Benzoate transport in Pseudomonas putida CSV86

Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?

Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L-1) and a eutrophic (105.35 μg C L-1) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.

Differential anaerobic oxidation of benzoate in Geotalea daltonii FRC-32

The efficient carbon source utilization in dynamic environments, including anoxic subsurface contaminated by aromatic compounds, is a challenge for anaerobic bacteria such as Geotalea daltonii strain FRC-32. The aim of this study was to elucidate the metabolic pathways employed by G. daltonii FRC-32 during anaerobic benzoate oxidation in the presence of acetate, a key intermediate in anaerobic organic matter degradation, to predict carbon source transport and utilization strategies. Simultaneous carbon source oxidation and monoauxic growth were observed in G. daltonii FRC-32 cultures grown on 1 mM benzoate + 5 mM acetate, 1 mM benzoate + 2 mM acetate, and 2 mM acetate spiked with 1 mM benzoate. Sequential carbon source oxidation and diauxic growth were observed only in cultures grown on 5 mM acetate spiked with 1 mM benzoate. Benzoate accumulation in G. daltonii FRC-32 whole cell lysates indicated that intracellular benzoate transport occurred during benzoate oxidation in the presence of acetate. Expression analyses of putative benzoate transporter BenK and protein-ligand binding affinity prediction suggested BenK's specificity for transporting benzoate. Relative expression levels for the gene benK, encoding BenK, and the genes bamNOPQ, involved in the benzoyl-CoA pathway, were significantly higher in cultures grown on both benzoate and acetate than in cultures grown on acetate as sole carbon source, indicating that intracellular benzoate accumulation facilitated the regulation of bamNOPQ. Our results demonstrated that G. daltonii FRC-32 can perform differential benzoate oxidation in the presence of acetate, by either simultaneous or sequential carbon source oxidation, which indicated the metabolic plasticity of G. daltonii FRC-32 in response to varying carbon source availability.IMPORTANCEThe contamination of anaerobic subsurface environments by crude oil derivatives including aromatic compounds is a global concern due to the persistence and toxicity of these pollutants. Anaerobic bacteria play a crucial role in the degradation of aromatic hydrocarbons under anoxic conditions; however, the potential mechanisms involved in metabolic regulation of aromatic degradation pathways are not well understood. This study contributed to elucidating how G. daltonii strain FRC-32 efficiently utilizes benzoate as a carbon source in the presence of acetate. Findings of intracellular benzoate accumulation and regulation of key genes associated with benzoate oxidation contributed to the understanding of G. daltonii FRC-32's aromatic degradation pathways, provided significant insights into potential mechanisms that modulate anaerobic benzoate oxidation in the presence of the energetically favorable carbon source acetate, and indicated metabolic strategies of G. daltonii FRC-32 in response to dynamic environmental conditions.

Metabolic engineering of Pseudomonas bharatica CSV86T to degrade Carbaryl (1-naphthyl-N-methylcarbamate) via the salicylate-catechol route

Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.

Detoxification of fluoroglucocorticoid by Acinetobacter pittii C3 via a novel defluorination pathway with hydrolysis, oxidation and reduction: Performance, genomic characteristics, and mechanism

Biological dehalogenation degradation was an important detoxification method for the ecotoxicity and teratogenic toxicity of fluorocorticosteroids (FGCs). The functional strain Acinetobacter pittii C3 can effectively biodegrade and defluorinate to 1 mg/L Triamcinolone acetonide (TA), a representative FGCs, with 86 % and 79 % removal proportion in 168 h with the biodegradation and detoxification kinetic constant of 0.031/h and 0.016/h. The dehalogenation and degradation ability of strain C3 was related to its dehalogenation genomic characteristics, which manifested in the functional gene expression of dehalogenation, degradation, and toxicity tolerance. Three detoxification mechanisms were positively correlated with defluorination pathways through hydrolysis, oxidation, and reduction, which were regulated by the expression of the haloacid dehalogenase (HAD) gene (mupP, yrfG, and gph), oxygenase gene (dmpA and catA), and reductase gene (nrdAB and TgnAB). Hydrolysis defluorination was the most critical way for TA detoxification metabolism, which could rapidly generate low-toxicity metabolites and reduce toxic bioaccumulation due to hydrolytic dehalogenase-induced defluorination. The mechanism of hydrolytic defluorination was that the active pocket of hydrolytic dehalogenase was matched well with the spatial structure of TA under the adjustment of the hydrogen bond, and thus induced molecular recognition to promote the catalytic hydrolytic degradation of various amino acid residues. This work provided an effective bioremediation method and mechanism for improving defluorination and detoxification performance.

Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications

Aromatic compounds are ubiquitous in nature; they are the building blocks of abundant lignin, and constitute a substantial proportion of synthetic chemicals and organic pollutants. Uptake and degradation of aromatic compounds by bacteria have relevance in bioremediation, bio-based plastic recycling, and microbial conversion of lignocellulosic biomass into high-value commodity chemicals. While remarkable progress has been achieved in understanding aromatic metabolism in biodegraders, the membrane transporter systems responsible for uptake and efflux of aromatic compounds and their degradation products are still poorly understood. Membrane transporters are responsible for the initial recognition, uptake, and efflux of aromatic compounds; thus, in addition to controlling influx and efflux, the transporter system also forms part of stress tolerance mechanisms through excreting toxic metabolites. This review discusses significant advancements in our understanding of the nature and identity of the bacterial membrane transporter systems for aromatics, the molecular and structural basis of substrate recognition, mechanisms of translocation, functional regulation, and biotechnological applications. Most of these developments were enabled through the availability of crystal structures, advancements in computational biophysics, genome sequencing, omics studies, bioinformatics, and synthetic biology. We provide a comprehensive overview of recently reported knowledge on aromatic transporter systems in bacteria, point gaps in our understanding of the underlying translocation mechanisms, highlight existing limitations in harnessing transporter systems in synthetic biology applications, and suggest future research directions.

A unique global metabolic trait of Pseudomonas bharatica CSV86T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids

Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86^T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86^T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86^T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86^T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.

Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.

Functional genome mining and taxono-genomics reveal eco-physiological traits and species distinctiveness of aromatic-degrading Pseudomonas bharatica sp. nov

Assistive eco-physiological traits are necessary for microbes to adapt and colonize at polluted niches, enabling efficient clean-up. To demarcate species distinctiveness and eco-physiological traits of aromatic compounds metabolizing Pseudomonas sp. CSV86^T (earlier identified as Pseudomonas putida), an Indian isolate from a petrol station soil, comparative genome mining, taxono-genomic, and physiological analyses were performed. A 6.79 Mbp genome (62.72 G + C mol%) of CSV86^T encodes 6798 CDS and 238 unique genes. Naphthalene metabolism and Co-Zn-Cd resistance gene clusters were part of distinct genomic islands. Abundance of transporters (aromatics, organic acids, amino acids, and metals) and mobile elements (integrases, transposases, conjugative proteins) differentiated CSV86^T from its closest relatives. Enhanced siderophore production for Fe-uptake during aromatic metabolism, indole acetic acid production, and fusaric acid resistance wasvalidated by genomic attributes. Full-length 16S-rRNA phylogeny revealed Pseudomonas japonica WL^T as a closest relative of CSV86^T . However, lower genomic indices (<97% gyrB-rpoB-rpoD homology, <90% ANI, <50% DNA-DNA relatedness) and taxonomic differences (assimilation of organic acids, amino acids, fatty acids composition) substantially differentiated CSV86^T from its closest relatives, indicating it to be a novel species as Pseudomonas bharatica. Preferential metabolism of aromatics with advantageous eco-physiological traits renders CSV86^T an ideal candidate for bioremediation and host for metabolic engineering.

Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation

Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICE_CSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.

Complete biodegradation of di-n-butyl phthalate (DBP) by a novel Pseudomonas sp. YJB6

Phthalate acid esters (PAEs) are environmentally ubiquitous and have aroused a worldwide concern due to their threats to environment and human health. Di-n-butyl phthalate (DBP) is one of the most frequently observed PAEs in the environment. In this study, a novel bacterium identified as Pseudomonas sp. YJB6 that isolated from PAEs-contaminated soil was determined to have strong DBP-degrading activity. A complete degradation of DBP in 200 mg/L was achieved within 3 days when YJB6 was cultivated at 31.4 °C with an initial inoculation size of 0.6 (OD600) in basic mineral salts liquid medium (MSM), pH 7.6. The degradation curves of DBP (50-2000 mg/L) fitted well the first-order kinetics model, with a half-life (t_1/2) ranging from 0.86 to 1.88 d. The main degradation intermediates were identified as butyl-ethyl phthalate (BEP), mono-butyl phthalate (MBP), phthalic acid (PA) and benzoic acid (BA), indicating a new complex and complete biodegradation pathway presented by YJB6. DBP might be metabolized through de-esterification, β-oxidation, and hydrolysis, followed by entering the Krebs cycle of YJB6 as a final step. Strain YJB6 was successfully immobilized with sodium alginate (SA), polyvinyl alcohol (PVA), and SA-PVA. The immobilization significantly improved the stability and adaptability of the cells thus resulting in high volumetric DBP-degrading rates compared to that of the freely suspended cells. In addition, these immobilized cells can be reused for many cycles with well conserved in DBP-degrading activity. The ideal DBP degrading ability of the free and immobilized YJB6 cells suggests that strain YJB6, especially the SA-PVA+ YJB6 promises great potential to remove hazardous PAEs.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1

Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD⁺-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain.

Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria

As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.

DdvK, a Novel Major Facilitator Superfamily Transporter Essential for 5,5'-Dehydrodivanillate Uptake by Sphingobium sp. Strain SYK-6

The microbial conversion of lignin-derived aromatics is a promising strategy for the industrial utilization of this large biomass resource. However, efficient application requires an elucidation of the relevant transport and catabolic pathways. In Sphingobium sp. strain SYK-6, most of the enzyme genes involved in 5,5'-dehydrodivanillate (DDVA) catabolism have been characterized, but the transporter has not yet been identified. Here, we identified SLG_07710 (ddvK) and SLG_07780 (ddvR), genes encoding a putative major facilitator superfamily (MFS) transporter and MarR-type transcriptional regulator, respectively. A ddvK mutant of SYK-6 completely lost the capacity to grow on and convert DDVA. DdvR repressed the expression of the DDVA O-demethylase oxygenase component gene (ligXa), while DDVA acted as the gene inducer. A DDVA uptake assay was developed by employing this DdvR-controlled ligXa transcriptional regulatory system. A Sphingobium japonicum UT26S transformant expressing ddvK acquired DDVA uptake capacity, indicating that ddvK encodes the DDVA transporter. DdvK, probably requiring the proton motive force, was suggested to be a novel MFS transporter on the basis of the amino acid sequence similarity. Subsequently, we evaluated the effects of ddvK overexpression on the production of the DDVA metabolite 2-pyrone-4,6-dicarboxylate (PDC), a building block of functional polymers. A SYK-6 mutant of the PDC hydrolase gene (ligI) cultured in DDVA accumulated PDC via 5-carboxyvanillate and grew by utilizing 4-carboxy-2-hydroxypenta-2,4-dienoate. The introduction of a ddvK-expression plasmid into a ligI mutant increased the growth rate in DDVA and the amounts of DDVA converted and PDC produced after 48 h by 1.35- and 1.34-fold, respectively. These results indicate that enhanced transporter gene expression can improve metabolite production from lignin derivatives.IMPORTANCE The bioengineering of bacteria to selectively transport and metabolize natural substrates into specific metabolites is a valuable strategy for industrial-scale chemical production. The uptake of many substrates into cells requires specific transport systems, and so the identification and characterization of transporter genes are essential for industrial applications. A number of bacterial major facilitator superfamily transporters of aromatic acids have been identified and characterized, but many transporters of lignin-derived aromatic acids remain unidentified. The efficient conversion of lignin, an abundant but unutilized aromatic biomass resource, to value-added metabolites using microbial catabolism requires the characterization of transporters for lignin-derived aromatics. In this study, we identified the transporter gene responsible for the uptake of 5,5'-dehydrodivanillate, a lignin-derived biphenyl compound, in Sphingobium sp. strain SYK-6. In addition to characterizing its function, we applied this transporter gene to the production of a value-added metabolite from 5,5'-dehydrodivanillate.