Zim17/Tim15 links mitochondrial iron–sulfur cluster biosynthesis to nuclear genome stability

Genomic instability is related to a wide-range of human diseases. Here, we show that mitochondrial iron–sulfur cluster biosynthesis is important for the maintenance of nuclear genome stability in Saccharomyces cerevisiae. Cells lacking the mitochondrial chaperone Zim17 (Tim15/Hep1), a component of the iron–sulfur biosynthesis machinery, have limited respiration activity, mimic the metabolic response to iron starvation and suffer a dramatic increase in nuclear genome recombination. Increased oxidative damage or deficient DNA repair do not account for the observed genomic hyperrecombination. Impaired cell-cycle progression and genetic interactions of ZIM17 with components of the RFC-like complex involved in mitotic checkpoints indicate that replicative stress causes hyperrecombination in zim17Δ mutants. Furthermore, nuclear accumulation of pre-ribosomal particles in zim17Δ mutants reinforces the importance of iron–sulfur clusters in normal ribosome biosynthesis. We propose that compromised ribosome biosynthesis and cell-cycle progression are interconnected, together contributing to replicative stress and nuclear genome instability in zim17Δ mutants.

Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis.

Pneumocystis species are fungal parasites colonizing mammal lungs with strict host specificity. Pneumocystis jirovecii is the human-specific species and can turn into an opportunistic pathogen causing severe pneumonia in immunocompromised individuals. This disease is currently the second most frequent life-threatening invasive fungal infection worldwide. The most efficient drug, cotrimoxazole, presents serious side effects, and resistance to this drug is emerging. The search for new targets for the development of new drugs is thus of utmost importance. The recent release of the P. jirovecii genome sequence opens a new era for this task. It can now be carried out on the actual targets to be inhibited instead of on those of the relatively distant model Pneumocystis carinii, the species infecting rats. We focused on the folic acid biosynthesis pathway because (i) it is widely used for efficient therapeutic intervention, and (ii) it involves several enzymes that are essential for the pathogen and have no human counterparts. In this study, we report the identification of two such potential targets within the genome of P. jirovecii, the dihydrofolate synthase (dhfs) and the aminodeoxychorismate lyase (abz2). The function of these enzymes was demonstrated by the rescue of the null allele of the orthologous gene of Saccharomyces cerevisiae.

Candida albicans Inhibits Pseudomonas aeruginosa Virulence through Suppression of Pyochelin and Pyoverdine Biosynthesis.

Bacterial-fungal interactions have important physiologic and medical ramifications, but the mechanisms of these interactions are poorly understood. The gut is host to trillions of microorganisms, and bacterial-fungal interactions are likely to be important. Using a neutropenic mouse model of microbial gastrointestinal colonization and dissemination, we show that the fungus Candida albicans inhibits the virulence of the bacterium Pseudomonas aeruginosa by inhibiting P. aeruginosa pyochelin and pyoverdine gene expression, which plays a critical role in iron acquisition and virulence. Accordingly, deletion of both P. aeruginosa pyochelin and pyoverdine genes attenuates P. aeruginosa virulence. Heat-killed C. albicans has no effect on P. aeruginosa, whereas C. albicans secreted proteins directly suppress P. aeruginosa pyoverdine and pyochelin expression and inhibit P. aeruginosa virulence in mice. Interestingly, suppression or deletion of pyochelin and pyoverdine genes has no effect on P. aeruginosa's ability to colonize the GI tract but does decrease P. aeruginosa's cytotoxic effect on cultured colonocytes. Finally, oral iron supplementation restores P. aeruginosa virulence in P. aeruginosa and C. albicans colonized mice. Together, our findings provide insight into how a bacterial-fungal interaction can modulate bacterial virulence in the intestine. Previously described bacterial-fungal antagonistic interactions have focused on growth inhibition or colonization inhibition/modulation, yet here we describe a novel observation of fungal-inhibition of bacterial effectors critical for virulence but not important for colonization. These findings validate the use of a mammalian model system to explore the complexities of polymicrobial, polykingdom infections in order to identify new therapeutic targets for preventing microbial disease.

Biosynthesis of panaxynol and panaxydol in Panax ginseng

The natural formation of the bioactive C17-polyacetylenes (−)-(R)-panaxynol and panaxydol was analyzed by 13C-labeling experiments. For this purpose, plants of Panax ginseng were supplied with 13CO2 under field conditions or, alternatively, sterile root cultures of P. ginseng were supplemented with [U-13C6]glucose. The polyynes were isolated from the labeled roots or hairy root cultures, respectively, and analyzed by quantitative NMR spectroscopy. The same mixtures of eight doubly 13C-labeled isotopologues and one single labeled isotopologue were observed in the C17-polyacetylenes obtained from the two experiments. The polyketide-type labeling pattern is in line with the biosynthetic origin of the compounds via decarboxylation of fatty acids, probably of crepenynic acid. The 13C-study now provides experimental evidence for the biosynthesis of panaxynol and related polyacetylenes in P. ginseng under in planta conditions as well as in root cultures. The data also show that 13CO2 experiments under field conditions are useful to elucidate the biosynthetic pathways of metabolites, including those from roots.

PEC1/AtABCG32 transport function in cuticle biosynthesis

Most aerial parts of the plants are covered by a hydrophobic coating called cuticle. The cuticle is formed of cutin, a complex mixture of esterified fatty acids that are embedded and associated with waxes. The cuticle often appears as a superposition of layers of different composition: The cuticle proper formed of cutin and a mixture of waxes and underneath, the cuticle layer containing cutin, intracuticular waxes and polysaccharides of the cell wall. In addition to its involvement in plant development by preventing organ fusions, the cuticle acts as a barrier to prevent water loss and protect plants against environmental aggressions such as excessive radiation or pathogens attacks. PEC1/AtABCG32 is an ABC transporter from the PDR family involved in cutin biosynthesis. Characterization of the peci mutant in Arabidopsis thaliana showed that PEC1 plays a significant role in the diffusion barrier formation in leaves and petals. The cuticles of leaves and flowers of peci are permeable and the cuticular layer rather than the cuticular proper was altered in the petals, underlining the importance of this particular layer in the maintenance of the diffusion barrier. Chemical analysis on the flower cutin monomer composition of ped mutant revealed a decrease in hydroxylated cutin monomers, suggesting a function of PEC1 in the incorporation of these monomers in the polymer cutin. However, the exact nature of the substrates of PEC1 remained elusive. PEC1 homologues in barley and rice, respectively HvABCG31/EIBI1 and OsABCG31, are also implicated in cuticle biosynthesis. Interestingly, the rice mutant displays more severe phenotypes such as dwarfism and spreading necrosis conducting to the seedling death. In this work, we further characterized osabcg31 mutant and hairpin-RNAi downregulated OsABCG31 plant lines showing reduced growth and cuticle permeability. Our analysis showed a decrease in hydroxylated cutin monomers and severe disruptions in the cuticle, which explain the permeability. Further insights into the function of the cuticle in rice resistance/susceptibility to Pathogens were obtained after inoculation with Magnaporthe oryzae, the fungus responsible for the rice blast disease. Osabcg31 as well as the transgenic lines downregulating OsABCG31 showed increased resistance to the fungus. However, only later steps of infection are reduced . and no impact is obseived on the germination or penetration stages, suggesting that the cuticle disruption per se is not responsible for the resistance. We further investigated the cause of the resistance by analyzing the expression of defense related gene in osabcg31 prior to infection. We found that osabcg31 constitutively express defense related genes, which may explain the resistance, the dwarfism and the cell death. osabcg31 is thus a tool to study the connection between cuticle, plant development and defense signaling networks in rice. The transport function of PEC1 family members is still unknown. In order to link cutin biosynthesis and transport activity, we combined ped mutation with mutations in cutin synthesis related genes. Here, we show that PEC1 acts independently from GPAT4 and GPAT8 pathway and partially overlaps with GPAT6 biosynthesis pathway that leads to the production of hydroxylated C16 cutin precursor 2-Mono(10,16-dihydroxyhexadecanoylJglycerol (2-MHG). In addition, we noticed that despite a comparable cutin monomer composition, ped mutant leaves cuticle are permeable while that of gpat6 mutant are not. This finding raises the possibility of PEC1 being required for the incorporation of C16 hydroxylated monomers and their structural arrangement rather than their direct transport towards the cuticle. A careful investigation of the cuticle permeability, cutin composition and ultrastructure during leave development in Wt plants and ped mutants revealed a possible different regulation of several pathways of cutin biosynthesis and showed the importance of PEC1 function early during leave cuticle maturation. In order to elucidate the transport activity of PEC1, we successfully expressed PEC1 in Nicotiana benthamiana plant system for direct transport experiments. This system will be used to test the PEC 1-dependent transport of potential substrates such as sn-2-monoacylglycerol loaded with a hydroxylated C16 fatty acid. -- Toutes les parties aériennes des plantes sont recouvertes d'une couche hydrophobe appelée «cuticule». Cette cuticule est composée de cutine, un polymère d'acides gras estérifiés, et de cires. La cuticule apparaît souvent sous forme de couches superposées: une première couche extérieure appelée «cuticle proper» formée de cutine et d'un mélange de cires, et une deuxième couche, la «cuticle layer», formée de cutine associée à des cires intracuticulaires et des polysaccharides pariétaux. La cuticule joue le rôle de barrière prévenant contre la perte d'eau et les agressions environnementales. AtABCG32/PEC1 est un transporteur ABC de la famille des PDR impliqué dans la synthèse de la cutine. L'étude du mutant peci d'Arabidopsis thaliana a révélé une fonction de PEC1 dans la formation de la barrière de diffusion. La cuticule des feuilles et fleurs de peci est perméable. Des altérations de la «cuticle layer» ont été démontrées, soulignant son importance dans le maintien de la barrière. L'analyse de la composition de la cutine de peci a montré une réduction spécifique en monomères hydroxylés, suggérant un rôle de PEC1 dans leur incorporation dans la cuticule. Cependant, la nature exacte des substrats de PEC1 n'a pas été identifiée. PEC1 possède deux homologues chez l'orge et le riz, respectivement HvABCG31 et OsABCG31, et qui sont impliqués dans la biosynthèse de la cuticule. Chez le riz, des phénotypes plus sévères ont été observés tels que nanisme et nécroses conduisant à la mort des jeunes plants. Dans cette étude, nous avons continué la caractérisation de osabcg31 ainsi que des lignées de riz sous exprimant le gène OsABCG31 et présentant une cuticule perméable tout en ayant une meilleure croissance. Notre étude a démontré une réduction des monomères hydroxylés de cutine et une désorganisation de la structure de la cuticule, aggravée dans le mutant osabcg31. Ce résultat explique la perméabilité observée. Des mformations P|us approfondies sur l'implication de la cuticule dans la résistance aux pathogènes ont été obtenues après inoculation du mutant osabcg31 et les lignées sous- exprimant OsABCG31 avec une souche virulente de Magnaporthe Oryzae, le champignon responsable de la pyriculariose du riz. Les différentes lignées testées ont démontré une résistance au pathogène. Cependant, seules les étapes tardives de l'infection sont réduites et aucun impact n'est observé sur la germination des spores ou la pénétration du champignon, suggérant que les modifications de la cuticule ne sont pas directement à l'origine de la résistance. L'analyse de l'expression de gènes impliqués dans la résistance à Magnaporthe.oryzae a mis en évidence l'expression constitutive de ces gènes en l'absence de tout contact avec le pathogène. Ceci explique la résistance, le nanisme et la mort cellulaire observés. Ainsi, osabcg31 représente un outil efficace pour l'étude intégrée des systèmes de régulation de la défense, de développement des plantes et la cuticule. La nature des substrats transportés par PEC1/AtABCG32 reste inconnue. Dans le but d'établir une liaison entre biosynthèse de cutine et transport des précurseurs par PEC1, la mutation peci a été combinée avec des mutants impliqués dans différentes voies de biosynthèse. Cette étude a démontré une fonction indépendante de PEC1 de la voie de biosynthèse impliquant les enzymes GPAT4 et GPAT8, et une fonction partiellement indépendante de la voie impliquant GPAT6 qui mène à la production de précurseurs sn-2- monoacylglycerol chargés en acides gras en C16 (2-MHG). De plus, malgré un profil similaire en monomères de cutine, gpat6 conserve une cuticule imperméable alors que celle de PEC1 est perméable. Ceci suggère que PEC1 est nécessaire à l'incorporation des monomères en C16 et leur arrangement structurel plutôt que simplement à leur transport direct. L'étude approfondie de la perméabilité cuticulaire, de la structure ainsi que de la composition en cutine pendant le développement des feuilles de peci et la plante sauvage a révélé l'existence de différentes régulations des voies de biosynthèses des monomères et a démontré l'importance de PEC1 dans les premières étapes de la mise en place de la cuticule. Pour identifier les substrats transportés, l'expression de PEC1 chez le système hétérologue Nicotiana benthamiana a été conduite avec succès. Ce système sera utilisé pour tester le transport de substrats potentiels tels que le sn-2-monoacylglycerol chargé en acide gras en C16.

The effect of lignin as a natural adhesive on the physico-mechanical properties of Vitis vinifera fiberboards

Lignin was used as a natural adhesive to manufacture Vitis vinifera fiberboards. The fiberboards were produced at laboratory scale by adding powdered lignin to material that had previously been steam-exploded under optimized pretreatment and pressing conditions. The kraft lignin used was washed several times with an acidic solution to eliminate any contaminants and low molecular weight compounds. This research studied the effects of amounts of lignin ranging from 5% to 20% on the properties of Vitis vinifera fiberboards. The fiberboard properties evaluated were density, water resistance in terms of thickness swelling, water absorption, and the mechanical properties in terms of modulus of rupture, modulus of elasticity, and internal bond. Results showed that fiberboards made from Vitis vinifera without lignin addition had weaker mechanical properties. However, the fiberboards obtained using acid-washed kraft lignin as a natural adhesive had good mechanical and water resistance properties that fully satisfied the relevant standard specifications

Wet oxidation of recalcitrant lignin waters: Experimental and kinetic studies

The dissertation is based on four articles dealing with recalcitrant lignin water purification. Lignin, a complicated substance and recalcitrant to most treatment technologies, inhibits seriously pulp and paper industry waste management. Therefore, lignin is studied, using WO as a process method for its degradation. A special attention is paid to the improvement in biodegradability and the reduction of lignin content, since they have special importance for any following biological treatment. In most cases wet oxidation is not used as a complete ' mineralization method but as a pre treatment in order to eliminate toxic components and to reduce the high level of organics produced. The combination of wet oxidation with a biological treatment can be a good option due to its effectiveness and its relatively low technology cost. The literature part gives an overview of Advanced Oxidation Processes (AOPs). A hot oxidation process, wet oxidation (WO), is investigated in detail and is the AOP process used in the research. The background and main principles of wet oxidation, its industrial applications, the combination of wet oxidation with other water treatment technologies, principal reactions in WO, and key aspects of modelling and reaction kinetics are presented. There is also given a wood composition and lignin characterization (chemical composition, structure and origin), lignin containing waters, lignin degradation and reuse possibilities, and purification practices for lignin containing waters. The aim of the research was to investigate the effect of the operating conditions of WO, such as temperature, partial pressure of oxygen, pH and initial concentration of wastewater, on the efficiency, and to enhance the process and estimate optimal conditions for WO of recalcitrant lignin waters. Two different waters are studied (a lignin water model solution and debarking water from paper industry) to give as appropriate conditions as possible. Due to the great importance of re using and minimizing the residues of industries, further research is carried out using residual ash of an Estonian power plant as a catalyst in wet oxidation of lignin-containing water. Developing a kinetic model that includes in the prediction such parameters as TOC gives the opportunity to estimate the amount of emerging inorganic substances (degradation rate of waste) and not only the decrease of COD and BOD. The degradation target compound, lignin is included into the model through its COD value (CODligning). Such a kinetic model can be valuable in developing WO treatment processes for lignin containing waters, or other wastewaters containing one or more target compounds. In the first article, wet oxidation of "pure" lignin water was investigated as a model case with the aim of degrading lignin and enhancing water biodegradability. The experiments were performed at various temperatures (110 -190°C), partial oxygen pressures (0.5 -1.5 MPa) and pH (5, 9 and 12). The experiments showed that increasing the temperature notably improved the processes efficiency. 75% lignin reduction was detected at the lowest temperature tested and lignin removal improved to 100% at 190°C. The effect of temperature on the COD removal rate was lower, but clearly detectable. 53% of organics were oxidized at 190°C. The effect of pH occurred mostly on lignin removal. Increasing the pH enhanced the lignin removal efficiency from 60% to nearly 100%. A good biodegradability ratio (over 0.5) was generally achieved. The aim of the second article was to develop a mathematical model for "pure" lignin wet oxidation using lumped characteristics of water (COD, BOD, TOC) and lignin concentration. The model agreed well with the experimental data (R2 = 0.93 at pH 5 and 12) and concentration changes during wet oxidation followed adequately the experimental results. The model also showed correctly the trend of biodegradability (BOD/COD) changes. In the third article, the purpose of the research was to estimate optimal conditions for wet oxidation (WO) of debarking water from the paper industry. The WO experiments were' performed at various temperatures, partial oxygen pressures and pH. The experiments showed that lignin degradation and organics removal are affected remarkably by temperature and pH. 78-97% lignin reduction was detected at different WO conditions. Initial pH 12 caused faster removal of tannins/lignin content; but initial pH 5 was more effective for removal of total organics, represented by COD and TOC. Most of the decrease in organic substances concentrations occurred in the first 60 minutes. The aim of the fourth article was to compare the behaviour of two reaction kinetic models, based on experiments of wet oxidation of industrial debarking water under different conditions. The simpler model took into account only the changes in COD, BOD and TOC; the advanced model was similar to the model used in the second article. Comparing the results of the models, the second model was found to be more suitable for describing the kinetics of wet oxidation of debarking water. The significance of the reactions involved was compared on the basis of the model: for instance, lignin degraded first to other chemically oxidizable compounds rather than directly to biodegradable products. Catalytic wet oxidation of lignin containing waters is briefly presented at the end of the dissertation. Two completely different catalysts were used: a commercial Pt catalyst and waste power plant ash. CWO showed good performance using 1 g/L of residual ash gave lignin removal of 86% and COD removal of 39% at 150°C (a lower temperature and pressure than with WO). It was noted that the ash catalyst caused a remarkable removal rate for lignin degradation already during the pre heating for `zero' time, 58% of lignin was degraded. In general, wet oxidation is not recommended for use as a complete mineralization method, but as a pre treatment phase to eliminate toxic or difficultly biodegradable components and to reduce the high level of organics. Biological treatment is an appropriate post treatment method since easily biodegradable organic matter remains after the WO process. The combination of wet oxidation with subsequent biological treatment can be an effective option for the treatment of lignin containing waters.

Methylene blue adsorption onto modified lignin from sugar cane bagasse

The adsorption kinetics and equilibrium of methylene blue (MB) onto reticulated formic lignin (RFL) from sugar cane bagasse was studied. The adsorption process is pH, temperature and ionic strength (µ) dependent and obeys the Langmuir model. Conditions for higher adsorption rate and capacity were determined. The faster adsorption (12 hours) and higher adsorption capacity (34.20 mg.g-1) were observed at pH = 5.8 (acetic acid-sodium acetate aqueous buffer), 50 ºC and 0.1 ionic strength. Under temperature (50 ºC) control and occasional mechanical stirring it took from 1 to 10 days to reach the equilibrium.

Biosynthesis of Yersinia enterocolitica serotype O:3 lipopolysaccharide outer core

Lipopolysacharide (LPS) present on the outer leaflet of Gram-negative bacteria is important for the adaptation of the bacteria to the environment. Structurally, LPS can be divided into three parts: lipid A, core and O-polysaccharide (OPS). OPS is the outermost and also the most diverse moiety. When OPS is composed of identical sugar residues it is called homopolymeric and when it is composed of repeating units of oligosaccharides it is called heteropolymeric. Bacteria synthesize LPS at the inner membrane via two separate pathways, Lipid A-core via one and OPS via the other. These are ligated together in the periplasmic space and the completed LPS molecule is translocated to the surface of the bacteria. The genes directing the OPS biosynthesis are often clustered and the clusters directing the biosynthesis of heteropolymeric OPS often contain genes for i) the biosynthesis of required NDP-sugar precursors, ii) glycosyltransferases needed to build up the repeating unit, iii) translocation of the completed O-unit to the periplasmic side of the inner membrane (flippase) and iv) polymerization of the repeating units to complete OPS. The aim of this thesis was to characterize the biosynthesis of the outer core (OC) of Yersinia enterocolitica serotype O:3 (YeO3). Y. enterocolitica is a member of the Gram-negative Yersinia genus and it causes diarrhea followed sometimes by reactive arthritis. The chemical structure of the OC and the nucleotide sequence of the gene cluster directing its biosynthesis were already known; however, no experimental evidence had been provided for the predicted functions of the gene products. The hypothesis was that the OC biosynthesis would follow the pathway described for heteropolymeric OPS, i.e. a Wzy-dependent pathway. In this work the biochemical activities of two enzymes involved in the NDP-sugar biosynthesis was established. Gne was determined to be a UDP-N-acetylglucosamine-4-epimerase catalyzing the conversion of UDP-GlcNAc to UDP-GalNAc and WbcP was shown to be a UDP-GlcNAc- 4,6-dehydratase catalyzing the reaction that converts UDP-GlcNAc to a rare UDP-2-acetamido- 2,6-dideoxy-d-xylo-hex-4-ulopyranose (UDP-Sugp). In this work, the linkage specificities and the order in which the different glycosyltransferases build up the OC onto the lipid carrier were also investigated. In addition, by using a site-directed mutagenesis approach the catalytically important amino acids of Gne and two of the characterized glycosyltranferases were identified. Also evidence to show the enzymes involved in the ligations of OC and OPS to the lipid A inner core was provided. The importance of the OC to the physiology of Y. enterocolitica O:3 was defined by determining the minimum requirements for the OC to be recognized by a bacteriophage, bacteriocin and monoclonal antibody. The biological importance of the rare keto sugar (Sugp) was also shown. As a conclusion this work provides an extensive overview of the biosynthesis of YeO3 OC as it provides a substantial amount of information of the stepwise and coordinated synthesis of the Ye O:3 OC hexasaccharide and detailed information of its properties as a receptor.

RELATIONSHIP BETWEEN LIGNIN CONTENT AND QUALITY OF Pinus taeda SEEDLINGS1

ABSTRACT The essay objective was to correlate lignin content resulting from tigmomorphogenesis induced by stem swaying with survival and post-planting growth of P. taeda seedlings. Seedlings were subjected to daily frequencies (0, 5, 10, 20 and 40 movements) of stem swaying for 60 days. By the end of the treatments, we determined lignin content of below and aboveground seedling tissues. Four replicates per treatment were planted in a area cultivated with pines. Ninety days after planting, survival and increments of seedling height, stem diameter and stem volume were quantified. Application of 20 stem swayings increased lignin in both below and aboveground plant tissues. Outplanted seedling survival was reduced with 40 stem swayings while growth increments were increased with both 10 and 20 stem swayings. Lignin content from belowground plant tissues was positively correlated with outplanted seedling survival while lignin from aboveground tissues correlated with height and stem volume increments. P. taeda seedlings with higher lignin content have higher survival chances after planting.

Purified lignin for demanding applications

Diplomityön tarkoituksena oli puhdistaa kraft ligniiniä. Raaka-aineena käytettiin pääasiassa Lignoboost -menetelmän kaltaisella menetelmällä havupuu- mustalipeästä saostettua ligniiniä. Diplomityön ensimmäisenä tavoitteena oli löytää menetelmä, jolla voidaan poistaa kraft ligniinistä tuhkaa. Työssä raaka-aineena käytetyn saostetun ligniinin tuhkapitoisuus oli noin 3 %. Tarkoituksena oli saada laskettua tuhkapitoisuutta uudelleenlieton, suodatuksen ja pesun avulla. Työn toisena tavoitteena oli hiilihydraattien poisto kraft ligniinistä. Hiilihydraatit, pääosin hemiselluloosaa, ovat kiinnittyneet ligniiniin vahvoin kovalenttisin sidoksin. Aiempien kokemusten perusteella hemiselluloosat eivät irtoa ligniinistä vesipesun yhteydessä, vaan niiden irrottaminen vaatii onnistuakseen happo-, entsyymi- tai mikrobikäsittelyn, mikäli halutaan säilyttää ligniinin rakenne muuttumattomana. Tässä työssä käytetyt kraft ligniinin puhdistusmenetelmät olivat lietto, happohydrolyysi ja entsymaattinen hydrolyysi, joista kumpikin sisälsi ligniinin uudelleenlieton, suodatuksen ja muodostuneen kakun pesun vedellä.

Biosynthesis of pyranonaphthoquinone polyketides:characterization of the alnumycin pathway

Alnumycin A is an aromatic pyranonaphthoquinone (PNQ) polyketide closely related to the model compound actinorhodin. While some PNQ polyketides are glycosylated, alnumycin A contains a unique sugar-like dioxane moiety. This unusual structural feature made alnumycin A an interesting research target, since no information was available about its biosynthesis. Thus, the main objective of the thesis work became to identify the steps and the enzymes responsible for the biosynthesis of the dioxane moiety. Cloning, sequencing and heterologous expression of the complete alnumycin gene cluster from Streptomyces sp. CM020 enabled the inactivation of several alnumycin biosynthetic genes and preliminary identification of the gene products responsible for pyran ring formation, quinone formation and dioxane biosynthesis. The individual deletions of the genes resulted in the production of several novel metabolites, which in many cases turned out to be pathway intermediates and could be used for stepwise enzymatic reconstruction of the complete dioxane biosynthetic pathway in vitro. Furthermore, the in vitro reactions with purified alnumycin biosynthetic enzymes resulted in the production of other novel compounds, both pathway intermediates and side products. Identification and molecular level studies of the enzymes AlnA and AlnB catalyzing the first step of dioxane biosynthesis – an unusual C-ribosylation step – led to a mechanistic proposal for the C-ribosylation of the polyketide aglycone. The next step on the dioxane biosynthetic pathway was found to be the oxidative conversion of the attached ribose into a highly unusual dioxolane unit by Aln6 belonging to an uncharacterized protein family, which unexpectedly occurred without any apparent cofactors. Finally, the last step of the pathway was found to be catalyzed by the NADPH-dependent reductase Aln4, which is able to catalyze the conversion of the formed dioxolane into a dioxane moiety. The work presented here and the knowledge gained of the enzymes involved in dioxane biosynthesis enables their use in the rational design of novel compounds containing C–C bound ribose, dioxolane and dioxane moieties.

An overview of lignin metabolism and its effect on biomass recalcitrance

Lignin, after cellulose, is the second most abundant biopolymer on Earth, accounting for 30% of the organic carbon in the biosphere. It is considered an important evolutionary adaptation of plants during their transition from the aquatic environment to land, since it bestowed the early tracheophytes with physical support to stand upright and enabled long-distance transport of water and solutes by waterproofing the vascular tissue. Although essential for plant growth and development, lignin is the major plant cell wall component responsible for biomass recalcitrance to industrial processing. The fact that lignin is a non-linear aromatic polymer built with chemically diverse and poorly reactive linkages and a variety of monomer units precludes the ability of any single enzyme to properly recognize and degrade it. Consequently, the use of lignocellulosic feedstock as a renewable and sustainable resource for the production of biofuels and bio-based materials will depend on the identification and characterization of the factors that determine plant biomass recalcitrance, especially the highly complex phenolic polymer lignin. Here, we summarize the current knowledge regarding lignin metabolism in plants, its effect on biomass recalcitrance and the emergent strategies to modify biomass recalcitrance through metabolic engineering of the lignin pathway. In addition, the potential use of sugarcane as a second-generation biofuel crop and the advances in lignin-related studies in sugarcane are discussed.