, and a decomposition temperature (T  decomp) of 268.6°C.