A peroxisomal thioesterase plays auxiliary roles in plant β‐oxidative benzoic acid metabolism

Peroxisomal β‐oxidative degradation of compounds is a common metabolic process in eukaryotes. Reported benzoyl‐coenzyme A (BA‐CoA) thioesterase activity in peroxisomes from petunia flowers suggests that, like mammals and fungi, plants contain auxiliary enzymes mediating β‐oxidation. Here we report the identification of Petunia hybrida thioesterase 1 (PhTE1), which catalyzes the hydrolysis of aromatic acyl‐CoAs to their corresponding acids in peroxisomes. PhTE1 expression is spatially, developmentally and temporally regulated and exhibits a similar pattern to known benzenoid metabolic genes. PhTE1 activity is inhibited by free coenzyme A (CoA), indicating that PhTE1 is regulated by the peroxisomal CoA pool. PhTE1 downregulation in petunia flowers led to accumulation of BA‐CoA with increased production of benzylbenzoate and phenylethylbenzoate, two compounds which rely on the presence of BA‐CoA precursor in the cytoplasm, suggesting that acyl‐CoAs can be exported from peroxisomes. Furthermore, PhTE1 downregulation resulted in increased pools of cytoplasmic phenylpropanoid pathway intermediates, volatile phenylpropenes, lignin and anthocyanins. These results indicate that PhTE1 influences (i) intraperoxisomal acyl‐CoA/CoA levels needed to carry out β‐oxidation, (ii) efflux of β‐oxidative products, acyl‐CoAs and free acids, from peroxisomes, and (iii) flux distribution within the benzenoid/phenylpropanoid metabolic network. Thus, this demonstrates that plant thioesterases play multiple auxiliary roles in peroxisomal β‐oxidative metabolism.     

A dominant‐negative form of Arabidopsis AP‐3 β‐adaptin improves intracellular pH homeostasis

Intracellular pH (pH_i) is a crucial parameter in cellular physiology but its mechanisms of homeostasis are only partially understood. To uncover novel roles and participants of the pH_i regulatory system, we have screened an Arabidopsis mutant collection for resistance of seed germination to intracellular acidification induced by weak organic acids (acetic, propionic, sorbic). The phenotypes of one identified mutant, weak acid‐tolerant 1‐1D (wat1‐1D) are due to the expression of a truncated form of AP‐3 β‐adaptin (encoded by the PAT2 gene) that behaves as a as dominant‐negative. During acetic acid treatment the root epidermal cells of the mutant maintain a higher pH_i and a more depolarized plasma membrane electrical potential than wild‐type cells. Additional phenotypes of wat1‐1D roots include increased rates of acetate efflux, K⁺ uptake and H⁺ efflux, the latter reflecting the in vivo activity of the plasma membrane H⁺‐ATPase. The in vitro activity of the enzyme was not increased but, as the H⁺‐ATPase is electrogenic, the increased ion permeability would allow a higher rate of H⁺ efflux. The AP‐3 adaptor complex is involved in traffic from Golgi to vacuoles but its function in plants is not much known. The phenotypes of the wat1‐1D mutant can be explained if loss of function of the AP‐3 β‐adaptin causes activation of channels or transporters for organic anions (acetate) and for K⁺ at the plasma membrane, perhaps through miss‐localization of tonoplast proteins. This suggests a role of this adaptin in trafficking of ion channels or transporters to the tonoplast.     

Role of Calcium on Phenolic Compounds and Enzymes Related to Lignification in Soybean (Glycine max L.) Root Growth

Changes in soluble and cell wall bound peroxidases activities, phenylalanine ammonia-lyase activity and phenolic compounds and lignin contents in roots of calcium-treated soybean (Glycine max (L.) Merr.) seedlings and their relationships with root growth were investigated. Three-day-old soybean seedlings were cultivated in nutrient solution with or without 0.025–5.0 mM calcium for 24 h. In general, length and fresh and dry weights of roots increased, while activities of enzymes (soluble and cell-wall peroxidases and phenylalanine ammonia-lyase) and phenolic compounds and lignin contents decreased against calcium concentrations. In the absence of calcium, phenylalanine ammonia-lyase and peroxidases activities increased by accumulating phenolic compounds and lignin due to restricted growth of roots. Enhanced calcium supply reduced the production of phenolic compounds and lignification due to low phenylalanine ammonia-lyase and peroxidases activities, reinforcing the essential role of calcium to improve the soybean root growth.     

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (?31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin‐derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin‐derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin‐derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.     

Changes in Cell Wall-bound Phenolic Compounds and Lignin in Roots of Date Palm Cultivars Differing in Susceptibility to Fusarium oxysporum f. sp. albedinis

The roots of date palm contain four cell wall‐bound phenolic acids identified as p‐hydroxybenzoic, p‐coumaric, ferulic and sinapic acids. The ferulic acid represents the major phenolic compound since it constitutes 48.2–55.8% of cell wall‐bound phenolic acids. All these phenolic acids were present in the resistant cultivar (BSTN) and the susceptible cultivar (JHL). However, the pre‐infection contents of p‐coumaric, ferulic and sinapic acids were greater in the resistant cultivar than in the susceptible one. For the contents of p‐hydroxybenzoic acid, there was no significant difference between the resistant cultivar and the susceptible cultivar. Similarly, the pre‐infection contents of lignin were approximately equal for both cultivars. Inoculation of the date palm roots by Fusarium oxysporum f. sp. albedinis induced important modifications to the contents of the cell wall‐bound phenolic compounds and lignin, which made it possible to distinguish between resistant and susceptible cultivars. The post‐infection contents of cell wall‐bound phenolic compounds underwent a rapid and intense increase with a maximum accumulation on the tenth day for p‐hydroxybenzoic acid (1.54 μmol/g), p‐coumaric acid (2.77 μmol/g) and ferulic acid (2.64 μmol/g) and on the fifteenth day for sinapic acid (1.85 μmol/g). The maximum contents accumulated in the resistant cultivar were greater than those in the susceptible cultivar, namely, 11 times for p‐hydroxybenzoic acid, 2.6 times for p‐coumaric acid, 1.8 times for ferulic acid and 12.3 times for sinapic acid. In the susceptible cultivar, p‐coumaric acid and ferulic acid contents also increased after inoculation although they did not reach the pre‐infection contents of the resistant cultivar. The contents of p‐hydroxybenzoic acid in the susceptible cultivar roots did not present post‐infection modification and those of sinapic acid decreased instead. The lignin contents increased in both cultivars with a maximum accumulation on the fifteenth day. However, the maximum contents accumulated in the resistant cultivar roots were 1.5 times greater than those of the susceptible cultivar. These results showed clear differences between the resistant BSTN and the susceptible JHL cultivars. The implication of cell wall‐bound phenolic compounds and lignin in the resistance of date palm to F. oxysporum f. sp. albedinis appears to be dependent on the speed and intensity of their accumulation with greater contents in the first stage of infection.     

Degradation of lignin β‐aryl ether units in Arabidopsis thaliana expressing LigD,LigF and LigG from Sphingomonas paucimobilis SYK‐6

Lignin is a major polymer in the secondary plant cell wall and composed of hydrophobic interlinked hydroxyphenylpropanoid units. The presence of lignin hampers conversion of plant biomass into biofuels; plants with modified lignin are therefore being investigated for increased digestibility. The bacterium Sphingomonas paucimobilis produces lignin‐degrading enzymes including LigD, LigF and LigG involved in cleaving the most abundant lignin interunit linkage, the β‐aryl ether bond. In this study, we expressed the LigD, LigF and LigG (LigDFG) genes in Arabidopsis thaliana to introduce postlignification modifications into the lignin structure. The three enzymes were targeted to the secretory pathway. Phenolic metabolite profiling and 2D HSQC NMR of the transgenic lines showed an increase in oxidized guaiacyl and syringyl units without concomitant increase in oxidized β‐aryl ether units, showing lignin bond cleavage. Saccharification yield increased significantly in transgenic lines expressing LigDFG, showing the applicability of our approach. Additional new information on substrate specificity of the LigDFG enzymes is also provided.     

Involvement and necessity of the Cpx regulon in the event of aberrant β‐barrel outer membrane protein assembly

The Cpx and σ^E regulons help maintain outer membrane integrity; the Cpx pathway monitors the biogenesis of cell surface structures, such as pili, while the σ^E pathway monitors the biogenesis of β‐barrel outer membrane proteins (OMPs). In this study we revealed the importance of the Cpx regulon in the event of β‐barrel OMP mis‐assembly, by utilizing mutants expressing either a defective β‐barrel OMP assembly machinery (Bam) or assembly defective β‐barrel OMPs. Analysis of specific mRNAs showed that ΔcpxR bam double mutants failed to induce degP expression beyond the wild type level, despite activation of the σ^E pathway. The synthetic conditional lethal phenotype of ΔcpxR in mutant Bam or β‐barrel OMP backgrounds was reversed by wild type DegP expressed from a heterologous plasmid promoter. Consistent with the involvement of the Cpx regulon in the event of aberrant β‐barrel OMP assembly, the expression of cpxP, the archetypal member of the cpx regulon, was upregulated in defective Bam backgrounds or in cells expressing a single assembly‐defective β‐barrel OMP species. Together, these results showed that both the Cpx and σ^E regulons are required to reduce envelope stress caused by aberrant β‐barrel OMP assembly, with the Cpx regulon principally contributing by controlling degP expression.     

Investigating the binding of β‐1,4‐galactan to Bacillus licheniformis β‐1,4‐galactanase by crystallography and computational modeling

Microbial β‐1,4‐galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH‐A of glycoside hydrolases, which cover many different poly‐ and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis β‐1,4‐galactanase and its inactive nucleophile mutant have been obtained with methyl‐β(1→4)‐galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the β‐1,4‐galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a β(1→4)‐galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite ?4 to +5. In particular, this analysis newly identified a conserved β‐turn, which contributes to subsites ?2 to +3. This β‐turn is unique to family 53 β‐1,4‐galactanases among all clan GH‐A families that have been structurally characterized and thus might be a structural signature for endo‐β‐1,4‐galactanase specificity. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Grapevine xylem response to fungi involved in trunk diseases

Grapevine trunk diseases (GTD), caused by a wide range of different fungi, are responsible for decline and productivity losses in vines at all growth stages. Grapevine responses to fungal attack include morphological and physiochemical defence mechanisms in the vascular system to reduce fungal infections. However, the extent to which these responses could control further spread by GTD‐fungi in the xylem vessels is poorly known. This study shows the formation of tyloses inside xylem vessels of diseased grapevines, as well as extracellular ligninolytic activities [lignin peroxidase, manganese peroxidase (MnP) and/or laccase] exhibited by some GTD‐fungi isolated here from symptomatic grapevines. In particular, Botryosphaeriaceae spp. and Phaeoacremonium minimum showed all three lignin‐degrading enzymatic activities. We also examined whether selected vine phenolic compounds, often located in the vascular system in response to fungal infection, could affect the lignin‐degrading activity from those GTD‐fungi as well as fungal colonisation. We found that phenolic compounds appeared to inhibit MnP activity, in addition to reducing fungal growth by causing anomalies in the hyphae morphology. Our results support that affected grapevines can initiate the tylosis formation in order to constrain fungi in the xylem vessels, while highlight the complementary action of the phenolic compounds to inhibit the fungi growth and colonisation. Phenolic compounds are therefore likely to have important role in alternative strategies for preventing trunk diseases.     

Mitochondrial β‐oxidation regulates organellar integrity and is necessary for conidial germination and invasive growth in Magnaporthe oryzae

Fatty acids stored as triglycerides, an important source of cellular energy, are catabolized through β‐oxidation pathways predicted to occur both in peroxisomes and mitochondria in filamentous fungi. Here, we characterize the function of Enoyl‐CoA hydratase Ech1, a mitochondrial β‐oxidation enzyme, in the model phytopathogen Magnaporthe oryzae. Ech1 was found to be essential for conidial germination and viability of older hyphae. Unlike wild‐type Magnaporthe, the ech1Δ failed to utilize C14 fatty acid and was partially impeded in growth on C16 and C18 fatty acids. Surprisingly, loss of β‐oxidation led to significantly altered mitochondrial morphology and integrity with ech1Δ showing predominantly vesicular/punctate mitochondria in contrast to the fused tubular network in wild‐type Magnaporthe. The ech1Δ appressoria were aberrant and displayed reduced melanization. Importantly, we show that the significantly reduced ability of ech1Δ to penetrate the host and establish therein is a direct consequence of enhanced sensitivity of the mutant to oxidative stress, as the defects could be remarkably reversed through exogenous antioxidants. Overall, our comparative analyses reveal that peroxisomal lipid catabolism is essential for appressorial function of host penetration, whereas mitochondrial β‐oxidation primarily contributes to conidial viability and maintenance of redox homeostasis during host colonization by Magnaporthe.     

Bioconversion of lignin model compounds with oleaginous <Emphasis Type="Italic">Rhodococci</Emphasis>

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.     

Re‐examining the role of Lys67 in class C β‐lactamase catalysis

Lys67 is essential for the hydrolysis reaction mediated by class C β‐lactamases. Its exact catalytic role lies at the center of several different proposed reaction mechanisms, particularly for the deacylation step, and has been intensely debated. Whereas a conjugate base hypothesis postulates that a neutral Lys67 and Tyr150 act together to deprotonate the deacylating water, previous experiments on the K67R mutants of class C β‐lactamases suggested that the role of Lys67 in deacylation is mainly electrostatic, with only a 2‐ to 3‐fold decrease in the rate of the mutant vs the wild type enzyme. Using the Class C β‐lactamase AmpC, we have reinvestigated the activity of this K67R mutant enzyme, using biochemical and structural studies. Both the rates of acylation and deacylation were affected in the AmpC K67R mutant, with a 61‐fold decrease in k_cat, the deacylation rate. We have determined the structure of the K67R mutant by X‐ray crystallography both in apo and transition state‐analog complexed forms, and observed only minimal conformational changes in the catalytic residues relative to the wild type. These results suggest that the arginine side chain is unable to play the same catalytic role as Lys67 in either the acylation or deacylation reactions catalyzed by AmpC. Therefore, the activity of this mutant can not be used to discredit the conjugate base hypothesis as previously concluded, although the reaction catalyzed by the K67R mutant itself likely proceeds by an alternative mechanism. Indeed, a manifold of mechanisms may contribute to hydrolysis in class C β‐lactamases, depending on the enzyme (wt or mutant) and the substrate, explaining why different mutants and substrates seem to support different pathways. For the WT enzyme itself, the conjugate base mechanism may be well favored.     

Community composition of root‐associated fungi in a Quercus‐dominated temperate forest: “codominance” of mycorrhizal and root‐endophytic fungi

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak‐dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal‐root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root‐associated fungal community was dominated by root‐endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root‐associated fungal communities of oak‐dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.     

Accumulation pattern of endogenous cytokinins and phenolics in different organs of 1‐year‐old cytokinin pre‐incubated plants: implications for conservation

A better understanding of phytohormone physiology can provide an essential basis to coherently achieve a conservation drive/strategy for valuable plant species. We evaluated the distribution pattern of cytokinins (CKs) and phenolic compounds in different organs of 1‐year‐old greenhouse‐grown Tulbaghia simmleri pre‐treated (during micropropagation) with three aromatic CKs (benzyladenine = BA, meta‐topolin = mT, meta‐topolin riboside = mTR). The test species is highly valuable due to its medicinal and ornamental uses. Based on UHPLC‐MS/MS quantification, mT and mTR pre‐treated plants had the highest total CK, mostly resulting from the isoprenoid CK‐type, which occurred at highest concentrations in the roots. Although occurring in much lower concentrations when compared to isoprenoid CKs, aromatic CKs were several‐fold more abundant in the root of mT pre‐treated plants than with other treatments. Possibly related to the enhanced aromatic CKs, free bases and ribonucleotides, plants pre‐treated with mT generally displayed better morphology than the other treatments. A total of 12 bioactive phenolic compounds, including four hydroxybenzoic acids, five hydroxycinnamic acids and three flavonoids at varying concentrations, were quantified in T. simmleri. The occurrence, distribution and levels of these phenolic compounds were strongly influenced by the CK pre‐treatments, thereby confirming the importance of CKs in phenolic biosynthesis pathways.