Regulation of genes in Streptomyces bacteria required for catabolism of lignin-derived aromatic compounds

Lignin Metabolism by Selected Fungi and Microbial Consortia for Plant Stimulation: Implications for Biologically Active Humus Genesis

Plant lignin is regarded as an important source for soil humic substances (HSs). Nonetheless, it remains unclear whether microbial metabolism on lignin is related to the genesis of unique HS biological activities (e.g., direct plant stimulation). Here, selected white-rot fungi (i.e., Ganoderma lucidum and Irpex lacteus) and plant litter- or mountain soil-derived microbial consortia were exploited to structurally modify lignin, followed by assessing the plant-stimulatory activity of the lignin-derived products. Parts solubilized by microbial metabolism on lignin were proven to exhibit organic moieties of phenol, carboxylic acid, and aliphatic groups and the enhancement of chromogenic features (i.e., absorbance at 450 nm), total phenolic contents, and radical-scavenging capacities with the cultivation times. In addition, high-resolution mass spectrometry revealed the shift of lignin-like molecules toward those showing either more molar oxygen-to-carbon or more hydrogen-to-carbon ratios. These results support the findings that the microbes involved, solubilize lignin by fragmentation, oxygenation, and/or benzene ring opening. This notion was also substantiated by the detection of related exoenzymes (i.e., peroxidases, copper radical oxidases, and hydrolases) in the selected fungal cultures, while the consortia treated with antibacterial agents showed that the fungal community is a sufficient condition to induce the lignin biotransformation. Major families of fungi (e.g., Nectriaceae, Hypocreaceae, and Saccharomycodaceae) and bacteria (e.g., Burkholderiaceae) were identified in the lignin-enriched cultures. All the microbially solubilized lignin products were likely to stimulate plant root elongation in the order selected white-rot fungi > microbial consortia > antibacterial agent-treated microbial consortia. Overall, this study supports the idea that microbial transformation of lignin can contribute to the formation of biologically active organic matter. IMPORTANCE Structurally stable humic substances (HSs) in soils are tightly associated with soil fertility, and it is thus important to understand how soil HSs are naturally formed. It is believed that microbial metabolism on plant matter contributes to natural humification, but detailed microbial species and their metabolisms inducing humic functionality (e.g., direct plant stimulation) need to be further investigated. Our findings clearly support that microbial metabolites of lignin could contribute to the formation of biologically active humus. This research direction appears to be meaningful not only for figuring out the natural processes, but also for confirming natural microbial resources useful for artificial humification that can be linked to the development of high-quality soil amendments.

Efficacy of the antifungal metabolites of Streptomyces philanthi RL-1-178 on aflatoxin degradation with its application to prevent aflatoxigenic fungi in stored maize grains and identification of the bioactive compound

Aflatoxin B₁ is a potent carcinogen produced by Aspergillus flavus (A. flavus) and Aspergillus. parasiticus (A. parasiticus), mainly during grain storage. The efficacy of the freeze-dried culture filtrate of Streptomyces philanthi (S. philanthi) strain RL-1-178 (DCF) on degradation of aflatoxin B₁ (AFB₁) were evaluated and its bioactive compounds were identified. The DCF at a concentration of 9.0% (w/v) completely inhibited growth and AFB₁ production of A. parasiticus TISTR 3276 and A. flavus PSRDC-4 after 7 days tested in yeast-extract sucrose (YES) medium and on stored maize grains after 28 and 14 days incubation, respectively. This indicated the more tolerance of A. parasiticus over A. flavus. The DCF and bacterial cells of S. philanthi were capable to degrade AFB₁ by 85.0% and 100% for 72 h and 8 days, respectively. This confirmed the higher efficacy of the DCF over the cells. After separation of the DCF on thin-layer chromatography (TLC) plate by bioautography bioassay, each active band was identified by liquid chromatography-quadrupole time of flight mass spectrometer (LC-Q-TOF MS/MS). The results revealed two compounds which were identified as azithromycin and an unknown based on mass ions of both ESI⁺ and ESI^- modes. The antifungal metabolites in the culture filtrate of S. philanthi were proved to degrade aflatoxin B₁. It could be concluded that the DCF may be applied to prevent the growth of the two aflatoxin-producing fungi as well as the occurrence of aflatoxin in the stored maize grains.

Comparative and pangenomic analysis of the genus Streptomyces

Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

Biological depolymerization of lignin using laccase harvested from the autochthonous fungus Schizophyllum commune employing various production methods and its efficacy in augmenting in vitro digestibility in ruminants

A laccase-producing hyper performer, Schizophyllum commune, a white-rot fungus, was evaluated for its ability to selectively degrade lignin of diverse crop residues in vitro. Relative analysis of crop residue treatment using laccase obtained from immobilized cells demonstrated degradation of 30-40% in finger millet straw and sorghum stover, 27-32% in paddy straw, 21% in wheat straw, and 26% in maize straw, while 20% lignin degradation was observed when purified and recombinant laccase was used. Further investigations into in vitro dry matter digestibility studies gave promising results recording digestibility of 54-59% in finger millet straw 33-36% in paddy straw and wheat straw, 16% in maize straw for laccase obtained from cell immobilization method, whereas 14% digestibility was observed when purified and recombinant laccase was used. Sorghum stover recorded digestibility of 13-15% across all straws treated with laccase. The results obtained elucidated the positive influence of laccase treatment on lignin degradation and in vitro dry matter digestibility. The present research gave encouraging figures confirming the production of laccase using the cell immobilization method to be an efficient production method commensurate with purified and recombinant laccase under conditions of submerged cultivation, proclaiming a cost-effective, environmentally safe green technology for effectual lignin depolymerization.

Responsiveness of Aromatoleum aromaticum EbN1T to Lignin-Derived Phenylpropanoids

The betaproteobacterial degradation specialist Aromatoleum aromaticum EbN1^T utilizes several plant-derived 3-phenylpropanoids coupled to denitrification. In vivo responsiveness of A. aromaticum EbN1^T was studied by exposing nonadapted cells to distinct pulses (spanning 100 µM to 0.1 nM) of 3-phenylpropanoate, cinnamate, 3-(4-hydroxyphenyl)propanoate, or p-coumarate. Time-resolved, targeted transcript analyses via quantitative reverse transcription-PCR of four selected 3-phenylpropanoid genes revealed a response threshold of 30 to 50 nM for p-coumarate and 1 to 10 nM for the other three tested 3-phenylpropanoids. At these concentrations, transmembrane effector equilibration is attained by passive diffusion rather than active uptake via the ABC transporter, presumably serving the studied 3-phenylpropanoids as well as benzoate. Highly substrate-specific enzyme formation (EbA5316 to EbA5321 [EbA5316-21]) for the shared peripheral degradation pathway putatively involves the predicted TetR-type transcriptional repressor PprR. Accordingly, relative transcript abundances of ebA5316-21 are lower in succinate- and benzoate-grown wild-type cells than in an unmarked in-frame ΔpprR mutant. In trans-complementation of pprR into the ΔpprR background restored wild-type-like transcript levels. When adapted to p-coumarate, the three genotypes had relative transcript abundances similar to those of ebA5316-21 despite a significantly longer lag phase of the pprR-complemented mutant (∼100-fold higher pprR transcript level than the wild type). Notably, transcript levels of ebA5316-21 were ∼10- to 100-fold higher in p-coumarate- than succinate- or benzoate-adapted cells across all three genotypes. This indicates the additional involvement of an unknown transcriptional regulator. Furthermore, physiological, transcriptional, and (aromatic) acyl-coenzyme A ester intermediate analyses of the wild type and ΔpprR mutant grown with binary substrate mixtures suggest a mode of catabolite repression of superior order to PprR.IMPORTANCE Lignin is a ubiquitous heterobiopolymer built from a suite of 3-phenylpropanoid subunits. It accounts for more than 30% of the global plant dry material, and lignin-related compounds are increasingly released into the environment from anthropogenic sources, i.e., by wastewater effluents from the paper and pulp industry. Hence, following biological or industrial decomplexation of lignin, vast amounts of structurally diverse 3-phenylpropanoids enter terrestrial and aquatic habitats, where they serve as substrates for microbial degradation. This raises the question of what signaling systems environmental bacteria employ to detect these nutritionally attractive compounds and to adjust their catabolism accordingly. Moreover, determining in vivo response thresholds of an anaerobic degradation specialist such as A. aromaticum EbN1^T for these aromatic compounds provides insights into the environmental fate of the latter, i.e., when they could escape biodegradation due to too low ambient concentrations.

Coelimycin Synthesis Activatory Proteins Are Key Regulators of Specialized Metabolism and Precursor Flux in Streptomyces coelicolor A3(2)

Many microbial specialized metabolites are industrially relevant agents but also serve as signaling molecules in intra-species and even inter-kingdom interactions. In the antibiotic-producing Streptomyces, members of the SARP (Streptomyces antibiotic regulatory proteins) family of regulators are often encoded within biosynthetic gene clusters and serve as their direct activators. Coelimycin is the earliest, colored specialized metabolite synthesized in the life cycle of the model organism Streptomyces coelicolor A3(2). Deletion of its two SARP activators cpkO and cpkN abolished coelimycin synthesis and resulted in dramatic changes in the production of the later, stationary-phase antibiotics. The underlying mechanisms of these phenotypes were deregulation of precursor flux and quorum sensing, as shown by label-free, bottom-up shotgun proteomics. Detailed profiling of promoter activities demonstrated that CpkO is the upper-level cluster activator that induces CpkN, while CpkN activates type II thioesterase ScoT, necessary for coelimycin synthesis. What is more, we show that cpkN is regulated by quorum sensing gamma-butyrolactone receptor ScbR.

Regulatory Control of Rishirilide(s) Biosynthesis in Streptomyces bottropensis

Streptomycetes are well-known producers of numerous bioactive secondary metabolites widely used in medicine, agriculture, and veterinary. Usually, their genomes encode 20-30 clusters for the biosynthesis of natural products. Generally, the onset and production of these compounds are tightly coordinated at multiple regulatory levels, including cluster-situated transcriptional factors. Rishirilides are biologically active type II polyketides produced by Streptomyces bottropensis. The complex regulation of rishirilides biosynthesis includes the interplay of four regulatory proteins encoded by the rsl-gene cluster: three SARP family regulators (RslR1-R3) and one MarR-type transcriptional factor (RslR4). In this work, employing gene deletion and overexpression experiments we revealed RslR1-R3 to be positive regulators of the biosynthetic pathway. Additionally, transcriptional analysis indicated that rslR2 is regulated by RslR1 and RslR3. Furthermore, RslR3 directly activates the transcription of rslR2, which stems from binding of RslR3 to the rslR2 promoter. Genetic and biochemical analyses demonstrated that RslR4 represses the transcription of the MFS transporter rslT4 and of its own gene. Moreover, DNA-binding affinity of RslR4 is strictly controlled by specific interaction with rishirilides and some of their biosynthetic precursors. Altogether, our findings revealed the intricate regulatory network of teamworking cluster-situated regulators governing the biosynthesis of rishirilides and strain self-immunity.

CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)-uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882-ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR-uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

Evolution and stabilization of environmental persistent free radicals during the decomposition of lignin by laccase

Soil microbial enzymes may induce lignin decomposition, accompanied by generation of free radicals. The evolution of environmentally persistent free radicals (EPFRs) and reactive oxygen species (ROS) during laccase-catalyzed lignin decomposition remains unclear. Characterization by electron paramagnetic resonance spectroscopy revealed gradually increased concentration of EPFRs, with maximum levels within 6 h that remained constant, accompanied by the increase in g-factor from 2.0037 to 2.0041. The results suggested the generation of oxygen-centered radicals on lignin. The EPFRs produced on solid samples slowly decreased by 17.2% over 17 d. ROS were also detected to have a similar trend as that of the evolution of EPFRs. Scanning electron microscopy, attenuated total reflectance-Fourier transform infrared spectroscopy, gel permeation chromatography and nuclear magnetic resonance analyses suggested the demethylation and oxidation of lignin. We clarify the biogeochemical transformation of lignin and potential contributions to the generation of EPFRs and ROS in soil.

A putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance

Mutations in rrn encoding ribosomal RNA (rRNA) and rRNA modification often confer resistance to ribosome-targeting antibiotics by altering the site of their interaction with the small (30S) and large (50S) subunits of the bacterial ribosome. The highly conserved central loop of domain V of 23S rRNA (nucleotides 2042-2628 in Escherichia coli; the exact position varies by species) of the 50S subunit, which is implicated in peptidyl transferase activity, is known to be important in macrolide interactions and resistance. In this study, we identified an A2302T mutation in the rrnA-23S rRNA gene and an A2281G mutation in the rrnC-23S rRNA gene that were responsible for resistance to erythromycin in the model actinomycete Streptomyces coelicolor A3(2) and its close relative Streptomyces lividans 66, respectively. Interestingly, genetic and phenotypic characterization of the erythromycin-resistant mutants indicated a possibility that under coexistence of the 23S rRNA mutation and mutations in other genes, S. coelicolor A3(2) and S. lividans 66 can produce abundant amounts of the pigmented antibiotics actinorhodin and undecylprodigiosin depending on the combinations of mutations. Herein, we report the unique phenomenon occurring by unexpected characteristics of the 23S rRNA mutations that can affect the emergence of additional mutations probably with an upswing in spontaneous mutations and enrichment in their variations in Streptomyces strains. Further, we discuss a putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance.

The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway

The outer potato periderm layer consists of dead suberized cells. Suberin, a protective biopolymer, is made of a polyaliphatic portion covalently linked to polyaromatic moieties. Evidence accumulates that Streptomyces scabies, the main causal agent of potato common scab, can degrade the suberin aliphatic part but its ability to degrade the aromatic portion has not been documented. This polyaromatic portion is mainly composed of cinnamic acids. In this study, two cinnamates (trans-ferulic or p-coumaric acids) were added to the culture medium of S. scabies strains EF-35 and 87.22. HPLC quantification revealed that both strains efficiently utilized these compounds. A proteomic study coupled with gene expression analysis led to the identification of putative catabolic pathways for cinnamates. Catabolism of both compounds appeared to occur via the β-ketoadipate pathway. Gene SCAB_15301, encoding for a putative vanillate monooxygenase, was partly deleted from S. scabies strain 87.22 genome. The mutant retained its ability to catabolize trans-ferulic acid into vanillate but lost its ability to further degrade the latter compound. When the wild-type mutant and complemented strains were grown in the presence of suberin-enriched potato periderm, accumulation of vanillic acid was observed only in the mutant culture medium. This work presents evidence that S. scabies can degrade not only the aliphatic part of suberin but also the constituents of suberin aromatic portion. This may provide ecological and pathological advantages to S. scabies as a saprophyte and pathogen.

Directed evolution of the PcaV allosteric transcription factor to generate a biosensor for aromatic aldehydes

Background

Transcription factor-based biosensors are useful tools for the detection of metabolites and industrially valuable molecules, and present many potential applications in biotechnology and biomedicine. However, the most common approach to develop biosensors relies on employing a limited set of naturally occurring allosteric transcription factors (aTFs). Therefore, altering the ligand specificity of aTFs towards the detection of new effectors is an important goal.

Results

Here, the PcaV repressor, a member of the MarR aTF family, was used to develop a biosensor for the detection of hydroxyl-substituted benzoic acids, including protocatechuic acid (PCA). The PCA biosensor was further subjected to directed evolution to alter its ligand specificity towards vanillin and other closely related aromatic aldehydes, to generate the Van2 biosensor. Ligand recognition of Van2 was explored in vitro using a range of biochemical and biophysical analyses, and extensive in vivo genetic-phenotypic analysis was performed to determine the role of each amino acid change upon biosensor performance.

Conclusions

This is the first study to report directed evolution of a member of the MarR aTF family, and demonstrates the plasticity of the PCA biosensor by altering its ligand specificity to generate a biosensor for aromatic aldehydes.

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

Lignin depolymerization and utilization by bacteria

Lignin compound wastes are generated as a result of agricultural and industrial practices. Microorganism-mediated bio-catalytic processes can depolymerize and utilize lignin eco-friendly. Although fungi have been studied since several decades for their ability to depolymerize lignin, strict growth conditions of fungus limit it's industrial application. Compared with fungi, bacteria can tolerate wider pH, temperature, oxygen ranges and are easy to manipulate. Several studies have focused on bacteria involved in the process of lignin depolymerization and utilization. Pseudomonas have been used for paper mill wastewater treatment while Rhodococcus are widely reported to accumulate lipid. In this review, the recent studies on bacterial utilization in paper wastewater treatment, lignin conversion to biofuels, bioplastic, biofertilizers and other value-added chemicals are summarized. As bacteria possess remarkable advantages in industrial production, they may play a promising role in the future commercial lignin utilization.

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures

Bacterial antibiotic resistance is a worldwide health problem that deserves important research attention in order to develop new therapeutic strategies. Recently, the World Health Organization (WHO) classified Pseudomonas aeruginosa as one of the priority bacteria for which new antibiotics are urgently needed. In this opportunistic pathogen, antibiotics efflux is one of the most prevalent mechanisms where the drug is efficiently expulsed through the cell-wall. This resistance mechanism is highly correlated to the expression level of efflux pumps of the resistance-nodulation-cell division (RND) family, which is finely tuned by gene regulators. Thus, it is worthwhile considering the efflux pump regulators of P. aeruginosa as promising therapeutical targets alternative. Several families of regulators have been identified, including activators and repressors that control the genetic expression of the pumps in response to an extracellular signal, such as the presence of the antibiotic or other environmental modifications. In this review, based on different crystallographic structures solved from archetypal bacteria, we will first focus on the molecular mechanism of the regulator families involved in the RND efflux pump expression in P. aeruginosa, which are TetR, LysR, MarR, AraC, and the two-components system (TCS). Finally, the regulators of known structure from P. aeruginosa will be presented.

A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor

In Streptomyces coelicolor, we identified a para-hydroxybenzoate (PHB) hydroxylase, encoded by gene pobA (SCO3084), which is responsible for conversion of PHB into PCA (protocatechuic acid), a substrate of the β-ketoadipate pathway which yields intermediates of the Krebs cycle. We also found that the transcription of pobA is induced by PHB and is negatively regulated by the product of SCO3209, which we named PobR. The product of this gene is highly unusual in that it is the apparent fusion of two IclR family transcription factors. Bioinformatic analyses, in vivo transcriptional assays, electrophoretic mobility shift assays (EMSAs), DNase I footprinting, and isothermal calorimetry (ITC) were used to elucidate the regulatory mechanism of PobR. We found that PobR loses its high affinity for DNA (i.e., the pobA operator) in the presence of PHB, the inducer of pobA transcription. PHB binds to PobR with a KD of 5.8 μM. Size-exclusion chromatography revealed that PobR is a dimer in the absence of PHB and a monomer in the presence of PHB. The crystal structure of PobR in complex with PHB showed that only one of the two IclR ligand binding domains was occupied, and defined how the N-terminal ligand binding domain engages the effector ligand.

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.

A valuable peroxidase activity from the novel species Nonomuraea gerenzanensis growing on alkali lignin

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Actinomycetes represent an attractive source of ligninolytic enzymes.

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43 actinomycetes were screened for laccase and peroxidase activities.

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The novel species N. gerenzanensis produces a valuable bacterial peroxidase activity.

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The dye-decolorizing activity paves the way for an industrial use of this peroxidase.

Degradation of lignin constitutes a key step in processing biomass to become useful monomers but it remains challenging. Compared to fungi, bacteria are much less characterized with respect to their lignin metabolism, although it is reported that many soil bacteria, especially actinomycetes, attack and solubilize lignin. In this work, we screened 43 filamentous actinomycetes by assaying their activity on chemically different substrates including a soluble and semi-degraded lignin derivative (known as alkali lignin or Kraft lignin), and we discovered a novel and valuable peroxidase activity produced by the recently classified actinomycete Nonomuraea gerenzanensis. Compared to known fungal manganese and versatile peroxidases, the stability of N. gerenzanensis peroxidase activity at alkaline pHs and its thermostability are significantly higher. From a kinetic point of view, N. gerenzanensis peroxidase activity shows a K_m for H₂O₂ similar to that of Phanerochaete chrysosporium and Bjerkandera enzymes and a lower affinity for Mn²⁺, whereas it differs from the six Pleurotus ostreatus manganese peroxidase isoenzymes described in the literature. Additionally, N. gerenzanensis peroxidase shows a remarkable dye-decolorizing activity that expands its substrate range and paves the way for an industrial use of this enzyme. These results confirm that by exploring new bacterial diversity, we may be able to discover and exploit alternative biological tools putatively involved in lignin modification and degradation.

Microbial utilization of lignin: available biotechnologies for its degradation and valorization

Lignocellulosic biomasses, either from non-edible plants or from agricultural residues, stock biomacromolecules that can be processed to produce both energy and bioproducts. Therefore, they become major candidates to replace petroleum as the main source of energy. However, to shift the fossil-based economy to a bio-based one, it is imperative to develop robust biotechnologies to efficiently convert lignocellulosic streams in power and platform chemicals. Although most of the biomass processing facilities use celluloses and hemicelluloses to produce bioethanol and paper, there is no consolidated bioprocess to produce valuable compounds out of lignin at industrial scale available currently. Usually, lignin is burned to provide heat or it remains as a by-product in different streams, thus arising environmental concerns. In this way, the biorefinery concept is not extended to completion. Due to Nature offers an arsenal of biotechnological tools through microorganisms to accomplish lignin valorization or degradation, an increasing number of projects dealing with these tasks have been described recently. In this review, outstanding reports over the last 6 years are described, comprising the microbial utilization of lignin to produce a variety of valuable compounds as well as to diminish its ecological impact. Furthermore, perspectives on these topics are given.

Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts

Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.

How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator

Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Å resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. The current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.

Cloning, expression, crystallization and crystallographic analysis of CouR from Rhodopseudomonas palustris

CouR from Rhodopseudomonas palustris is a member of the MarR transcriptional regulator family. It regulates the expression of CouA and CouB, enzymes that are involved in the degradation of p-coumarate. In vivo, CouR binds to a DNA fragment containing the couAB promoter and suppresses the expression of CouA and CouB, while binding of p-coumaroyl-CoA attenuates its affinity towards DNA and activates the expression of CouA and CouB. Here, the crystallization and X-ray diffraction analyses of CouR alone and in complex with p-coumaroyl-CoA are reported. Apo and ligand-complexed CouR crystals diffracted to 2.5 and 3.3 Å resolution, respectively. The crystals of apo CouR belonged to space group P22121, with unit-cell parameters a = 62.78, b = 76.15, c = 87.38 Å, whereas the crystals of the CouR-ligand complex belonged to space group P212121, with unit-cell parameters a = 61.37, b = 69.82, c = 70.32 Å. The crystals were predicted to contain two CouR molecules or CouR-ligand complexes per asymmetric unit.

An overview on transcriptional regulators in Streptomyces

Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.

The regulatory role of Streptomyces coelicolor TamR in central metabolism

Trans-aconitate methyltransferase regulator (TamR) is a member of the ligand-responsive multiple antibiotic resistance regulator (MarR) family of transcription factors. In Streptomyces coelicolor, TamR regulates transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase) and sacA (encoding aconitase); up-regulation of these genes promotes metabolic flux through the citric acid cycle. DNA binding by TamR is attenuated and transcriptional derepression is achieved on binding of ligands such as citrate and trans-aconitate to TamR. In the present study, we show that three additional genes are regulated by S. coelicolor TamR. Genes encoding malate synthase (aceB1; SCO6243), malate dehydrogenase (mdh; SCO4827) and isocitrate dehydrogenase (idh; SCO7000) are up-regulated in vivo when citrate and trans-aconitate accumulate, and TamR binds the corresponding gene promoters in vitro, a DNA binding that is attenuated by cognate ligands. Mutations to the TamR binding site attenuate DNA binding in vitro and result in constitutive promoter activity in vivo. The predicted TamR binding sites are highly conserved in the promoters of these genes in Streptomyces species that encode divergent tam-tamR gene pairs, suggesting evolutionary conservation. Like aconitase and trans-aconitate methyltransferase, malate dehydrogenase, isocitrate dehydrogenase and malate synthase are closely related to the citric acid cycle, either catalysing individual reaction steps or, in the case of malate synthase, participating in the glyoxylate cycle to produce malate that enters the citric acid cycle to replenish the intermediate pool. Taken together, our data suggest that TamR plays an important and conserved role in promoting metabolic flux through the citric acid cycle.

Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene

The past decade has witnessed a large influx of research toward the creation of sustainable, biologically derived fuels. While significant effort has been exerted to improve production capacity in common hosts, such as Escherichia coli or Saccharomyces cerevisiae, studies concerning alternate microbes comparatively lag. In an effort to expand the breadth of characterized hosts for fuel production, we map the terpene biosynthetic pathway in a model actinobacterium, Streptomyces venezuelae, and further alter secondary metabolism to afford the advanced biofuel precursor bisabolene. Leveraging information gained from study of the native isoprenoid pathway, we were able to increase bisabolene titer nearly 5-fold over the base production strain, more than 2 orders of magnitude greater than the combined terpene yield in the wild-type host. We also explored production on carbon sources of varying complexity to, notably, define this host as one able to perform consolidated bioprocessing.

BadR and BadM Proteins Transcriptionally Regulate Two Operons Needed for Anaerobic Benzoate Degradation by Rhodopseudomonas palustris

The bacterium Rhodopseudomonas palustris grows with the aromatic acid benzoate and the alicyclic acid cyclohexanecarboxylate (CHC) as sole carbon sources. The enzymatic steps in an oxygen-independent pathway for CHC degradation have been elucidated, but it was unknown how the CHC operon (badHI aliAB badK) encoding the enzymes for CHC degradation was regulated. aliA and aliB encode enzymes for the conversion of CHC to cyclohex-1-enecarboxyl-coenzyme A (CHene-CoA). At this point, the pathway for CHC degradation merges with the pathway for anaerobic benzoate degradation, as CHene-CoA is an intermediate in both degradation pathways. Three enzymes, encoded by badK, badH, and badI, prepare and cleave the alicyclic ring of CHene-CoA to yield pimelyl-CoA. Here, we show that the MarR transcription factor family member, BadR, represses transcription of the CHC operon by binding near the transcription start site of badH. 2-Ketocyclohexane-1-carboxyl-CoA, an intermediate of CHC and benzoate degradation, interacts with BadR to abrogate repression. We also present evidence that the transcription factor BadM binds to the promoter of the badDEFGAB (Bad) operon for the anaerobic conversion of benzoate to CHene-CoA to repress its expression. Contrary to previous reports, BadR does not appear to control expression of the Bad operon. These data enhance our view of the transcriptional regulation of anaerobic benzoate degradation by R. palustris.

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.

Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.

Ligand-binding pocket bridges DNA-binding and dimerization domains of the urate-responsive MarR homologue MftR from Burkholderia thailandensis

Members of the multiple antibiotic resistance regulator (MarR) family often regulate gene activity by responding to a specific ligand. In the absence of ligand, most MarR proteins function as repressors, while ligand binding causes attenuated DNA binding and therefore increased gene expression. Previously, we have shown that urate is a ligand for MftR (major facilitator transport regulator), which is encoded by the soil bacterium Burkholderia thailandensis. We show here that both mftR and the divergently oriented gene mftP encoding a major facilitator transport protein are upregulated in the presence of urate. MftR binds two cognate sites in the mftR-mftP intergenic region with equivalent affinity and sensitivity to urate. Mutagenesis of four conserved residues previously reported to be involved in urate binding to Deinococcus radiodurans HucR and Rhizobium radiobacter PecS significantly reduced protein stability and DNA binding affinity but not ligand binding. These data suggest that residues equivalent to those implicated in ligand binding to HucR and PecS serve structural roles and that MftR relies on distinct residues for ligand binding. MftR exhibits a two-step melting transition suggesting independent unfolding of the dimerization and DNA-binding regions; urate binding or mutations in the predicted ligand-binding sites result in one-step unfolding transitions. We suggest that MftR binds the ligand in a cleft between the DNA-binding lobes and the dimer interface but that the mechanism of ligand-mediated attenuation of DNA binding differs from that proposed for other urate-responsive MarR homologues. Since DNA binding by MftR is attenuated at 37 °C, our data also suggest that MftR responds to both ligand and a thermal upshift by attenuated DNA binding and upregulation of the genes under its control.

Poly R decolorization and APPL production by Streptomyces violaceoruber and Streptomyces spiroverticillatus

Two mesophilic streptomycetes (S. violaceoruber and S. spiroverticillatus) were selected to study their Poly R-478 decolorization ability and lignocellulose solubilizing activity. Both strains were able to degrade Poly R-478 dye and ferulic acid during growth on a minimal salts medium. The Poly R-478 decolorizing activities of both strains were induced by adding different carbon sources to the culture media. S. violaceoruber could decolorize 63% of Poly R-478 after 24 h. Both strains could solubilize straw and produce acid-precipitable polymeric lignin (APPL) with different efficiency. From the major extracellular enzymes recovery of both strains on rice and wheat straw, we can predicate that the biodegradation process was partial indicating a possible utilization in biological delignification.

Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete

We announce the availability of the genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a plant biomass-degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized component of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.

Study of PcaV from Streptomyces coelicolor yields new insights into ligand-responsive MarR family transcription factors

MarR family proteins constitute a group of >12 000 transcriptional regulators encoded in bacterial and archaeal genomes that control gene expression in metabolism, stress responses, virulence and multi-drug resistance. There is much interest in defining the molecular mechanism by which ligand binding attenuates the DNA-binding activities of these proteins. Here, we describe how PcaV, a MarR family regulator in Streptomyces coelicolor, controls transcription of genes encoding β-ketoadipate pathway enzymes through its interaction with the pathway substrate, protocatechuate. This transcriptional repressor is the only MarR protein known to regulate this essential pathway for aromatic catabolism. In in vitro assays, protocatechuate and other phenolic compounds disrupt the PcaV-DNA complex. We show that PcaV binds protocatechuate in a 1:1 stoichiometry with the highest affinity of any MarR family member. Moreover, we report structures of PcaV in its apo form and in complex with protocatechuate. We identify an arginine residue that is critical for ligand coordination and demonstrate that it is also required for binding DNA. We propose that interaction of ligand with this arginine residue dictates conformational changes that modulate DNA binding. Our results provide new insights into the molecular mechanism by which ligands attenuate DNA binding in this large family of transcription factors.

Pretreatment of yellow pine in an acidic ionic liquid: extraction of hemicellulose and lignin to facilitate enzymatic digestion

The acidic ionic liquid 1-H-3-methylimidazolium chloride can effectively pretreat yellow pine wood chips under mild conditions for enzymatic saccharification. Wood samples were treated at temperatures between 110 and 150°C for up to 5 h in the ionic liquid and three fractions collected; a cellulose rich fraction, lignin, and an aqueous fraction. This treatment caused the hemicellulose and the lignin to be degraded and dissolved from the cell walls of the pine wood. The lignin was depolymerized and subsequently dissolved in the ionic liquid. This process occurred more quickly at higher temperatures, although at the highest temperatures tested, significant cellulose degradation also occurred. The cellulose rich fraction was saccharified using cellulase from Trichoderma viride, with longer pretreatment times at 130°C resulting in higher glucose yields.

Transcriptomic study for screening genes involved in the oxidative bioconversions of Streptomyces avermitilis

Streptomyces avermitilis is a well known organism producing avermectin antibiotics, and has been utilized as an industrial host for oxidation bioconversion processes. Recently, gene screening strategies related to bioconversions have received much focus, as attempts are made to optimize oxidation and biodegradation pathways to maximize yield and productivity. Here, we have demonstrated the oxidative metabolisms of three molecules, daidzein, p-coumaric acid and mevastatin, where S. avermitilis converted each substrate to 3',4',7-trihydroxyisoflavone, caffeic acid and hydroxyl-mevastatin to yield 9.3, 32.5 and 15.0 %, respectively. Microarray technology was exploited to investigate genome-wide analysis of gene expression changes, which were induced upon the addition of each substrate. Cytochrome P450 hydroxylases (pteC, cyp28 and olmB), diooxygenases (xylE, cdo1 and putatives) and LuxAB-like oxygenase were identified. One of them, cyp28, was indeed a gene encoding P450 hydroxylase responsible for the oxidative reaction of daidzein. Furthermore, possible electron transfer chain (fdrC → pteE → pteC) supporting cytochrome P450 dependent hydroxylation of daidzein has been suggested based on the interpretation of expression profiles. The result provided a potential application of transcriptomic study on uncovering enzymes involved in oxidative bioconversions of S. avermitilis.

The transcriptional regulator TamR from Streptomyces coelicolor controls a key step in central metabolism during oxidative stress

Multiple antibiotic resistance regulator (MarR) family transcriptional regulators usually regulate gene activity by responding to specific ligands. Here we show that TamR (trans-aconitate methyltransferase regulator), a MarR homologue from Streptomyces coelicolor, functions in oxidative stress responses to regulate a key step in central metabolism. The gene encoding TamR is oriented divergently from the tam gene, which encodes trans-aconitate methyltransferase. Trans-aconitate methyltransferase methylates trans-aconitate, which is formed when cis-aconitate is released during aconitase-mediated isomerization of citrate to isocitrate; trans-aconitate, but not its methyl ester, is a potent inhibitor of aconitase. We show that TamR binds with high affinity to the intergenic region between the tamR and tam genes. Notably, trans-aconitate attenuates DNA-binding by TamR, as do citrate, cis-aconitate and isocitrate, which are the substrate, intermediate and product of aconitase respectively. In vivo, hydrogen peroxide and citrate induce significant upregulation of the tam (SCO3132), tamR (SCO3133) and aconitase (SCO5999) genes. Since oxidative stress leads to disassembly of the [4Fe-4S] cluster that is essential for aconitase activity, resulting in accumulation of citrate and release of cis-aconitate and its subsequent conversion to trans-aconitate, we propose that TamR mediates a novel regulatory function in which the inhibitory effects of trans-aconitate and accumulated citrate are alleviated.

Depolymerization of oak wood lignin under mild conditions using the acidic ionic liquid 1-H-3-methylimidazolium chloride as both solvent and catalyst

Oak wood lignin, which was separated from the wood using dissolution in the ionic liquid 1-methyl-3-ethylimidazolium acetate and subsequent precipitation, was successfully depolymerized in the acidic ionic liquid 1-H-3-methylimidazolium chloride under mild conditions (110-150 °C). Based on gel permeation chromatography results, an increase in temperature from 110 to 150 °C increased the rate of reaction, but did not significantly change the final size of the lignin fragments. Nuclear magnetic resonance and infrared spectroscopy were utilized to demonstrate that the depolymerization proceeded via a hydrolysis reaction that cleaved the alkyl-aryl ether linkages. Coupling of the lignin fragments was also shown to occur in the reaction mixture. These hydrolysis results are consistent with the literature on acid catalyzed depolymerization of lignin in conventional solvents and with recent model compound studies involving guaiacylglycerol-β-guaiacyl ether and veratrylglycerol-β-guaiacyl ether done in acidic ionic liquids.

Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A

The phenylpropanoid p-coumarate and structurally related aromatic compounds are produced in large amounts by green plants and are excellent carbon sources for many soil bacteria. Aerobic bacteria remove the acyl side chain from phenylpropanoids to leave an aromatic aldehyde, which then enters one of several possible central pathways of benzene ring degradation. We investigated the pathway for the anaerobic degradation of p-coumarate by the phototrophic bacterium Rhodopseudomonas palustris and found that it also follows this metabolic logic. We characterized enzymes for the conversion of p-coumarate to p-hydroxybenzaldehyde and acetyl coenzyme A (acetyl-CoA) encoded by the couAB operon. We also identified a MarR family transcriptional regulator that we named CouR. A couR mutant had elevated couAB expression. In addition, His-tagged CouR bound with high affinity to a DNA fragment encompassing the couAB promoter region, and binding was abrogated by the addition of nanomolar quantities of p-coumaroyl-CoA but not by p-coumarate. Footprinting demonstrated binding of CouR to an inverted repeat sequence that overlaps the -10 region of the couAB promoter. Our results provide evidence for binding of a CoA-modified aromatic compound by a MarR family member. Although the MarR family is widely distributed in bacteria and archaea and includes over 12,000 members, ligands have been identified for relatively few family members. Here we provide biochemical evidence for a new category of MarR ligand.

Bioconversion of lignin model compounds with oleaginous Rhodococci

Although economically efficient biomass conversion depends on the utilization of the complete cell wall (biorefinery concept), including polysaccharides and lignin, current biofuels research concentrate mostly on cellulose conversion, while lignin is viewed as a side-product that is used primarily as a thermal resource. Microbiological conversion of lignin is almost exclusive to fungi, usually resulting in increased cell mass and lignolytic enzymes. Some bacteria can also degrade lignin-related compounds using the β-ketoadipate pathway; for example, Rhodococcus opacus DSM 1069 can degrade coniferyl alcohol and grow on it as sole carbon source. Moreover, this strain belongs to the actinomycetes group that is also known for oleaginous species with lipid accumulation over 20%. Present work shows that R. opacus DSM 1069 and PD630 strains under nitrogen limiting conditions can convert lignin model compounds into triacylglycerols, also known as neutral lipids. 4-Hydroxybenzoic and vanillic acid lignin model compounds were used as sole carbon sources, and after brief adaptation periods, the cells not only began growing but accumulated lipids to the level of oleaginicity. These lipids were extracted for transesterification and analysis of fatty acid methyl esters showed good composition for biodiesel applications with no aromatics. Furthermore, the two strains showed distinct substrate metabolism and product profiles.

Cleaving the β--O--4 bonds of lignin model compounds in an acidic ionic liquid, 1-H-3-methylimidazolium chloride: an optional strategy for the degradation of lignin

The hydrolysis of β--O--4 bonds in two lignin model compounds was studied in an acidic ionic liquid, 1-H-3-methylimidazolium chloride. The β--O--4 bonds of both guaiacylglycerol-β-guaiacyl ether and veratrylglycerol-β-guaiacyl ether underwent catalytic hydrolysis to produce guaiacol as the primary product with more than 70 % yield at 150 °C. Up to 32 wt % substrate concentration could be treated in the system without a decrease in guaiacol production. The ionic liquid could be reused without loss of activity in guaiacol production from both guaiacylglycerol-β-guaiacyl ether and veratrylglycerol-β-guaiacyl ether. A possible mechanism accounting for the guaiacol production is presented.

Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators

Bacteria and archaea encode members of the large multiple antibiotic resistance regulator (MarR) family of transcriptional regulators. Generally, MarR homologs regulate activity of genes involved in antibiotic resistance, stress responses, virulence or catabolism of aromatic compounds. They constitute a diverse group of transcriptional regulators that includes both repressors and activators, and the conventional mode of regulation entails a genetic locus in which the MarR homolog and a gene under its regulation are encoded divergently; binding of the MarR homolog to the intergenic region typically represses transcription of both genes, while binding of a specific ligand to the transcription factor results in attenuated DNA binding and hence activated gene expression. For many homologs, the natural ligand is unknown. Crystal structures reveal a common architecture with a characteristic winged helix domain for DNA binding, and recent structural information of homologs solved both in the absence and presence of their respective ligands, as well as biochemical data, is finally converging to illuminate the mechanisms by which ligand-binding causes attenuated DNA binding. As MarR homologs regulate pathways that are critical to bacterial physiology, including virulence, a molecular understanding of mechanisms by which ligands affect a regulation of gene activity is essential. Specifying the position of ligand-binding pockets further has the potential to aid in identifying the ligands for MarR homologs for which the ligand remains unknown.