A CMP-N-acetylneuraminic acid synthetase purified from a marine bacterium, Photobacterium leiognathi JT-SHIZ-145

A cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) synthetase was found in a crude extract prepared from Photobacterium leiognathi JT-SHIZ-145, a marine bacterium that also produces a β-galactoside α2,6-sialyltransferase. The CMP-Neu5Ac synthetase was purified from the crude extract of the cells by a combination of anion-exchange and gel filtration column chromatography. The purified enzyme migrated as a single band (60 kDa) on sodium dodecylsulfate-polyacrylamide gel electrophoresis. The activity of the enzyme was maximal at 35 °C at pH 9.0, and the synthetase required Mg(2+) for activity. Although these properties are similar to those of other CMP-Neu5Ac synthetases isolated from bacteria, this synthetase produced not only CMP-Neu5Ac from cytidine triphosphate and Neu5Ac, but also CMP-N-glycolylneuraminic acid from cytidine triphosphate and N-glycolylneuraminic acid, unlike CMP-Neu5Ac synthetase purified from Escherichia coli.     

Purification, cloning, and expression of an alpha/beta-galactoside alpha-2,3-sialyltransferase from a luminous marine bacterium, Photobacterium phosphoreum

A novel sialyltransferase, alpha/beta-galactoside alpha-2,3-sialyltransferase, was purified from the cell lysate of a luminous marine bacterium, Photobacterium phosphoreum JT-ISH-467, isolated from the Japanese common squid (Todarodes pacificus). The gene encoding the enzyme was cloned from the genomic library of the bacterium using probes derived from the NH(2)-terminal and internal amino acid sequences. An open reading frame of 409 amino acids was identified, and the sequence had 32% identity with that of beta-galactoside alpha-2,6-sialyltrasferase in Photobacterium damselae JT0160. DNA fragments that encoded the full-length protein and a protein that lacked the sequence between the 2nd and 24th residues at the NH(2) terminus were amplified by polymerase chain reactions and cloned into an expression vector. The full-length and truncated proteins were expressed in Escherichia coli, producing active enzymes of 0.25 and 305 milliunits, respectively, per milliliter of the medium in the lysate of E. coli. The truncated enzyme was much more soluble without detergent than the full-length enzyme. The enzyme catalyzed the transfer of N-acetylneuraminic acid from CMP-N-acetylneuraminic acid to disaccharides, such as lactose and N-acetyllactosamine, with low apparent K(m) and to monosaccharides, such as alpha-methyl-galactopyranoside and beta-methyl-galactopyranoside, with much lower apparent K(m). Thus, this sialyltransferase is unique and should be very useful for achieving high productivity in E. coli with a wide substrate range.     

Anti-oxidation of agar oligosaccharides produced by agarase from a marine bacterium

In order to prepare the active agar oligosaccharide, agarase extracted from a strain of unidentified marine bacterium from the South China Sea coast was selected for the agar depolymerization. The optimum decomposing conditions were determined to be pH 7.0, 35 °C and halophilic properties 2%. Three main degraded products, AOS-1, AOS-2 and AOS-3, were separated by ethanol fractionation and anion exchange chromatography. The molecular mass was analyzed by MALDI-TOF-MS. The agar oligosaccharides exhibited antioxidative activities in scavenging hydroxyl free radical, scavenging superoxide anion radical and inhibiting lipid peroxidation. The fragment with the sulfate group showed stronger antioxidative activities than that without the sulfate group. Higher antioxidative activities were found when the molecular mass was increased. The results indicated that the antioxidative activities were closely related to the molecular mass of the agar oligosaccharides and the substitute groups binding the carbohydrate ring.     

Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition

Sialyltransferases are a family of glycosyltransferases that catalyze the transfer of N-acetylneuraminic acid residues from cytidine monophosphate N-acetylneuraminic acid (CMP-NeuAc) as a donor substrate to the carbohydrate groups of glycoproteins and glycolipids as acceptor substrates. We determined the crystal structure of Delta16psp26ST, the N-terminal truncated form of alpha2,6-sialyltransferase from Vibrionaceae Photobacterium sp. JT-ISH-224, complexed with a donor product CMP and an acceptor substrate lactose. Delta16psp26ST has three structural domains. Domain 1 belongs to the immunoglobulin-like beta-sandwich fold, and domains 2 and 3 form the glycosyltransferase-B structure. The CMP and lactose were bound in the deep cleft between domains 2 and 3. In the structure, only Asp232 was within hydrogen-binding distance of the acceptor O6 carbon of the galactose residue in lactose, and His405 was within hydrogen-binding distance of the phosphate oxygen of CMP. Mutation of these residues greatly decreased the activity of the enzyme. These structural and mutational results indicated that Asp232 might act as a catalytic base for deprotonation of the acceptor substrate, and His405 might act as a catalytic acid for protonation of the donor substrate. These findings are consistent with an in-line-displacement reaction mechanism in which Delta16psp26ST catalyzes the inverting transfer reaction. Unlike the case with multifunctional sialyltransferase (Delta24PmST1) complexed with CMP and lactose, the crystal structure of which was recently reported, the alpha2,6 reaction specificity of Delta16psp26ST is likely to be determined by His123.     

Production of RNA by a marine photosynthetic bacterium, Rhodovulum sp.

The marine photosynthetic bacterium, Rhodovulum sp. PS88, produces RNA not only in cells but also as an extracellular polymeric substance during aerobic continuous cultivation in the dark. At a dilution rate of 0.32–0.5 h^–1, the maximum RNA production was 460 mg RNA l^–1 broth (200 mg RNA g^–1 suspended solids) which is a value about 2–3 times more than that of yeast cells.     

Promotion of growth and flocculation of a marine photosynthetic bacterium, Rhodovulum sp. by metal cations

A marine photosynthetic bacterium, Rhodovulum sp., (PS88) isolated from a sea sediment mud self-flocculated during aerobic cultivation in the dark. Flocculation and growth of PS88 were especially by Mg2 up to 10 mM in culture medium. Ca2 had a lesser stimulating effect. © Rapid Science Ltd. 1998     

Removal of a high load of ammonia by a marine bacterium,Vibrio alginolyticus in biofilter

A newly isolated heterotrophic marine bacterium,Vibrio alginolyticus, was used to remove a high load of ammonia gas under non-sterile condition. The cells were inoculated onto an inorganic packing material in a fixed-bed reactor (biofilter), and a high bad of ammonia, in the range of ammonia gas concentration of 170 ppm to 880 ppm, was introduced continuously. Sucrose solution and 3% NaCl was supplied intermittently to supplement the carbon source and water to the biofilter. The average percentage of gas removed exceeded 85% for 107-day operation. The maximum removal capacity and the complete removal capacity were 19 g-N kg⁻¹ dry packing material day⁻¹ and 16 g-N kg⁻¹ dry packing material day⁻¹, respectively, which were about three times greater than those obtained in nitrifying sludge inoculated onto the same packing material. On day 82, the enhanced pressure drop was restored to the normal one by NaOH treatment, and efficient removal characteristics were later observed. During this operation, the non-sterile condition had no significantly adverse effect on the removability of ammonia byV. alginolyticus.     

Removal characteristics of high load ammonia gas by a biofilter seeded with a marine bacterium, Vibrio alginolyticus

When the cells of the newly isolated marine bacterium, Vibrio alginolyticus, were inoculated on to an inorganic packing material in biofilter, and a load of ammonia of 2.4–22.5 g-N kg^–1dry packing material was introduced continuously under non-sterile conditions, the average amount of NH₃removed exceeded 85% over 61-d operation. The maximum removal capacity and the complete removal capacity were 22.8 g-N kg^–1dry packing material dand 18.6 g-N kg^–1dry packing material d, respectively, which were about four times larger than those obtained in autotrophic nitrifying sludge inoculated on the same packing material.     

The dimeric assembly of Photobacterium leiognathi and Salmonella typhimurium SodC1 Cu,Zn superoxide dismutases is affected differently by active site demetallation and pH: an analytical ultracentrifuge study

To establish whether the species-specific variations at the subunit interface of bacterial Cu,Zn superoxide dismutases affect dimer assembly, the association state of the Photobacterium leiognathi (PlSOD) and Salmonella typhimurium (StSOD) enzymes, which differ in 11 out of 19 interface residues, was investigated by analytical ultracentrifugation.The same linkage pattern correlates quaternary assembly, active site metallation, and pH in the two enzymes albeit with quantitative differences. Both holo-enzymes are stable dimers at pH 6.8 and 8.0, although their shape is altered at alkaline pH. In contrast, dimer stability is affected differently by metal removal. Thus, apo-StSOD is a stable dimer at pH 6.8 whereas apo-PlSOD is in reversible monomer-dimer equilibrium. In both apoproteins a pH increase to 8.0 favors monomerization. These effects prove the existence of long-range communication between the active site and the subunit interface and provide a structural explanation for the known functional differences between the two enzymes.     

Physicochemical and rheological properties of a novel emulsifier,EPS-R,produced by the marine bacterium<Emphasis Type="Italic">Hahella chejuensis</Emphasis>

The rheological properties of an exopolysaccharide, EPS-R, produced by the marine bacteriumHahella chejuensis strain 96CJ10356 were investigated. The E₂₄ of 0.5% EPS-R was 89.2%, which was higher than that observed in commercial polysaccharides such as xanthan gum (67.8%), gellan gum (2.01%) or sodium alginate (1.02%). Glucose and galactose are the main sugars in EPS-R, with a molar ratio of ∼1∶6.8, xylose and ribose are minor sugar components. The average molecular mass, as determined by gel filtration chromatography, was 2.2×10³ KDa. The intrinsic viscosities of EPS-R were calculated to be 16.5 and 15.9 dL/g using the Huggins and Kraemer equations, respectively, with a 2.3 dL/g overlap. In terms of rigidity, the conformation of EPS-R was similar to that of caboxymethyl cellulose (5.0×10⁻²). The rheological behavior of EPS-R dispersion indicated that the formation of a structure intermediate between that of a random-coil polysaccharide and a weak gel. The aqueous dispersion of EPS-R at concentrations ranging from 0.25 to 1.0% (w/w) showed a marked shear-thinning property in accordance with Power-law behavior. In aqueous dispersions of 1.0% EPS-R, the consistency index (K) and flow behavior index (n) were 1,410 and 0.73, respectively. EPS-R was stable to pH and salts.     

A major flagellum sialoglycoprotein in sea urchin sperm contains a novel polysialic acid, an alpha2,9-linked poly-N-acetylneuraminic acid chain, capped by an 8-O-sulfated sialic acid residue

A new type of polysialic acid (polySia) structure was demonstrated to occur in a major unknown sialoglycoprotein with a diverse molecular mass of 40-80 kDa in sea urchin sperm. The polySia-containing glycan structure was determined to be HSO(3)-->8Neu5Acalpha2-->9(Neu5Acalpha2-->9)(n-2) Neu5Acalpha2-->6GalNAcalpha1-->Ser/Thr (n, on average 15), based on carbohydrate analysis of the sialoglycopeptide obtained by an exhaustive protease digestion of whole sperm, fluorometric anion-exchange high-performance liquid chromatography, and methylation analysis. The sulfate group was predominantly localized to the nonreducing terminus of the polySia chain. This is the first example of an alpha2,9-linked polySia structure in animal sperm. The polySia-containing sialoglycoprotein was present in sperm flagellum but not in the head. Furthermore, this sialoglycoprotein localized in the sperm lipid raft, which contains an enriched ganglioside (Neu5Acalpha2-->8Neu5Acalpha2-->6GlcCer), a receptor for sperm-activating peptide (speract), and its associated guanylate cyclase.     

A stable alpha-helix-rich intermediate is formed by a single mutation of the beta-sheet protein, src SH3, at pH 3

Recently, we have found a transient intermediate on the folding pathway of src SH3. Intending to investigate the structure of the transient intermediate, we tested a mutant of src SH3, named A45G, using circular dichroism, fluorescence and X-ray solution scattering, and incidentally found that it forms a stable alpha-helix-rich intermediate (I(eq)) (different from the native beta-sheet-based secondary structure) at pH 3.0, but contains only beta-sheets at pH 6.0, whereas wild-type SH3 forms only beta-sheets at both pH 3.0 and pH 6.0. The intermediate I(eq) shows a circular dichroism measured at theta(222)=-10,300 deg.cm(2) dmol(-1), indicating a 31% alpha-helix proportion, as estimated by the CONTIN program. X-ray scattering gave the radius of gyration for I(eq) as 19.1 A at pH 3.0 and 15.4 A at pH 6.0, and Kratky plots showed a clear peak at pH 3.0, 4.0 and 6.0, indicating that I(eq) too is compact. In these parameters, I(eq) closely resembles the kinetically-obtained intermediate I(kin) which we found on the folding pathway of wild-type SH3 at pH 3.0 (radius of gyration 18.7 A and theta(222)=-8700 deg.cm(2)dmol(-1)), indicating a 26% alpha-helix proportion in our previous paper. Refolding experiments with A45G were done at pH 6.0 by stopped-flow apparatus monitored by circular dichroism, and compared to kinetic experiments with wild-type SH3 at pH 6.0. The result showed an alpha-helix-rich intermediate at the same dichroism amplitude, but nine times slower in formation-rate. A pH-jump experiment from pH 3.0 to pH 5.9 on A45G was also performed. This showed no bursts, and the rate of conformation-change was almost as fast as the refolding rate of A45G at pH 6.0. These kinetic experiment data would be consistent with I(eq) being nearly identical to the I(kin), which appeared on the folding pathways of both wild-type SH3 and A45G at pH 3.