Metabolism of Lignin Model Compounds of the Arylglycerol-β-Aryl Ether Type by Pseudomonas acidovorans D 3

Identification of the two-component guaiacol demethylase system from Rhodococcus rhodochrous and expression in Pseudomonas putida EM42 for guaiacol assimilation

A diversity of softwood lignin depolymerization processes yield guaiacol as the main low molecular weight product. This key aromatic compound can be utilized as a carbon source by several microbial species, most of which are Gram positive bacteria. Microbial degradation of guaiacol is known to proceed initially via demethylation to catechol, and this reaction is catalyzed by cytochrome P450 monooxygenases. These enzymes typically require a set of redox partner proteins, whose number and identities were not described until very recently in the case of guaiacol. In this work we identified two proteins involved in guaiacol demethylation by the actinomycete Rhodococcus rhodochrous. Additionally, we constructed four different polycistronic operons carrying combinations of putative redox partners of this guaiacol demethylation system in an inducible expression plasmid that was introduced into the Gram negative host Pseudomonas putida EM42, and the guaiacol consumption dynamics of each resulting strain were analyzed. All the polycistronic operons, expressing a cytochrome P450 together with a putative ferredoxin reductase from R. rhodochrous and putative ferredoxins from R. rhodochrous or Amycolatopsis ATCC 39116 enabled P. putida EM42 to metabolize and grow on guaiacol as the sole carbon source.

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGST_Nu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans We solved the crystal structure of NaGST_Nu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr⁵¹, Tyr¹⁶⁶, and Tyr²²⁴) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases.

Carbon Sources for Polyhydroxyalkanoates and an Integrated Biorefinery

Polyhydroxyalkanoates (PHAs) are a group of bioplastics that have a wide range of applications. Extensive progress has been made in our understanding of PHAs’ biosynthesis, and currently, it is possible to engineer bacterial strains to produce PHAs with desired properties. The substrates for the fermentative production of PHAs are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. This paper gives an overview of the current carbon sources used for PHA production and the methods used to transform these sources into fermentable forms. This allows us to identify the opportunities and restraints linked to future sustainable PHA production. Hemicellulose hydrolysates and crude glycerol are identified as two promising carbon sources for a sustainable production of PHAs. Hemicellulose hydrolysates and crude glycerol can be produced on a large scale during various second generation biofuels’ production. An integration of PHA production within a modern biorefinery is therefore proposed to produce biofuels and bioplastics simultaneously. This will create the potential to offset the production cost of biofuels and reduce the overall production cost of PHAs.

Formation of Guaiacol by Spoilage Bacteria from Vanillic Acid, a Product of Rice Koji Cultivation, in Japanese Sake Brewing

The formation of guaiacol, a potent phenolic off-odor compound in the Japanese sake brewing process, was investigated. Eight rice koji samples were analyzed, and one contained guaiacol and 4-vinylguaiacol (4-VG) at extraordinarily high levels: 374 and 2433 μg/kg dry mass koji, respectively. All samples contained ferulic and vanillic acids at concentrations of mg/kg dry mass koji. Guaiacol forming microorganisms were isolated from four rice koji samples. They were identified as Bacillus subtilis, B. amyloliquefaciens/subtilis, and Staphylococcus gallinarum using 16S rRNA gene sequence. These spoilage bacteria convert vanillic acid to guaiacol and ferulic acid to 4-VG. However, they convert very little ferulic acid or 4-VG to guaiacol. Nine strains of koji fungi tested produced vanillic acid at the mg/kg dry mass koji level after cultivation. These results indicated that spoilage bacteria form guaiacol from vanillic acid, which is a product of koji cultivation in the sake brewing process.

Phylogenetic and kinetic characterization of a suite of dehydrogenases from a newly isolated bacterium, strain SG61-1L, that catalyze the turnover of guaiacylglycerol-β-guaiacyl ether stereoisomers

Lignin is a complex aromatic polymer found in plant cell walls that makes up 15 to 40% of plant biomass. The degradation of lignin substructures by bacteria is of emerging interest because it could provide renewable alternative feedstocks and intermediates for chemical manufacturing industries. We have isolated a bacterium, strain SG61-1L, that rapidly degrades all of the stereoisomers of one lignin substructure, guaiacylglycerol-β-guaiacyl ether (GGE), which contains a key β-O-4 linkage found in most intermonomer linkages in lignin. In an effort to understand the rapid degradation of GGE by this bacterium, we heterologously expressed and kinetically characterized a suite of dehydrogenase candidates for the first known step of GGE degradation. We identified a clade of active GGE dehydrogenases and also several other dehydrogenases outside this clade that were all able to oxidize GGE. Several candidates exhibited stereoselectivity toward the GGE stereoisomers, while others had higher levels of catalytic performance than previously described GGE dehydrogenases for all four stereoisomers, indicating a variety of potential applications for these enzymes in the manufacture of lignin-derived commodities.

Pathways for degradation of lignin in bacteria and fungi

Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.

Alicyclobacillusspp. in the Fruit Juice Industry: History, Characteristics, and Current Isolation/Detection Procedures

The first Alicyclobacillus spp. was isolated in 1982, and was originally thought to be strictly limited to thermophilic and acidic environments. Two years later, another Alicyclobacillus sp., A. acidoterrestris, was identified as the causative agent in spoilage of commercially pasteurized apple juice. Subsequent studies soon found that Alicyclobacillus spp. are soilborne bacteria, and do not strictly require thermophilic and acidic environments. Alicyclobacillus spp. posess several distinct characteristics; the major one is their ability to survive commercial pasteurization processes and produce off-flavors in fruit juices. The fruit juice industry has acknowledged Alicyclobacillus spp. as a major quality control target microorganism. Guaiacol and halophenols were identified as the offensive smelling agent in many Alicyclobacillus spp. related spoilage. Though the exact formation pathway of these off-flavors by Alicyclobacillus spp. are not yet identified, studies report that the presence of Alicyclobacillus spp. in the medium may be a major contributor to the formation of these off-flavors. Many identification methods and isolation media were developed in the last two decades. However, most of these methods were developed specifically for A. acidoterrestris, which was the first identified off-flavor producing Alicyclobacillus. However, recent studies indicate that other species of Alicyclobacillus may also produce guaiacol or the halophenols. In this respect, all Alicyclobacillus spp. should be monitored as potential spoilage bacteria in fruit juices. This article includes an overall review of the history of Alicyclobacillus spp., characteristics, suggested off-flavor production pathways, and commonly used identification methods for the currently identified Alicyclobacillus spp.

Biodegradation of kraft-lignin by Bacillus sp. isolated from sludge of pulp and paper mill

Eight bacterial strains were isolated on kraft lignin (KL) containing mineral salt medium (L-MSM) agar with glucose and peptone from the sludge of pulp and paper mill. Out of these, ITRC-S8 was selected for KL degradation, because of its fast growth at highest tested KL concentration and use of various lignin-related low molecular weight aromatic compounds (LMWACs) as sole source of carbon and energy. The bacterium was identified by biochemical tests as Gram-positive, rod-shaped and non-motile. Subsequent 16S rRNA gene sequencing showed 95% base sequence homology and it was identified as Bacillus sp. In batch experiments, a decrease in pH was observed initially followed by an increase till it reached an alkaline pH, which did not alter the culture growth significantly. The bacterium reduced the colour and KL content of 500 mg l(-1 )KL in MSM, in the presence of glucose and peptone, at pH 7.6, temperature 30 degrees C, agitation of 120 rpm and 6 days of incubation by 65 and 37% respectively. Significant reduction in colour and KL content in subsequent incubations is indicative of a co-metabolism mechanism, possibly due to initial utilization of added co-substrates for energy followed by utilization of KL as a co-metabolic. The degradation of KL by bacterium was confirmed by GC-MS analysis indicating formation of several LMWACs such as t-cinnamic acid, 3, 4, 5-trimethoxy benzaldehyde and ferulic acid as degradation products, which were not present in the control (uninoculated) sample. This favours the idea of biochemical modification of the KL polymer to a single monomer unit.

Determination of six bioactive components ofSaussurea katochaete by capillary electrophoresis

The simultaneous determination of 3,4-dimethoxy-3'-hydroxy propiophenone, 5-hydroxy-7-methoxy coumarin, 7-hydroxy coumarin, 3',5'-dimethoxy apigenin, apigenin and 4-hydroxy cinnamic acid in the extract of S. katochaete has been investigated by capillary electrophoresis for the first time. The six active components were completely separated within 10 min in 20 mM Na(2)HPO(4) buffer at pH 11.00 with 10% (v/v) methanol and detected at 214 nm. The applied voltage was 15 kV and the temperature was kept at 25 degrees C. The effects of buffer pH, the concentration of Na(2)HPO(4) and the concentration of methanol on the separation efficiency were studied systematically. The regression equations revealed good linear relationships (correlation coefficients were 0.9987-0.9998) between the peak area of each analyte and its concentration. The relative standard deviations (RSD) of migration time and peak areas were <1.63 and <4.03%, respectively. The application of this method for the separation and determination of the six bioactive components in S. katochaete was reported. The contents of the six analytes ranged from 0.023 to 0.131 mg/g and recoveries ranged from 94.7 to 104.8%.

Formation of guaiacol in chocolate milk by the psychrotrophic bacterium Rahnella aquatilis

AIMS

The aim of this study was to identify the causative agent of a smoky/phenolic taint in refrigerated full cream chocolate milk.

METHODS AND RESULTS

Microbiological examination of spoiled and unspoiled milk samples from the same processor showed high numbers of the psychrotrophic coliform Rahnella aquatilis in the spoiled samples only. Gas chromatography/mass spectrometry (GC/MS) was used to identify and quantify the taint compound as guaiacol (2-methoxyphenol) in the spoiled milk. Challenge studies in UHT chocolate and white milks inoculated with the isolate and incubated at 4-5 degrees C and 8-9 degrees C for 6 d showed the production of guaiacol in chocolate milk only, which was confirmed and quantified by GC/MS.

CONCLUSIONS

The results indicate that if present in refrigerated chocolate milk, Rah. aquatilis can produce guaiacol within the expected shelf-life of the product, even without temperature abuse.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that the coliform Rah. aquatilis can produce guaiacol in refrigerated chocolate milk products.

Bioavailability of Chlorocatechols in Naturally Contaminated Sediment Samples and of Chloroguaiacols Covalently Bound to C 2 -Guaiacyl Residues

Bacteria in anaerobic enrichment cultures that dechlorinated a range of chlorocatechols were used to examine the stability of endogenous chlorocatechols in a contaminated sediment sample and in interstitial water prepared from it. During incubation of the sediment sample for 450 days with or without added cells, there was a decrease in the concentration of solvent-extractable chlorocatechols but not in that of the total chlorocatechols, including sediment-associated components. In the presence of azide, the decrease in the concentrations of the former was eliminated or substantially decreased. Control experiments in which 3,4,5-trichlorocatechol was added to the sediment suspensions after 130 days showed that its dechlorination was accomplished not only by the added cells but also by the endemic microbial flora. It was concluded that the endogenous chlorocatechols in the sediment were not accessible to microorganisms with dechlorinating activity. On the other hand, microorganisms were apparently responsible for decreasing the solvent extractability of the chlorocatechols, and this effect decreased with increasing length of exposure time. Similar experiments carried out for 70 days with the sediment interstitial water showed that the chlorocatechols that were known to be associated with organic matter were also inaccessible to microbial dechlorination. Experiments with model compounds in which 4,5,6-trichloroguaiacol and tetrachloroguaiacol were covalently linked to C 2 -guaiacyl residues showed that these compounds were resistant to O demethylation or dechlorination during incubation with a culture having these activities. The only effect of microbial action was the quantitative reduction in 12 days of the C′1 keto group to an alcohol which was stable against further transformation for up to 65 days. The results of these experiments are consistent with the existence of chlorocatechols and chloroguaiacols in contaminated sediments and illustrate the cardinal significance of bioavailability in determining their recalcitrance to dechlorination and O demethylation, respectively. It is suggested that bioavailability is an important factor in determining the persistence of xenobiotics in natural ecosystems and that its omission represents a serious limitation in the interpretation of many laboratory experiments directed towards determining the persistence of xenobiotics in aquatic ecosystems.

Possible initial steps in the catabolism of 1,2-diphenylethanone (deoxybenzoin) by Pseudomonas fluorescens DB-5

A natural bacterial strain, identified as Pseudomonas fluorescens DB-5, was isolated in enrichment cultures containing 1,2-diphenylethanone as the only source of carbon and energy. On the basis of characteristic features observed in the mass spectra of degradation intermediates, it is proposed that metabolism of 1,2-diphenylethanone is initiated by two hydroxylations on the benzyl ring. Phenol, presumably arising from the benzoyl ring, was transiently detected as a catabolic intermediate.

Limited bacterial mineralization of fungal degradation intermediates from synthetic lignin

The ability of selected bacterial strains and consortia to mineralize degradation intermediates produced by Phanerochaete chrysosporium from 14C-labeled synthetic lignins was studied. Three different molecular weight fractions of the intermediates were subjected to the action of the bacteria, which had been grown on a lignin-related dimeric compound. Two consortia isolated from wood being decayed naturally by a Ganoderma species of white rot fungus (the palo podrido system) mineralized 10 to 11% of the fraction with a molecular weight of approximately 500 but less than 4% of the higher- and lower-molecular-weight fractions. The consortia mineralized 5 to 9% of the original lignins. The ability of two pseudomonads isolated earlier from lignin-rich environments to mineralize the original lignins or fungus degradation products was much lower.

Degradation and oligomerization of syringic acid by distinctive ecological groups of fungi

Forty-four terrestrial and aeroaquatic and aquatic fungi, including fifteen species causing white-rot, four species causing brown-rot, and some species causing soft-rot of wood, were tested for their ability to degrade the monomer syringic acid, which is released during decay of angiosperm lignin. None of the white- or brown-rot species caused any detectable degradation of syringic acid under the test conditions; however, six typical white-rot fungi strongly oligomerized syringic acid, both with and without cosubstrate. The main polymerization product was identified as a 1,3-dimethylpyrogallol oligomer by(13)C-NMR. Other minor metabolic products were methylated and hydroxylated derivatives. Oligomerization depended on the presence of 1 or 2 methoxy groups in ortho position to the hydroxy group of the substrate.Among the remaining fungi,Exophiala jeanselmei, Fusarium eumartii, andPaecilomyces variotii completely and rapidly degraded syringic acid (5 g/liter) within 48 to 100 hours. A further seven species were able to degrade syringic acid to some extent when glucose was added. Methylated and demethylated metabolic intermediates were identified by GC/MS.

Detection and localization of a new enzyme catalyzing the beta-aryl ether cleavage in the soil bacterium (Pseudomonas paucimobilis SYK-6)

Cleavage of the arylglycerol-beta-aryl ether linkage is the most important process in the biological degradation of lignin. We determined the activity of the enzyme cleaving the beta-aryl ether linkage in membranes of Pseudomonas paucimobilis SYK-6. This enzyme was tightly associated with the cellular membrane and catalyzed the unique and reductive cleavage of compound II but not cleavage of compound I. This enzymatic activity was stimulated by addition of NADH. On the basis of this evidence, we present a model of the specific cellular assimilation of beta-aryl ether by P. paucimobilis SYK-6.