Properties of the halophilic nuclease of a moderate halophile, Micrococcus varians subsp. halophilus

Domain organization of DNase from Thioalkalivibrio sp. provides insights into retention of activity in high salt environments

Our study indicates that DNA binding domains are common in many halophilic or halotolerant bacterial DNases and they are potential activators of enzymatic activity at high ionic strength. Usually, proteins adapt to high ionic strength by increasing the number of negatively charged residues on the surface. However, in DNases such adaptation would hinder the binding to negatively charged DNA, a step critical for catalysis. In our study we demonstrate how evolution has solved this dilemma by engaging the DNA binding domain. We propose a mechanism, which enables the enzyme activity at salt concentrations as high as 4 M of sodium chloride, based on collected experimental data and domain structure analysis of a secreted bacterial DNase from the extremely halotolerant bacterium Thioalkalivibrio sp. K90mix. The enzyme harbors two domains: an N-terminal domain, that exhibits DNase activity, and a C-terminal domain, comprising a duplicate DNA binding helix-hairpin-helix motif. Here we present experimental data demonstrating that the C-terminal domain is responsible for the enzyme's resistance to high ionic strength.

Halophilic hydrolases as a new tool for the biotechnological industries

Halophilic micro-organisms are able to survive in high salt concentrations because they have developed diverse biochemical, structural and physiological modifications, allowing the catalytic synthesis of proteins with interesting physicochemical and structural properties. The main characteristic of halophilic enzymes that allows them to be considered as a novel alternative for use in the biotechnological industries is their polyextremophilicity, i.e. they have the capacity to be thermostable, tolerate a wide range of pH, withstand denaturation and tolerate high salt concentrations. However, there have been relatively few studies on halophilic enzymes, with some being based on their isolation and others on their characterisation. These enzymes are scarcely researched because attention has been focused on other extremophile micro-organisms. Only a few industrial applications of halophilic enzymes, principally in the fermented food, textile, pharmaceutical and leather industries, have been reported. However, it is important to investigate applications of these enzymes in more biotechnological processes at both the chemical and the molecular level. This review discusses the modifications of these enzymes, their industrial applications and research perspectives in different biotechnological areas.

Halophilic Nuclease of a Moderately Halophilic Bacillus sp.: Production, Purification, and Characterization

A moderately halophilic bacterium, Bacillus sp., isolated from rotting wood on the seashore in Nauru, produced an extracellular nuclease when cultivated aerobically in media containing 1 to 2 M NaCl. The enzyme was purified from the culture filtrate to an electrophoretically homogeneous state by ethanol precipitation, DEAE-Sephadex A-50 column chromatography, and Sephadex G-200 gel filtration. The enzyme consisted of two charge isomers and showed both RNase and DNase activities. Molecular weight was estimated to be 138,000 by Sephadex G-200 gel filtration. The enzyme had marked halophilic properties, showing maximal activities in the presence of 1.4 to 3.2 M NaCl or 2.3 to 3.2 M KCl. The enzyme hydrolyzed thymidine-5'-monophosphate-p-nitrophenyl ester at a rate that increased with NaCl concentration up to 4.8 M. In the presence of both Mg and Ca, activity was greatly enhanced. The activity was lost by dialysis against water and low-salt buffer, but it was protected when 10 mM Ca was added to the dialysis buffer. When the inactivated enzyme was dialyzed against 3.5 M NaCl buffer as much as 68% of the initial activity could be restored. The enzyme exhibited maximal activity at pH 8.5 and at 50 degrees C on DNA and at 60 degrees C on RNA and attacked RNA and DNA exonucleolytically and successively, producing 5'-mononucleotides.

Marinimicrobium haloxylanilyticum sp. nov., a new moderately halophilic, polysaccharide-degrading bacterium isolated from Great Salt Lake, Utah

A new moderately halophilic, strictly aerobic, Gram-negative bacterium, strain SX15(T), was isolated from hypersaline surface sediment of the southern arm of Great Salt Lake (Utah, USA). The strain grew on a number of carbohydrates and carbohydrate polymers such as xylan, starch, carboxymethyl cellulose and galactomannan. The strain grew at salinities ranging from 2 to 22% NaCl (w/v). Optimal growth occurred in the presence of 7-11% NaCl (w/v) at a temperature of 35°C and a pH of 6.7-8.2. Major whole-cell fatty acids were C16:0 (30.5%), C18:0 (14.8%), C18:1ω7c (13.1%) and C12:0 (7.8%). The G+C content of the DNA was 60 ± 0.5 mol%. By 16S rRNA gene sequence analysis, strain SX15(T) was shown to be affiliated to members of the gammaproteobacterial genus Marinimicrobium with pair wise identity values of 92.9-94.6%. The pheno- and genotypic properties suggest that strain SX15(T) represents a novel species of the genus Marinimicrobium for which the name Marinimicrobium haloxylanilyticum is proposed. The type strain is SX15(T) (= DSM 23100(T) = CCUG 59572(T)).

Biology of moderately halophilic aerobic bacteria

The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms.

Effect of amino acid residues at the cleavable site of substrates on the remarkable activation of thermolysin by salts

The activity of thermolysin in the hydrolysis of N-[3-(2-furyl)acryloyl]-glycyl-L-leucine amide and N-carbobenzoxy-L-aspartyl-L-phenylalanine methyl ester is remarkably enhanced in the presence of high concentrations (1-5 M) of neutral salts [Inouye (1992) J. Biochem. (Tokyo) 112, 335-340]. In this study, the effect of salts on such activity has been examined using a series of substrates, furylacryloyl dipeptide amides, which have various hydrophobic amino acids at the cleavable bond. Although the enzyme activity varies widely depending on the substrate employed, the degree of activation at a given concentration of NaCl is considerably similar. This indicates that the degree of activation is not dependent on the hydrophobicity of the amino acid side chains at the scissile bond of the substrates. The molecular activity, kcat, and Michaelis constant, Km, were evaluated separately for substrates N[3-(2-furyl)acryloyl]-L-leucyl-L-alanine amide and N-[3-(2-furyl)acryloyl]L-phenyl-alanyl-L-alanine amide, and the activation was found to be brought about only by an increase in k(cat'). The effectiveness of monovalent cations on the increase of k(cat) was determined to follow the order of Na(+)>K(+)>Li(+).

Immobilized nucleases

Nucleases are important analytical enzymes and are used widely for the determination of nucleic acid structure. Their application depends on the specificity and mode of action of the particular enzyme. Nucleases have also found application in the production of flavor enhancers like 5' IMP and 5' GMP, removal of nucleic acids in single cell protein preparations, and as therapeutic agents. Immobilization of nucleases and the use of immobilized nucleases for various biotechnological applications have been reviewed.

Production of 5′ Nucleotide by Using Halophilic Nuclease H Preferentially Adsorbed on Flocculated Cells of the Halophile Micrococcus varians subsp. halophilus

A bioreactor with a column of flocculated cells of the moderate halophile Micrococcus varians subsp. halophilus which adsorbed the halophilic nuclease H was designed to be used in the production of 5′ nucleotides from RNA. A remarkable characteristic of the flocculated cells was that they preferentially adsorbed much exogenous nuclease, excluding adsorbed 5′ nucleotidase. Furthermore, desalting treatment of the flocculated cells in the presence of 2% MgSO 4 · 7H 2 O gave rise to selective inactivation of 5′ nucleotidase without the loss of nuclease H activity, and 5′-guanylic acid was produced with the bioreactor.

Application of halophilic nuclease H of Micrococcus varians subsp. halophilus to commercial production of flavoring agent 5'-GMP

RNA was degraded at 60 degrees C for 24 h by halophilic nuclease H in supernatants from broth cultures of Micrococcus varians subsp. halophilus containing 12% NaCl. Since contaminating 5'-nucleotidase exhibited almost no activity under these conditions, the 5'-GMP formed could be recovered from the reaction mixture, and the yield was 805 mg from 5 g of RNA.

The halophilic properties of pyruvate kinase from Vibrio costicola, a moderate halophile

Pyruvate kinase from Vibrio costicola, a moderate halophile, appears to be adapted to functioning in the presence of salt. Its stability depends on the ionic strength of the medium. The amino acid composition resembles that of other halophilic enzymes. It is proposed that the halophilic pyruvate kinase utilizes preferentially the Mn++ cofactor which forms more stable complexes in the presence of physiological concentrations of salt.