Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.

Psychrobacter cryohalolentis strain K5T is a Gram-negative organism first isolated in 2006. It has a complex O-antigen that contains, in addition to l-rhamnose and d-galactose, two diacetamido- and a triacetamido-sugar. The biochemical pathways for the production of these unusual sugars are presently unknown. Utilizing the published genome sequence of the organism, we hypothesized that the genes 0612, 0638, and 0637 encode for a 4,6-dehydratase, an aminotransferase, and an N-acetyltransferase, respectively, which would be required for the biosynthesis of one of the diacetamido-sugars, 2,4-diacetamido-2,4,6-trideoxy-d-glucose, starting from UDP-N-acetylglucosamine. Here we present functional and structural data on the proteins encoded by the 0638 and 0637 genes. The kinetic properties of these enzymes were investigated by a discontinuous HPLC assay. An X-ray crystallographic structure of 0638, determined in its external aldimine form to 1.3 Å resolution, demonstrated the manner in which the UDP ligand is positioned into the active site. It is strikingly different from that previously observed for PglE from Campylobacter jejuni, which functions on the same substrate. Four X-ray crystallographic structures were also determined for 0637 in various complexed states at resolutions between 1.3 and 1.55 Å. Remarkably, a tetrahedral intermediate mimicking the presumed transition state was trapped in one of the complexes. The data presented herein confirm the hypothesized functions of these enzymes and provide new insight into an unusual sugar biosynthetic pathway in Gram-negative bacteria. We also describe an efficient method for acetyl-CoA synthesis that allowed us to overcome its prohibitive cost for this analysis.

Structural insights into inhibition of lipid I production in bacterial cell wall synthesis.

Antibiotic-resistant bacterial infection is a serious threat to public health. Peptidoglycan biosynthesis is a well-established target for antibiotic development. MraY (phospho-MurNAc-pentapeptide translocase) catalyses the first and an essential membrane step of peptidoglycan biosynthesis. It is considered a very promising target for the development of new antibiotics, as many naturally occurring nucleoside inhibitors with antibacterial activity target this enzyme. However, antibiotics targeting MraY have not been developed for clinical use, mainly owing to a lack of structural insight into inhibition of this enzyme. Here we present the crystal structure of MraY from Aquifex aeolicus (MraYAA) in complex with its naturally occurring inhibitor, muraymycin D2 (MD2). We show that after binding MD2, MraYAA undergoes remarkably large conformational rearrangements near the active site, which lead to the formation of a nucleoside-binding pocket and a peptide-binding site. MD2 binds the nucleoside-binding pocket like a two-pronged plug inserting into a socket. Further interactions it makes in the adjacent peptide-binding site anchor MD2 to and enhance its affinity for MraYAA. Surprisingly, MD2 does not interact with three acidic residues or the Mg(2+) cofactor required for catalysis, suggesting that MD2 binds to MraYAA in a manner that overlaps with, but is distinct from, its natural substrate, UDP-MurNAc-pentapeptide. We have determined the principles of MD2 binding to MraYAA, including how it avoids the need for pyrophosphate and sugar moieties, which are essential features for substrate binding. The conformational plasticity of MraY could be the reason that it is the target of many structurally distinct inhibitors. These findings can inform the design of new inhibitors targeting MraY as well as its paralogues, WecA and TarO.

Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis.

Arsenosugars are a group of arsenic-containing ribosides that are found predominantly in marine algae but also in terrestrial organisms. It has been proposed that arsenosugar biosynthesis involves a key intermediate 5'-deoxy-5'-dimethylarsinoyl-adenosine (DDMAA), but how DDMAA is produced remains elusive. Now, we report characterization of ArsS as a DDMAA synthase, which catalyzes a radical S-adenosylmethionine (SAM)-mediated alkylation (adenosylation) of dimethylarsenite (DMAsIII ) to produce DDMAA. This radical-mediated reaction is redox neutral, and multiple turnover can be achieved without external reductant. Phylogenomic and biochemical analyses revealed that DDMAA synthases are widespread in distinct bacterial phyla with similar catalytic efficiencies; these enzymes likely originated from cyanobacteria. This study reveals a key step in arsenosugar biosynthesis and also a new paradigm in radical SAM chemistry, highlighting the catalytic diversity of this superfamily of enzymes.

Lipid Requirements for the Enzymatic Activity of MraY Translocases and in Vitro Reconstitution of the Lipid II Synthesis Pathway.

Screening of new compounds directed against key protein targets must continually keep pace with emerging antibiotic resistances. Although periplasmic enzymes of bacterial cell wall biosynthesis have been among the first drug targets, compounds directed against the membrane-integrated catalysts are hardly available. A promising future target is the integral membrane protein MraY catalyzing the first membrane associated step within the cytoplasmic pathway of bacterial peptidoglycan biosynthesis. However, the expression of most MraY homologues in cellular expression systems is challenging and limits biochemical analysis. We report the efficient production of MraY homologues from various human pathogens by synthetic cell-free expression approaches and their subsequent characterization. MraY homologues originating from Bordetella pertussis, Helicobacter pylori, Chlamydia pneumoniae, Borrelia burgdorferi, and Escherichia coli as well as Bacillus subtilis were co-translationally solubilized using either detergent micelles or preformed nanodiscs assembled with defined membranes. All MraY enzymes originating from Gram-negative bacteria were sensitive to detergents and required nanodiscs containing negatively charged lipids for obtaining a stable and functionally folded conformation. In contrast, the Gram-positive B. subtilis MraY not only tolerates detergent but is also less specific for its lipid environment. The MraY·nanodisc complexes were able to reconstitute a complete in vitro lipid I and lipid II forming pipeline in combination with the cell-free expressed soluble enzymes MurA-F and with the membrane-associated protein MurG. As a proof of principle for future screening platforms, we demonstrate the inhibition of the in vitro lipid II biosynthesis with the specific inhibitors fosfomycin, feglymycin, and tunicamycin.

Pretreatment of fibrous biomass and growth of biosurfactant-producing Bacillus subtilis on biomass-derived fermentable sugars.

Pretreatment of six fibrous biomasses (switchgrass, alfalfa, soy hulls, soy fiber, DDGS and Baggase) and subsequent hydrolysis using cellulolytic enzymes at a 2.5% (v/v) and 5% (v/v) loading 2.5 (v/v) and 5% (v/v) loading was compared for higher amounts of sugars released. Soaking of biomasses of switchgrass, alfalfa, soy hulls and bagasse in 15% w/w ammonia was optimal at 60 °C for 12 h, followed by enzymatic hydrolysis, yielding 72, 70, 80 and 75% carbohydrate conversions, respectively. However, soaking in ammonia was not needed for soy fiber and DDGS as these contained very little lignin. Ultrasonication for 3 min @ 100% amplitude (170 µM) was found to be optimal for soy fiber and DDGS from which 77 and 83% carbohydrate conversion, respectively, was obtained following enzyme treatment at 5% (w/v) enzyme. The sugars released by enzymatic hydrolysis of pretreated biomass were utilized as an energy source by Bacillus subtilis in fermentation media at 2% (w/v) of concentration. In shake flask trials, cell growth was 15-20% higher on hydrolysates of ammonia-treated switchgrass and alfalfa vs. glucose-based control media due to the presence of a wider range of monomeric sugars (glucose, xylose, arabinose, mannose and galactose). In contrast, growth was less on soy hull hydrolysates prepared with ammonia pretreatment.

Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.

A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

Biosynthesis of a water-soluble lipid I analogue and a convenient assay for translocase I.

Translocase I (MraY/MurX) is an essential enzyme in growth of the vast majority of bacteria that catalyzes the transformation from UDP-MurNAc-pentapeptide (Park's nucleotide) to prenyl-MurNAc-pentapeptide (lipid I), the first membrane-anchored peptidoglycan precursor. MurX has received considerable attention in the development of new tuberculosis (TB) drugs due to the fact that the MurX inhibitors kill exponentially growing Mycobacterium tuberculosis (Mtb) much faster than clinically used TB drugs. Lipid I isolated from Mtb contains the C50-prenyl unit that shows very poor water solubility; thus, this chemical characteristic of lipid I renders MurX enzyme assays impractical for screening and lacks reproducibility of the enzyme assays. We have established a scalable chemical synthesis of Park's nucleotide-N(ε)-dansylthiourea 2 that can be used as a MurX enzymatic substrate to form lipid I analogues. In our investigation of the minimum structure requirement of the prenyl phosphate in the MraY/MurX-catalyzed lipid I analogue synthesis with 2, we found that neryl phosphate (C10 phosphate) can be recognized by MraY/MurX to generate the water-soluble lipid I analogue in quantitative yield under the optimized conditions. Here, we report a rapid and robust analytical method for quantifying MraY/MurX inhibitory activity of library molecules.

Patterns of major metabolites biosynthesis by different mushroom fungi grown on glucose-based submerged cultures.

The biosynthetic potential of four basidiomycetes (Agrocybe aegerita, Flammulina velutipes, Ganoderma applanatum and Pleurotus pulmonarius) and one ascomycete (Morchella esculenta) was examined in regard to biomass, intracellular (endopolysaccharides and lipids) and extracellular (exopolysaccharides) compounds' production in liquid media with glucose as substrate, in static and agitated cultures. Exopolysaccharides' production presented significant negative correlation with biomass, endopolysaccharides and lipids, while biomass was positively related to the production of endopolysaccharides and lipids. Maximum values of biomass, endo- and exo-polysaccharides obtained were quite impressive: P. pulmonarius produced 22.5 g/L of biomass, A. aegerita 60.4 % (w/w) of endopolysaccharides and F. velutipes 1.2 g/L of exopolysaccharides. Polysaccharides and lipids synthesized at the early growth stages were subjected to degradation as the fermentation proceeded. Mycelial lipids of all strains were highly unsaturated, dominated by linoleic acid, whereas glucose was the main building block of endopolysaccharides. The ability of the examined mushroom fungi to synthesize in high quantities biomass and polysaccharides, products with biotechnological and medicinal interest, renders these fungi as potential candidates in sugar-based bio-refineries.

[Cellulolytic activity of Fenellia flavipes and Fusarium oxysporum strains].

The production of cellulolytic enzymes by Fenellia flavipes and Fusarium oxysporum strains in submerged culture with plant residues as carbon source was studied. It was established that the majority of studied strains was able to hydrolyze the filter paper, husk of sunflower seeds, wheat straw and corn stalks. The ability to synthesize enzymes depended on the strain of microscopic fungi, type of substrate and duration of cultivation. As a result two fungal strains were selected: F. flavipes 655 with maximum of cellulolytic activity 2 U/ml in the medium with wheat straw and 1.6 U/ml in the medium with corn stalks on the 4th day of cultivation and F. oxysporum 420 which synthesized 0.875 mg/ml of reducing sugars.

[Antifungal and antiviral substances of Pseudomonas chlororaphis subsp. aureofaciens strains--components of gaupsin].

Phenazine-1-carboxylic, 2-hydroxy-phenazine-carboxylic acid and 2-hydroxy-phenazine active against phytopathogenic fungi were detected in fermentation broth of Pseudomonas chlororaphis subsp.aureofaciens strains UCM B-111 and UCM B-306--components of insectofungicide biopreparation gaupsin using chromato-mass-spectrometric methods; strain B-306 produced antifungal antibiotic pyrrolnitrin together with phenazines. Supernatants of fermentation broth of P chlororaphis subsp. aureofaciens B-111 and B-306 strains grown in King A medium and exopolymers preparations obtained from these supernatants using evaporation, dialysis and liophylisation were highly active against tobacco mosaic virus (TMV). At a dose of 10 mg/ml they reduced TMV infectivity by 76-96%, at concentrations 1 and 0.1 mg/ml the antiviral effect was decreased to 40-62 and 14-27%, respectively. Dialysis did not influence the antiviral activity of isolated preparations. The latter contained 2-7.6 % of carbohydrates including neutral monosaccharides: fucose, mannose, galactose and glucose.

Metabolic manipulation of glycosylation disorders in humans and animal models.

In the last decade, over 40 inherited human glycosylation disorders were identified. Most patients have hypomorphic, rather than null alleles. The phenotypic spectrum is broad and most of the disorders affect embryonic and early post-natal development; a few appear in adult life. Some deficiencies can be treated with simple dietary sugar (monosaccharide) supplements. Here we focus on four glycosylation disorders that have been treated with supplements in patients or in model systems, primarily the mouse. Surprisingly, small differences in the amount of exogenous sugar have a major impact on the diseases in specific cells or organs while others are unaffected. The underlying mechanisms are mostly unknown, but changes in the contributions of the de novo, salvage and dietary pathways may contribute to the beneficial outcome. Clearly, the metabolic chart is not flat; all arrows are not equally robust at all points of time and space. This metabolic perspective may help explain some of these observations and guide the development of other vertebrate models of glycosylation disorders that can respond to dietary manipulation.

Methylthioxylose--a jewel in the mycobacterial crown?

Ten years ago an unusual sugar was discovered in a cell wall polysaccharide of Mycobacterium tuberculosis. Structural elucidation revealed the presence of the first thiosugar in a bacterial polysaccharide. Synthetic studies have helped to define its relative and absolute configuration as α-D-methylthioxylofuranosyl. While its biosynthetic origins remain the subject of speculation, work has begun to define its possible biological roles.

Formation of a vitamin C conjugate of acrolein and its paraoxonase-mediated conversion into 5,6,7,8-tetrahydroxy-4-oxooctanal.

Vitamin C (ascorbic acid) has been reported to participate in Michael addition reactions in vitro to form vitamin C conjugates with alpha,beta-unsaturated aldehydes, such as acrolein. This study shows evidence for the formation and metabolism of the vitamin C conjugate of acrolein (AscACR) in cultured human monocytic THP-1 cells exposed to acrolein diacetate. By using (18)O and (13)C labeling in combination with liquid chromatography-tandem mass spectrometry, AscACR was shown to undergo hydrolytic conversion of the ascorbyl lactone into an intermediate carboxylic acid. Subsequent decarboxylation of the carboxylic acid yielded 5,6,7,8-tetrahydroxy-4-oxooctanal (THO). When THP-1 cells were pretreated with ascorbic acid (1 mM, 18 h) and then exposed to acrolein diacetate, THO was detected as its pentafluorobenzyl oxime derivative in the cell lysates and medium. Treatment of THP-1 cells with both ascorbic acid and acrolein diacetate was required for THO formation. The formation of THO from AscACR was facilitated by the lactonase enzymes, human recombinant paraoxonases 1 and 2. THP-1 cells exhibited PON activity, which explains the catalytic conversion of AscACR into THO in these cells. THO was formed in addition to metabolites of the glutathione conjugate of acrolein, indicating that THO formation contributes to the elimination of acrolein in a cellular environment.

Comparison of Ethanol Yield Coefficients Using Saccharomyces cerevisiae, Candida lusitaniae, and Kluyveromyces marxianus Adapted to High Concentrations of Galactose with Gracilaria verrucosa as Substrate.

The red seaweed Gracilaria verrucosa has been used for the production of bioethanol. Pretreatment for monosaccharide production was carried out with 12% (w/v) G. verrucosa slurry and 500 mM HNO3 at 121°C for 90 min. Enzymatic hydrolysis was performed with a mixture of commercial enzymes (Cellic C-Tec 2 and Celluclast 1.5 L; 16 U/ml) at 50°C and 150 rpm for 48 h. G. verrucosa was composed of 66.9% carbohydrates. In this study, 61.0 g/L monosaccharides were obtained from 120.0 g dw/l G. verrucosa. The fermentation inhibitors such as hydroxymethylfurfural (HMF), levulinic acid, and formic acid were produced during pretreatment. Activated carbon was used to remove HMF. Wildtype and adaptively evolved Saccharomyces cerevisiae, Candida lusitaniae, and Kluyveromyces marxianus were used for fermentation to evaluate ethanol production.

Metabolism of hibifolin by human intestinal bacteria.

Hibifolin, the highest-content bioactive flavonoid of the flowers of Abelmoschus manihot, was incubated with human intestinal bacteria, and four metabolites (1-4) were obtained from the incubated solution by chromatographic methods. The structures of the four metabolites were elucidated as gossypetin 8-O-beta-D-4''-deoxy- Delta(4'')-glucuropyranoside (1), gossypetin (2), quercetin (3), and 8-methoxy-quercetin (4), respectively, on the basis of UV, NMR, and MS data. Metabolite 1 was obtained as a new compound with a specific beta-D-4''-deoxy-Delta(4'')-glucuropyranosyl moiety, which was formed through a unique and novel metabolic pathway that has not been reported previously.

Extracellular polysaccharides produced by cooling water tower biofilm bacteria and their possible degradation.

The extracellular polymers (EPS) of biofilm bacteria that can cause heat and mass transfer problems in cooling water towers in the petrochemical industry were investigated. In addition, these microorganisms were screened for their ability to grow and degrade their own EPS and the EPS of other species. Twelve bacteria producing the most EPS were isolated from cooling water towers and characterized biochemically by classic and commercial systems. These were species of Pseudomonas, Burkholderia, Aeromonas, Pasteurella, Pantoea, Alcaligenes and Sphingomonas. EPS of these species were obtained by propan-2-ol precipitation and centrifugation from bacterial cultures in media enriched with glucose, sucrose or galactose. EPS yields were of 1.68-4.95 g l(-1). These EPS materials were characterized for total sugar and protein contents. Their total sugar content ranged from 24 to 56% (g sugar g(-1) EPS), and their total protein content ranged from 10 to 28% (g protein g(-1) EPS). The monosaccharide compositions of EPS were determined by HPLC. Generally, these compositions were enriched in galactose and glucose, with lesser amounts of mannose, rhamnose, fructose and arabinose. All bacteria were investigated in terms of EPS degradation. Eight of the bacteria were able to utilize EPS from Burkholderia cepacia, seven of the bacteria were able to utilize EPS from Pseudomonas sp. and Sphingomonas paucimobilis. The greatest viscosity reduction of B. cepacia was obtained with Pseudomonas sp. The results show that the bacteria in this study are able to degrade EPS from biofilms in cooling towers.

Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.

High-throughput sequencing of microbial genomes has allowed the application of functional genomics methods to species lacking well-developed genetic systems. For the model hyperthermophile Thermotoga maritima, microarrays have been used in comparative genomic hybridization studies to investigate diversity among Thermotoga species. Transcriptional data have assisted in prediction of pathways for carbohydrate utilization, iron-sulfur cluster synthesis and repair, expolysaccharide formation, and quorum sensing. Structural genomics efforts aimed at the T. maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins. The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes.

Enzyme structures of the bacterial peptidoglycan and wall teichoic acid biogenesis pathways.

The bacterial cell wall is a complex polymeric structure with essential roles in defence, survival and pathogenesis. Common to both Gram-positive and Gram-negative bacteria is the mesh-like peptidoglycan sacculus that surrounds the outer leaflet of the cytoplasmic membrane. Recent crystallographic studies of enzymes that comprise the peptidoglycan biosynthetic pathway have led to significant new understanding of all stages. These include initial multi-step cytosolic formation of sugar-pentapeptide precursors, transfer of the precursors to activated polyprenyl lipids at the membrane inner leaflet and flippase mediated relocalization of the resulting lipid II precursors to the outer leaflet where glycopolymerization and subsequent peptide crosslinking are finalized. Additional, species-specific enzymes allow customized peptidoglycan modifications and biosynthetic regulation that are important to bacterial virulence and survival. These studies have reinforced the unique and specific catalytic mechanisms at play in cell wall biogenesis and expanded the atomic foundation to develop novel, structure guided, antibacterial agents.

Metabolism of indole-3-acetic acid in rice: identification and characterization of N-beta-D-glucopyranosyl indole-3-acetic acid and its conjugates.

A search was made for conjugates of indole-3-acetic acid (IAA) in rice (Oryza sativa) using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) in order to elucidate unknown metabolic pathways for IAA. N-beta-d-Glucopyranosyl indole-3-acetic acid (IAA-N-Glc) was found in an alkaline hydrolysate of rice extract. A quantitative analysis of 3-week-old rice demonstrated that the total amount of IAA-N-Glc was equal to that of IAA. A LC-ESI-MS/MS-based analysis established that the major part of IAA-N-Glc was present as bound forms with aspartate and glutamate. Their levels were in good agreement with the total amount of IAA-N-Glc during the vegetative growth of rice. Further detailed analysis showed that both conjugates highly accumulated in the root. The free form of IAA-N-Glc accounted for 60% of the total in seeds but could not be detected in the vegetative tissue. An incorporation study using deuterium-labeled compounds showed that the amino acid conjugates of IAA-N-Glc were biosynthesized from IAA-amino acids. IAA-N-Glc and/or its conjugates were also found in extracts of Arabidopsis, Lotus japonicus, and maize, suggesting that N-glucosylation of indole can be the common metabolic pathway of IAA in plants.

Byelyankacin: a novel melanogenesis inhibitor produced by Enterobacter sp. B20.

A novel melanogenesis inhibitor, byelyankacin (1), was isolated from the fermentation broth of a bacterial strain. The producing organism, designated B20, was identified as a member of the genus Enterobacter based on taxonomic characteristics. 1 was obtained as a white powder from the culture medium by solvent extraction and serial chromatographic purification. The structure of 1 was determined as (E)-4-(2-isocyanovinyl)phenyl alpha-L-rhamnopyranoside on the basis of spectroscopic data. 1 potently inhibited mushroom tyrosinase and melanogenesis of B16-2D2 melanoma cells with IC50 value of 2.1 nM and 30 nM, respectively.