Mutational analysis in Corynebacterium stationis MFS transporters for improving nucleotide bioproduction.

Product secretion from an engineered cell can be advantageous for microbial cell factories. Extensive work on nucleotide manufacturing, one of the most successful microbial fermentation processes, has enabled Corynebacterium stationis to transport nucleotides outside the cell by random mutagenesis; however, the underlying mechanism has not been elucidated, hindering its applications in transporter engineering. Herein, we report the nucleotide-exporting major facilitator superfamily (MFS) transporter from the C. stationis genome and its hyperactive mutation at the G64 residue. Structural estimation and molecular dynamics simulations suggested that the activity of this transporter improved via two mechanisms: (1) enhancing interactions between transmembrane helices through the conserved "RxxQG" motif along with substrate binding and (2) trapping substrate-interacting residue for easier release from the cavity. Our results provide novel insights into how MFS transporters change their conformation from inward- to outward-facing states upon substrate binding to facilitate efflux and can contribute to the development of rational design approaches for efflux improvements in microbial cell factories. KEYPOINTS: • An MFS transporter from C. stationis genome and its mutation at residue G64 were assessed • It enhanced the transporter activity by strengthening transmembrane helix interactions and trapped substrate-interacting residues • Our results contribute to rational design approach development for efflux improvement.

Effusibacillus dendaii sp. nov. isolated from farm soil.

A Gram-positive, rod-shaped, spore-forming, thermophilic, and acidophilic bacterium, designated as strain skT53T, was isolated from farm soil in Tokyo, Japan. Under aerobic conditions, the strain grew at 35-55 °C (optimum temperature 44-55 °C) and pH 4.0-6.0 (optimum pH 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was moderately related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.2 mol%, and MK-7 was the predominant respiratory quinone in the strain. The major fatty acids were anteiso-C15:0, iso-C15:0, and iso-C16:0. Based on the phenotypic and chemotaxonomic characteristics, as well as 16S rRNA gene sequence similarity and whole genome analyses, strain skT53T represents a novel species in the genus Effusibacillus, for which the name Effusibacillus dendaii sp. nov. has been proposed. The type strain is skT53T (= NBRC 114101 T = TBRC 11241 T).

Complete Genome Sequence of Effusibacillus sp. Strain skT53, Isolated from Farm Soil.

This study reports the complete genome sequence of Effusibacillus sp. strain skT53. The genome is 3,454,394 bp in length and has a G+C content of 48.22 mol%.

The impact of the C-terminal domain on the gating properties of MscCG from Corynebacterium glutamicum.

The mechanosensitive (MS) channel MscCG from the soil bacterium Corynebacterium glutamicum functions as a major glutamate exporter. MscCG belongs to a subfamily of the bacterial MscS-like channels, which play an important role in osmoregulation. To understand the structural and functional features of MscCG, we investigated the role of the carboxyl-terminal domain, whose relevance for the channel gating has been unknown. The chimeric channel MscS-(C-MscCG), which is a fusion protein between the carboxyl terminal domain of MscCG and the MscS channel, was examined by the patch clamp technique. We found that the chimeric channel exhibited MS channel activity in Escherichia coli spheroplasts characterized by a lower activation threshold and slow closing compared to MscS. The chimeric channel MscS-(C-MscCG) was successfully reconstituted into azolectin liposomes and exhibited gating hysteresis in a voltage-dependent manner, especially at high pipette voltages. Moreover, the channel remained open after releasing pipette pressure at membrane potentials physiologically relevant for C. glutamicum. This contribution to the gating hysteresis of the C-terminal domain of MscCG confers to the channel gating properties highly suitable for release of intracellular solutes.

Glutamate is excreted across the cytoplasmic membrane through the NCgl1221 channel of Corynebacterium glutamicum by passive diffusion.

The NCgl1221 gene, which encodes a mechanosensitive channel, has been reported to be critically involved in glutamate (Glu) overproduction by Corynebacterium glutamicum, but direct evidence of Glu excretion through this channel has not yet been provided. In this study, by electrophysiological methods, we found direct evidence of Glu excretion through this channel by passive diffusion. We found that the introduction into Phe-producing Escherichia coli of mutant NCgl1221 genes that induce Glu overproduction by C. glutamicum improved productivity. This suggests a low-substrate preference of this channel, indicates its potential as a versatile exporter, and more broadly, indicates the potential of exporter engineering.

Down-regulation of UDP-arabinopyranose mutase reduces the proportion of arabinofuranose present in rice cell walls.

Arabinoxylans may account for up to 25% of the mass of grass cell walls. The interactions of these polysaccharides with themselves and with cellulose and lignin is believed to affect the walls physical properties and increase the walls resistance to biochemical conversion to fermentable sugars. Arabinoxylans have a backbone composed of 1,4-linked ß-D-xylosyl residues, some of which are substituted at O-2 or O-3 with single arabinofuranosyl (Araf) residues. The Araf residues are likely transferred from UDP-Araf to the xylan backbone by arabinofuranosyltransferases. UDP-Araf is itself formed from UDP-arabinopyranose (UDP-Arap) by UDP-arabinopyranose mutase (UAM). In this study, RNA interference (RNAi) was used to suppress UAM expression in rice plants and thereby reduce the amounts of UDP-Araf available for cell wall synthesis. Several of the transgenic plants had reduced proportions of Araf in their walls together with a decrease in the extent of substitution of the xylan backbone, and a reduction of between 25% and 80% in ferulic acid and p-coumaric acid contents of the cell walls. Those transgenic plants with >25% reduction in the amounts of Araf were dwarfed and infertile.

An arginyl residue in rice UDP-arabinopyranose mutase is required for catalytic activity and autoglycosylation.

Plants use UDP-arabinofuranose (UDP-Araf) to donate Araf residues in the biosynthesis of Araf-containing complex carbohydrates. UDP-Araf itself is formed from UDP-arabinopyranose (UDP-Arap) by UDP-arabinopyranose mutase (UAM). However, the mechanism by which this enzyme catalyzes the interconversion of UDP-Arap and UDP-Araf has not been determined. To gain insight into this reaction, functionally recombinant rUAMs were reacted with UDP-Glc or UDP-Araf. The glycosylated recombinant UAMs were fragmented with trypsin, and the glycopeptides formed were then identified and sequenced by LC-MS/MS. The results of these experiments, together with site-directed mutagenesis studies, suggest that in functional UAMs an arginyl residue is reversibly glycosylated with a single glycosyl residue, and that this residue is required for mutase activity. We also provide evidence that a DXD motif is required for catalytic activity.

Purification and biochemical characterization of recombinant rice UDP-arabinopyranose mutase generated in insect cells.

Plants utilize UDP-arabinofuranose (UDP-Araf) in the biosynthesis of Araf-containing complex carbohydrates. UDP-Araf is synthesized from UDP-arabinopyranose by UDP-arabinopyranose mutases (UAMs). Here we describe the heterologous expression of rice (Oryza sativa) UAM genes in insect cells and report some of their enzymatic properties. Recombinant UAMs might serve as useful tools for the biosynthesis of UDP-Araf and might be better than chemical synthesis.

Defects in flagellin glycosylation affect the virulence of Pseudomonas syringae pv. tabaci 6605.

Flagellar motility and its glycosylation are indispensable for the virulence of Pseudomonas syringae pv. tabaci 6605. Six serine residues of the flagellin protein at positions 143, 164, 176, 183, 193 and 201 are glycosylated, and the glycan structure at 201 was determined to consist of a trisaccharide of two L-rhamnosyl residues and a modified 4-amino-4,6-dideoxyglucosyl (viosamine) residue. To investigate the glycan structures attached to the other serine residues and to identify the glycans important for virulence, Ser/Ala-substituted mutants were generated. Six mutant strains that each retained a single glycosylated serine residue were generated by replacing five of the six serine residues with alanine residues. MALDI-TOF mass analysis of flagellin proteins revealed that the major component of each glycan was a trisaccharide basically similar to that at position 201, but with heterogeneity in glycoform distribution. Swarming motility and amounts of acylhomoserine lactones (AHLs) as quorum-sensing signal molecules were significantly reduced, especially in the S143-5S/A, S164-5S/A and S201-5S/A mutants, whereas tolerance to antibiotics was increased in these three mutants. All the mutants showed lower ability to cause disease on host tobacco plants. These results supported our previous finding that glycosylation of the most externally located sites on the surface of the flagellin molecule, such as S176 and S183, is required for virulence in P. syringae pv. tabaci 6605. Furthermore, it is speculated that flagellum-dependent motility might be correlated with quorum sensing and antibiotic resistance.

Structural characterization of an O-linked tetrasaccharide from Pseudomonas syringae pv. tabaci flagellin.

The flagellin of Pseudomonas syringae pv. tabaci is a glycoprotein that contains O-linked oligosaccharides composed of rhamnosyl and 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methylglucosyl residues. These O-linked glycans are released by hydrazinolysis and then labeled at their reducing ends with 2-aminopyridine (PA). A PA-labeled trisaccharide and a PA-labeled tetrasaccharide are isolated by normal-phase high-performance liquid chromatography. These oligosaccharides are structurally characterized using mass spectrometry and NMR spectroscopy. Our data show that P. syringae pv. tabaci flagellin is glycosylated with a tetrasaccharide, 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methyl-Glcp-(1-->3)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->2)-alpha-L-Rha-(1-->, as well a trisaccharide, 4,6-dideoxy-4-(3-hydroxybutanamido)-2-O-methyl-Glcp-(1-->3)-alpha-L-Rhap-(1-->2)-alpha-L-Rha-(1-->, which was identified in a previous study.

Genetic analysis of genes involved in synthesis of modified 4-amino-4,6-dideoxyglucose in flagellin of Pseudomonas syringae pv. tabaci.

Glycosylation of flagellin contributes to swimming and swarming motilities, adhesion ability, and consequently virulence in Pseudomonas syringae pv. tabaci 6605. Glycans attached to six serine residues are located in the central region of the flagellin polypeptide. The glycan structure at position Ser 201 was recently revealed to consist of two L-rhamnoses and one modified 4-amino-4,6-dideoxyglucose (viosamine). To clarify the mechanisms for glycosylation of modified viosamine, genes encoding dTDP-viosamine aminotransferase (vioA), dTDP-viosamine acetyltransferase (vioB), and viosamine-derivative transferase (vioT) were isolated and defective mutants were generated. MALDI-TOF-MS analysis of a lysyl endopeptidase-digested peptide including all six glycosylation sites from each flagellin indicated that the molecular masses of the three flagellin mutants were reduced with highly heterogeneous patterns at regular intervals of 146 Da in the mass range from m/z 13,819 to 15,732. The data indicated that the glycopeptides obtained from mutants had glycans consisting only of deoxyhexose instead of the flagellin glycans including the viosamine derivatives determined previously. The motility and virulence on host tobacco leaves were strongly impaired in the Delta vioA mutant and were weakly reduced in the Delta vioB and Delta vioT mutant strains. These results suggest that the genes vioA, vioB, and vioT are essential for glycosylation of flagellin, and accordingly are required for bacterial virulence.

Properties of family 79 beta-glucuronidases that hydrolyze beta-glucuronosyl and 4-O-methyl-beta-glucuronosyl residues of arabinogalactan-protein.

The carbohydrate moieties of arabinogalactan-proteins (AGPs), which are mainly composed of Gal, L-Ara, GlcA, and 4-Me-GlcA residues, are essential for the physiological functions of these proteoglycans in higher plants. For this study, we have identified two genes encoding family 79 beta-glucuronidases, designated AnGlcAase and NcGlcAase, in Aspergillus niger and Neurospora crassa, respectively, based on the amino acid sequence of a native beta-glucuronidase purified from a commercial pectolytic enzyme preparation from A. niger. Although the deduced protein sequences of AnGlcAase and NcGlcAase were highly similar, the recombinant enzymes expressed in Pichia pastoris exhibited distinct substrate specificity toward 4-Me-GlcA residues of AGPs: recombinant AnGlcAase (rAnGlcAase) substantially liberated both GlcA and 4-Me-GlcA residues from radish AGPs, whereas recombinant NcGlcAase (rNcGlcAase) activity on the 4-Me-GlcA residues of AGPs was very low. Maximum activity of rAnGlcAase hydrolyzing PNP beta-GlcA occurred at pH 3.0-4.0, whereas the maximum rNcGlcAase activity was at pH 6.0. The apparent Km values of rAnGlcAase were 30.4 microM for PNP beta-GlcA and 422 microM for beta-GlcA-(1-->6)-Gal, and those of rNcGlcAase were 38.3 microM and 378 microM, respectively. Similar to the native enzyme, rAnGlcAase was able to catalyze the transglycosylation of GlcA residues from PNP beta-GlcA to various monosaccharide acceptors such as Glc, Gal, and Xyl. We propose that both AnGlcAase and NcGlcAase are instances of a novel type of beta-glucuronidase with the capacity to hydrolyze beta-GlcA and 4-Me-beta-GlcA residues of AGPs, although they differ significantly in their preferences.

Chain elongation of pectic beta-(1-->4)-galactan by a partially purified galactosyltransferase from soybean (Glycine max Merr.) hypocotyls.

Pectin is one of the major cell wall polysaccharides found in dicotyledonous plants. We have solubilized and partially purified a beta-(1-->4)-galactosyltransferase (GalT) involved in the synthesis of the beta-(1-->4)-galactan side chains of pectin. The enzyme protein was almost completely solubilized by mixing a crude microsomal preparation of etiolated 6-day-old soybean (Glycine max Merr.) hypocotyls with a detergent, Triton X-100 (0.75%, w/v), in buffer. The solubilized enzyme was partially purified by ion-exchange chromatography. The crude membrane-bound GalT transferred Gal from UDP-Gal onto 2-aminobenzamide (AB)-derivatized beta-(1-->4)-galactoheptaose (Gal(7)-AB), leading to the formation of Gal(8-11)-AB by attachment of a series of one to four galactosyl residues; this is similar to what has previously been observed for 2-aminopyridine-derivatized beta-(1-->4)-galactooligomer acceptors (Konishi et al. in Planta 218:833-842, 2004). The partially purified GalT, by contrast, was able to transfer more than 25 galactosyl residues and elongated the chains to about Gal(35)-AB, thus almost reaching the length (43-47 Gal units) of native beta-(1-->4)-galactan side chains found in pectic polysaccharides from soybean cotyledons (Nakamura et al. in Biosci Biotechnol Biochem 66:1301-1313, 2002). Enzyme activity increased with increasing chain length of beta-(1-->4)-galactooligomers and reached maximal activity at heptaose, whereas galactooligomers higher than heptaose showed lower acceptor efficiency.

Properties and physiological functions of UDP-sugar pyrophosphorylase in Arabidopsis.

UDP-sugar pyrophosphorylase catalyzes the conversion of various monosaccharide 1-phosphates to the respective UDP-sugars in the salvage pathway. Using the genomic database, we cloned a putative gene for UDP-sugar pyrophosphorylase from Arabidopsis. Although relatively stronger expression was detected in the vascular tissue of leaves and the pollen, AtUSP is expressed in most cell types of Arabidopsis, indicating a housekeeping function in nucleotide sugar metabolism. Recombinant AtUSP expressed in Escherichia coli exhibited broad specificity toward monosaccharide 1-phosphates, resulting in the formation of various UDP-sugars such as UDP-glucose, -galactose, -glucuronic acid, -xylose and -L-arabinose. A loss-of-function mutation in the AtUSP gene caused by T-DNA insertion completely abolished male fertility. These results indicate that AtUSP functions as a UDP-sugar pyrophosphorylase in the salvage pathway, and that the generation of UDP-sugars from monosaccharide 1-phosphates catalyzed by AtUSP is essential for pollen development in Arabidopsis.

An alpha-L-arabinofuranosidase/beta-D-xylosidase from immature seeds of radish (Raphanus sativus L.).

The carbohydrate moieties of arabinogalactan proteins (AGPs) are essential for their physiological functions and undergo rapid turnover in vivo. Degradation of the carbohydrate moieties of AGPs seems to occur by concerted action of several glycosidases, among them alpha-L-arabinofuranosidase, beta-D-galactosidase, and beta-D-glucuronidase. Here, a bifunctional alpha-L-arabinofuranosidase/beta-D-xylosidase from immature seeds of radish (Raphanus sativus L.), which hydrolyses alpha-L-arabinofuranosyl residues of the carbohydrate moieties of AGPs, has been cloned by reverse transcriptase-PCR. The gene, designated RsAraf1, contained an open reading frame of 2343 bp (780 amino acids), including a putative signal sequence (33 amino acids) at the N-terminus. RsAraf1 is highly similar to barley alpha-L-arabinofuranosidase/beta-D-xylosidases and belongs to family 3 of the glycosyl hydrolases based on sequence homology. Southern blot analysis revealed that several related genes exist in the radish genome. RsAraf1 is expressed throughout seed development and weakly expressed in young seedlings. It was found that alpha-L-arabinofuranosidase activity in a cell-wall protein fraction prepared from transgenic Arabidopsis plants with enhanced expression of RsAraf1 was significantly higher than that in a wild-type protein fraction; the crude enzyme preparation released L-arabinose from radish AGPs as well as alpha-(1-->5)-arabinan and arabinoxylan. Accordingly, the amount of L-arabinosyl residues in the cell walls of transgenic plants was significantly decreased. These results indicate that RsAraf1 encodes a bifunctional alpha-L-arabinofuranosidase/beta-D-xylosidase and suggest that RsAraf1 is involved in the hydrolysis of the carbohydrate moieties of AGPs in immature radish seeds.

Molecular cloning of a {beta}-galactosidase from radish that specifically hydrolyzes {beta}-(1->3)- and {beta}-(1->6)-galactosyl residues of Arabinogalactan protein.

A basic beta-galactosidase with high specificity toward beta-(1-->3)- and beta-(1-->6)-galactosyl residues was cloned from radish (Raphanus sativus) plants by reverse transcription-PCR. The gene, designated RsBGAL1, contained an open reading frame consisting of 2,532 bp (851 amino acids). It is expressed in hypocotyls and young leaves. RsBGAL1 was highly similar to beta-galactosidases having exo-beta-(1-->4)-galactanase activity found in higher plants and belongs to family 35 of the glycosyl hydrolases. Recombinant RsBGAL1 was expressed in Pichia pastoris and purified to homogeneity. The recombinant enzyme specifically hydrolyzed beta-(1-->3)- and beta-(1-->6)-galactooligosaccharides, the same substrates as the native enzyme isolated from radish seeds (Sekimata et al., 1989). It split off about 90% of the carbohydrate moieties of an arabinogalactan protein extracted from radish roots in concerted action with microbial alpha-l-arabinofuranosidase and beta-glucuronidase. These results suggest that RsBGAL1 is a new kind of beta-galactosidase with different substrate specificity than other beta-galactosidases that exhibit exo-beta-(1-->4)-galactanase activity. The C-terminal region (9.6 kD) of RsBGAL1 is significantly similar to the Gal lectin-like domain, but this region is not retained in the native enzyme. Assuming posttranslational processing of RsBGAL1 with elimination of the Gal lectin-like domain results in a protein consisting of two subunits with molecular masses of 46 and 34 kD (calculated from the RsBGAL1 gene sequence). This is in good agreement with the SDS-PAGE and matrix-assisted laser desorption/ionization-time-of flight mass spectrometry measurements for subunits of the native enzyme (45 and 34 kD) and may thus partially explain the formation process of the native enzyme.

Potentiometric immunosensor using artificial antibody based on molecularly imprinted polymers.

A potentiometric artificial immunosensor based on a molecularly imprinted polymer was prepared as a detecting element in micro total analysis systems with the intent of providing easy clinical analysis. As the structure and transducing mechanism of this sensor are very simple, construction of a single microsensor should be quite easy. Multimicrosensor arrays applicable to several kinds of analytes will be attainable by both changing the template molecule to be imprinted and reducing the sensor size. The response characteristics of this sensor were evaluated by measuring the response potential to serotonin, which was used as a model material. The obtained sensor was highly responsive to serotonin in water but not to tryptamine, acetaminophen, or procainamide. This phenomenon confirms that the sensor recognizes serotonin and that it functions as a specific artificial immunosensor. Quick measurement is possible because the response time, defined as the time required to achieve 95% of the magnitude of the equilibrated signal, correspond to approximately 12 s. The sensor's determination and detection limits were found to be 1 mumol/L and 100 pmol/L, respectively. These results suggest that our strategy can be applied to construction of a potentiometric artificial immunosensor.

Three novel cantharidin-related compounds from the Chinese blister beetle, Mylabris phalerata Pall.

Three novel cantharidin analogues were isolated from the Chinese blister beetle, Mylabris phalerata PALL. (Meloidae), which has been used in traditional Chinese medicine for the treatment of cancer. Their structures were determined on the basis of heteronuclear multiple-bond connectivity and nuclear Overhauser effect spectroscopy experiments, and chemical data confirmed them to be so-called cantharimides, in which the anhydride oxygen atoms are replaced by the basic amino acid L-lysine, L-ornithine, and L-arginine moieties.

Biosynthesis of pectic galactan by membrane-bound galactosyltransferase from soybean ( Glycine max Merr) seedlings.

We investigated the properties of a galactosyltransferase (GalT) that is involved in the synthesis of beta-(1-->4)-galactan side chains of pectins. A membrane preparation of etiolated 6-day-old soybean ( Glycine max Merr.) hypocotyls transferred [(14)C]Gal from UDP-[(14)C]Gal into intact and partially hydrolyzed lupin beta-(1-->4)-galactans of various chain lengths as exogenous acceptors, while activity to endogenous acceptors was negligible. Maximal activity occurred at pH 6.5 and 20-25 degrees C in the presence of 25 mM Mn(2+) and 0.75% Triton X-100. The transfer reaction onto the unmodified commercial pectic galactan ( M(r)>150000) from lupin we used was very low but increased when the M(r) of the galactan was reduced by partial acid hydrolysis. Among the partially hydrolyzed galactans, high- M(r) (average M(r) 60000) beta-(1-->4)-galactan was a more efficient acceptor [specific activity 2000-3000 pmol min(-1) (mg protein)(-1)] than low- M(r) (average M(r) 10000 and 5000) polymers. Digestion of the radiolabeled product from high- M(r) galactan with endo-beta-(1-->4)-galactanase released mainly radioactive beta-(1-->4)-galactobiose and Gal, indicating that the transfer of [(14)C]Gal occurred through beta-(1-->4)-linkages. HPLC analysis showed that the enzyme also catalyzes incorporation of Gal into pyridylaminated (PA) beta-(1-->4)-galactooligomers with degree of polymerization at least 5. Gal(7)-PA chains were elongated by attachment of one, two, or three Gal residues leading to the formation of Gal(8-10)-PA.