Occurrence of Free Ceramide in Acetobacter xylinum

Oryzacystatin, a proteinaceous cysteine proteinase inhibitor (cystatin) from rice seeds and probably the first well-defined cystatin superfamily member of plant origin, was immunologically investigated for its occurrence in rice seeds during maturation and germination. The enzyme-linked immunosorbent assay (ELISA) using anti-oryzacystatin Immunoglobulin G showed that all the investigated 23 cultivars of rice, Oryza sativa L. japónica, contained oryzacystatin at 1 ~ 4 mg % in their seeds. Particularly, oryzacystatin levels were high in precocious cultivars and low in sticky rice cultivars. The use of the ELISA method for the representative rice cultivar, Nipponbare, gave the result that in the seed maturation process, oryzacystatin was synthesized in precedence to total seed protein. In the germination process, oryzacystatin tended to decrease in accordance with degradation of total seed protein.     

Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli

In recent years, Escherichia coli has served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely used E. coli K-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenic E. coli strains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling in E. coli, we now propose a general and systematic dgc and pde nomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains of E. coli in future studies.     

A Novel Type of D-Mannitol Dehydrogenase from Acetobacter xylinum: Occurrence,Purification, and Basic Properties

We purified a novel type of D-mannitol dehydrogenase, which contains a c-type cytochrome and an unknown chromophore in the soluble fraction of an acetic acid bacterium, Acetobacter xylinum KU-1, to homogeneity. The enzyme showed the maximum activity at pH 5 and 40°C. It was stable up to 60°C at pH 6, and was inhibited by Hg²⁺ and p-quinone (K_i = 0.18 mm). The molecular weight of the enzyme was about 140,000, and those of the subunits were 69,000, 51,000, and 20,000; the enzyme is hetero-trimeric and contained 8 g-atoms of Fe per mole. The α-helix content was estimated to be about 52.9%. The enzyme catalyzed phenazine methosulfate dependent oxidation of d-mannitol with an apparent K_m of 98 μm (for d-mannitol) and V_max of 213 μmol/min/mg. The reduced form of the enzyme showed the absorption maxima at 386, 416, 480, 518, 550, and 586 nm, which are attributable to a c-type cytochrome in the enzyme.     

Conserved Spatial Organization of FG Domains in the Nuclear Pore Complex

Selective transport through the nuclear pore complex (NPC) requires nucleoporins containing natively unfolded phenylalanine-glycine (FG) domains. Several differing models for their dynamics within the pore have been proposed. We characterize the behavior of the FG nucleoporins in vivo using polarized fluorescence microscopy. Using nucleoporins tagged with green fluorescent protein along their FG domains, we show that some of these proteins are ordered, indicating an overall orientational organization within the NPC. This orientational ordering of the FG domains depends on their specific context within the NPC, but is independent of active transport and cargo load. For most nups, behavior does not depend on the FG motifs. These data support a model whereby local geometry constrains the orientational organization of the FG nups. Intriguingly, homologous yeast and mammalian proteins show conserved behavior, suggesting functional relevance. Our findings have implications for mechanistic models of NPC transport.     

Genetic analysis of acetan biosynthesis in Acetobacter xylinum: DNA sequence analysis of the aceM gene encoding an UDP-glucose dehydrogenase

Analysis of the nucleotide sequence of a 1592 bp region of Acetobacter xylinum genomic DNA involved in acetan biosynthesis revealed the presence of an open-reading frame (aceM) encoding a protein of 449 amino acids with a molecular weight of 48.5 kDa. The deduced amino acid sequence of aceM displayed high homology to the protein sequences of genes encoding UDP-glucose dehydrogenase (UGDH) activities from other organisms. AceM is likely to encode the UGDH involved in the biosynthesis of UDP-glucuronic acid required for acetanbiosynthesis. This revised version was published online in November 2006 with corrections to the Cover Date.     

Phosphorylation of glycerol and dihydroxyacetone in Acetobacter xylinum and its possible regulatory role.

Extracts of Acetobacter xylinum catalyze the phosphorylation of glycerol and dihydroxyacetone (DHA) by adenosine 5'-triphosphate (ATP) to form, respectively, L-alpha-glycerophosphate and DHA phosphate. The ability to promote phosphorylation of glycerol and DHA was higher in glycerol-grown cells than in glucose- or succinate-grown cells. The activity of glycerol kinase in extracts is compatible with the overall rate of glycerol oxidation in vivo. The glycerol-DHA kinase has been purified 210-fold from extracts, and its molecular weight was determined to be 50,000 by gel filtration. The glycerol kinase to DHA kinase activity ratio remained essentially constant at 1.6 at all stages of purification. The optimal pH for both reactions was 8.4 to 9.2. Reaction rates with the purified enzyme were hyperbolic functions of glycerol, DHA, and ATP. The Km for glycerol is 0.5 mM and that for DHA is 5 mM; both are independent of the ATP concentration. The Km for ATP in both kinase reactions is 0.5 mM and is independent of glycerol and DHA concentrations. Glycerol and DHA are competitive substrates with Ki values equal to their respective Km values as substrates. D-Glyceraldehyde and l-Glyceraldehyde were not phosphorylated and did not inhibit the enzyme. Among the nucleotide triphosphates tested, only ATP was active as the phosphoryl group donor. Fructose diphosphate (FDP) inhibited both kinase activities competitively with respect to ATP (Ki= 0.02 mM) and noncompetitively with respect to glycerol and DHA. Adenosine 5'-diphosphate (ADP) and adenosine 5'-monophosphate (AMP) inhibited both enzymic activities competitively with respect to ATP (Ki (ADP) = 0.4 mM; Ki (AMP) =0.25 mM). A. xylinum cells with a high FDP content did not grow on glycerol. Depletion of cellular FDP by starvation enabled rapid growth on glycerol. It is concluded that a single enzyme from A. xylinum is responsible for the phosphorylation of both glycerol and DHA. This as well as the sensitivity of the enzyme to inhibition by FDP and AMP suggest that it has a regulatory role in glycerol metabolism.     

Characterization of the Biosynthetic Pathway of Cellulose from Glucose and Fructose in Acetobacter xylinum

For characterization of the biosynthetic pathway of cellulose in a cellulose-producing Acetobacter xylinum strain BPR2001, the activities of several enzymes were measured. The activity of phosphoglucose isomerase catalyzing the conversion of fructose-6- phosphate into glucose-6-phosphate was greatly increased by fructose in the medium. The UDP-glucose pyrophosphorylase activity catalyzing the synthesis of UDP-glucose was very high in strain BPR2001, consistent with the idea that this is the key enzyme in cellulose biosynthesis. Strain BPR2001 was found to have a fructose-specific phosphoenolpyruvate-dependent phosphotransferase system (PTS).     

Activities of citrate synthase and other enzymes of Acetobacter xylinum in situ and in vitro.

The activities of a number of enzymes, extracted from Acetobacter xylinum, that are involved in carbohydrate metabolism may be accounted for in situ in permeabilized cells. The kinetic properties of citrate synthase and glycerokinase observed in vitro are also retained in situ. So is the regulatory sensitivity of these enzymes. Both in vitro and in situ, (a) citrate synthase, in contrast with the enzyme for other Gram-negative bacteria, is inhibited by ATP and is insensitive to NADH, and (b) glycerokinase is inhibited by fructose diphosphate and the ratio of its activities towards glycerol and dihydroxyacetone is the same.     

A family of IS1031 elements in the genome of Acetobacter xylinum: nucleotide sequences and strain distribution

An insertion sequence (here called IS 1031A) from Acetobacter xylinum ATCC 23769 has recently been isolated. This study describes the complete nucleotide sequence of IS 1031A as well as the sequences of two novel iso-IS 1031 elements, IS1031C and IS1031D, from A. xylinum ATCC 23769. The three ISs are all exactly 930 bp long, have imperfect terminal inverted repeats of 24 bp for IS1031A and 21 bp for IS1031C and IS1031D, are flanked by three base pair direct repeats, and contain an open reading frame encoding a putative basic protein of 278 amino acids. Because of nucleotide substitutions, IS1031C and IS1031D differ from IS 1031A by 12.9% while IS1031C differs from IS1031D by only 0.6%. Hybridization analyses of total DNA from nine A. xylinum strains showed that all strains contained IS 1031-like elements varying in copy number from three to at least 16. None of three Acetobacter aceti strains examined contained IS1031-like elements. Taken together, the results suggest that A. xylinum contains a family of IS 1031 elements with considerably diversified nucleotide sequences.     

Cellulose component of Acetobacter xylinum pellicle: morphology and its significance for the mechanism of microfibril formation

The cellulose component of native, minimally disturbed pellicles of Acetobacter sylinum has a three-dimensional, microfibrillar, interconnected, ‘brush-wood’ structure. This structure could not originate from a spinneret or extrusion mechanism of cellulose microfibril formation. It may be produced by a mechanism of spontaneous association and post factor crystallization of preformed, transient I → 4β glucans.     

Cloning of the Acetobacter xylinum cellulase gene and its expression in Escherichia coli and Zymomonas mobilis

A DNA fragment corresponding to carboxymethylcellulase activity of Acetobacter xylinum IFO 3288 was isolated and cloned in Escherichia coli, and the DNA sequence was determined. The DNA fragment sequenced had an open-reading frame of 654 base pairs that encoded a protein of 218 amino acid residues with a deduced molecular mass of 23,996 Da. The protein encoded in the DNA fragment expressed in E. coli hydrolyzed a carboxymethylcellulose. This gene was subcloned into the shuttle vector [pZA22; Misawa et al. (1986) Agric Biol Chem 50:3201–3203] between Zymomonas mobilis and E. coli. The recombinant plasmid pZAAC21 was introduced into Z. mobilis IFO 13756 by electroporation. The carboxymethylcellulase gene was efficiently expressed in both bacteria, although the level of expression in Z. mobilis was ten times greater than that in E. coli. Approximately 75% of the total carboxymethylcellulase activity detected in Z. mobilis was located in the periplasmic space (outside of the cytoplasmic space). Enzyme activity was not detected in the periplasmic space, but in the cytoplasm of E. coli.     

AtNHX5 and AtNHX6 Control Cellular K+ and pH Homeostasis in Arabidopsis: Three Conserved Acidic Residues Are Essential for K+ Transport

AtNHX5 and AtNHX6, the endosomal Na⁺,K⁺/H⁺ antiporters in Arabidopsis, play an important role in plant growth and development. However, their function in K⁺ and pH homeostasis remains unclear. In this report, we characterized the function of AtNHX5 and AtNHX6 in K⁺ and H⁺ homeostasis in Arabidopsis. Using a yeast expression system, we found that AtNHX5 and AtNHX6 recovered tolerance to high K⁺ or salt. We further found that AtNHX5 and AtNHX6 functioned at high K⁺ at acidic pH while AtCHXs at low K⁺ under alkaline conditions. In addition, we showed that the nhx5 nhx6 double mutant contained less K⁺ and was sensitive to low K⁺ treatment. Overexpression of AtNHX5 or AtNHX6 gene in nhx5 nhx6 recovered root growth to the wild-type level. Three conserved acidic residues, D164, E188, and D193 in AtNHX5 and D165, E189, and D194 in AtNHX6, were essential for K⁺ homeostasis and plant growth. nhx5 nhx6 had a reduced vacuolar and cellular pH as measured with the fluorescent pH indicator BCECF or semimicroelectrode. We further show that AtNHX5 and AtNHX6 are localized to Golgi and TGN. Taken together, AtNHX5 and AtNHX6 play an important role in K⁺ and pH homeostasis in Arabidopsis. Three conserved acidic residues are essential for K⁺ transport.     

Behavior of Freezable Bound Water in the Bacterial Cellulose Produced by Acetobacter xylinum: An Approach Using Thermoporosimetry

The aim of the study is to examine thermal behavior of water within reticulated structure of bacterial cellulose (BC) films by sub-ambient differential scanning calorimetry (DSC). BC films with different carbon source, either manitol (BC (a)) or glycerol (BC (b)), were produced by Acetobacter xylinum using Hestrin and Shramm culture medium under static condition at 30 ± 0.2°C for 3 days. BC samples were characterized by electron scanning microscopy and X-ray diffraction spectroscopy. The pore analysis was done by B.H.J. nitrogen adsorption. The pre-treated with 100% relative humidity, at 30.0 ± 0.2°C for 7 days samples were subjected to a between 25 and −150°C-cooling–heating cycle of DSC at 5.00°C/min rate. The pre-treated samples were also hydrated by adding 1 μl of water and thermally run with identical conditions. It is observed that cellulose fibrils of BC (a) were thinner and reticulated to form slightly smaller porosity than those of BC (b). They exhibited slightly but non-significantly different crystalline features. The freezable bound water behaved as a water confinement within pores rather than a solvent of polymer which is possible to use thermoporosimetry based on Gibb–Thomson equation to approach pore structure of BC. In comparison with nitrogen adsorption, it was found that thermoporosimetry underestimated the BC porosity, i.e., the mean diameters of 23.0 nm vs. 27.8 nm and 27.9 nm vs. 33.9 nm for BC (a) and BC (b), respectively, by thermoporosimetry vs. B.H.J. nitrogen adsorption. It may be due to large non-freezable water fraction interacting with cellulose, and the validity of pore range based on thermodynamic assumptions of Gibb–Thomson theory.     

Intermediatry steps in Acetobacter xylinum cellulose synthesis: studies with whole cells and cell-free preparations of the wild type and a celluloseless mutant.

Intermediatry steps in cellulose synthesis in Acetobacter xylinum were studied with resting cells and particulate-membranous preparations of the wild-type strain and of a celluloseless mutant. Exogenously supplied [1-14C]glucose was rapidly converted by resting cells of both types into glucose 6-phosphate, glucose 1-phosphate, and uridine glucose 5'-diphosphate (UDP)-glucose and incorporated into lipid-, water-, and alkali-soluble cellular fractions. The decrease in the level of labeled hexose-phosphates and UDP-glucose upon depletion of the exogenous substrate was accounted for by a continuous incorporation of [14C]glucose into cellulose in the wild type and into the above-mentioned cellular components in the mutant. [14C]glucose retained in the alkali- and water-soluble fractions of pulse-labeled wild-type cells was quantitatively chased into cellulose. Sonic extracts of both strains catalyzed the transfer of glucose from UDP-glucose into lipid-, water-, and alkali-soluble materials, as well as into an alkali-insoluble cellulosic beta-1,4-glucan. The results strongly support the sequence glucose leads to glucose 6-phosphate leads to glucose 1-phosphate leads to UDP-glucose leads to cellulose and indicate that lipid- and protein-linked cellodextrins may function as intermediates between UDP-glucose and cellulose in A. xylinum.     

Competence of Genetic Transformation correlated with the Occurrence of Fimbriae in Three Bacterial Species

THE involvement of bacterial fimbriae (pili) in some cases of phage infection and in bacterial conjugation has been known or presumed for some years¹. Studies in our laboratories show that fimbriae are also associated with genetic transformation in several bacterial species.