Degradation of Nucleic Acids and their Related Compounds by Microbial Enzymes

Seven strains of microorganisms selected by the previous screening tests were further compared on their ability to produce extracellular enzyme systems capable of degrading RNA into 5′-ribonucleotides. As a result, two strains of Streptomyces were finally concluded to be most preferable. When these two were applied, the rate of 5′-nucleotide production reached up to 70%.

Bacillus subtilis was outstanding in its activity to degrade RNA, but its PDase activity producing 5′-nucleotides from RNA was found to be lower than those of Streptomyces strains. A pathway involving 3′- and 5′-nucleotides as intermediates was proposed for the degradation of RNA by the Bacillus enzyme system. The activity of RNA-degrading enzyme system of Bacillus subtilis contained in the supernatant of culture fluid was found to be lost at 700°C but remained to certain extent at 100°C, a possible mechanism for the phenomenon being discussed. Usability of the Bacillus enzyme system in the practical production of 5′-nucleotides under the condition of high RNA concentration was discussed.     

Excretion of 5′-Nucleotides from Bacterial Cells

Incubating the dried cells of Brevibacterium sojae No. 425-40 in alkaline buffer, the excretion of 5′-nucleotides accompanying with the decrease of intracellular RNA was observed. Then the determination of the optimum condition of the excretion and the investigation on the enzyme responsible for the degradation of endogenous RNA were carried out.

In the experiments using sonicate and disrupted cells, it appeared that orthophos-phate and Mg⁺⁺ might be accelerative or essential for the degradation of endogenous RNA and, in addition to four 5′-nucleotides (AMP, GMP, UMP and CMP), each nucleoside 5′-diphosphate was also contained in its degraded products. Nucleoside 2′- or 3′-monophos-phates were not detected. Although it was not clear whether phosphodiesterase concerned with the degradation of intracellular RNA or not, it was suggested that polynucleotide phos-phorylase acted mainly on the degradation.

The maximal excretion of 5′-nucleotides from dried cells was obtained by suspending 1 to 2% of dried cells in 0.05 M carbonate-bicarbonate buffer (pH 10) and incubating it at 60°C for two to three hours. Orthophosphate and Mg⁺⁺ were not required for the excretion.     

Excretion of 5′-Nucleotides by Bacteria

A Bacillus accumulated 5′-nucleotides in the culture fluid during cultivation. These nucleotides consisted mainly of ribonucleoside 5′-monophosphates and of traces of nucleoside 5′-diphosphates. The composition of the accumulated nucleotides resembled that of the nucleotides of intracellular RNA. Therefore an intimate relationship between the accumulation of nucleotides and the metabolism of endogenous RNA was suggested.

The excretion of 5′-nucleotides into the culture fluid took place in parallel with the reduction of intracellular RNA, and it was presumed that the accumulated nucleotides were products of degradation of intracellular RNA.     

Studies on Metabolic Pathway of NAD in Yeast

Quantitative studies on yeast 5′-nucIeotidase are presented.

K_m values for purine 5′-nucleotides were generally smaller than those for pyrimidine 5′-nucleotides and, among purine series, K_m value for 5′-AMP was the smallest, while their V values were almost same.

The enzyme activity was inhibited in the competitive type by bases, nucleosides, 3′- or 2′-nucleotides, and NMN and in the mixed type by NAD and NADP.

Base-, ribose-, 3′- or 5′-phosphate moiety of nucleoside and nucleotide had some effects on binding with enzyme; especially the structure of base moiety characterizes the K_m or K_i value.

The enzyme activity was accelerated by Ni⁺⁺ or Co⁺⁺, which increases V value but never affects K_m value.

The relationship between the structure of substrate and its affinity towards enzyme is discussed.     

Difference in NaCl tolerance of membrane-bound 5′-nucleotidases purified from deep-sea and brackish water Shewanella species

Shewanella species are widely distributed in sea, brackish, and fresh water areas, growing psychrophilically or mesophilically, and piezophilically or piezo-sensitively. Here, membrane-bound 5′-nucleotidases (NTases) from deep-sea Shewanella violacea and brackish water Shewanella amazonensis were examined from the aspect of NaCl tolerance to gain an insight into protein stability against salt. Both NTases were single polypeptides with molecular masses of ~59 kDa, as determined on mass spectroscopy. They similarly required 10 mM MgCl₂ for their activities, and they exhibited the same pH dependency and substrate specificity for 5′-nucleotides. However, S. violacea 5′-nucleotidase (SVNTase) was active enough in the presence of 2.5 M NaCl, whereas S. amazonensis 5′-nucleotidase (SANTase) exhibited significantly reduced activity with the same concentration of the salt. Although SVNTase and SANTase exhibited high sequence identity (69.7%), differences in the ratio of acidic to basic amino acid residues and the number of potential salt bridges maybe being responsible for the difference in the protein stability against salt. 5′-Nucleotidases from these Shewanella species will provide useful information regarding NaCl tolerance, which may be fundamental for understanding bacterial adaptation to growth environments.

     

Osservazioni Preliminari sui Sistemi Degradanti dell'RNA nei semi di Ricino

Abstract

Preliminary observations on the enzymatic degradation of RNA in castor bean seeds. — Cocucci, Maggio, Monroy and Marrè have shown the decrease of RNA content during ripening in castor bean seeds, and its increase during germination. Furthermore, these Authors have demonstrated that in the dry ripe seeds the ribosomes are undetectable, and that they increase rapidly during germination. Two peaks of ribosomes are easily detected upon ultracentrifugal analysis in germinating seeds (Cocucci and Sturani). These observations were the basis for our investigations of the enzymes of RNA metabolism in castor bean seeds. This paper deals with our preliminary observations on RNA degrading enzymes in these tissues. We have been able to measure RNase activity, phosphodiesterase, 3′-,5′- and 2′-nucleotidases in castor bean seeds at different stages of development. RNase activity (measured in crude extracts) changes little during the ripening process, its rate corresponding to 40–50 μMoles of nucleotides liberated from RNA per hour and per gram of fresh weight. In the dry seeds, RNase activity is 30–40 μMoles of nucleotides/h.g.f.w., and it increases to about 60–70 μMoles/h/g.f.w. after 72 hours of germination.

Phosphodiesterase activity is about 4–5 μMoles/h.g.f.w.

The following rates have been found in seeds almost completely ripe seeds for 3′-, 5′- and 2′-nucleotidase activities, respectively 45–50 μMoles/h.g.f.w.; 6–7 μMoles/h.g.f.w.; 8 μMoles/h.g.f.w.; ATP-ase activity was of about 80–100 μMoles of phosphate liberated /h.g.f.w. - The high activity of 3′-nucleotidase, of the same order of that of RNase, suggests that these two enzymes are responsible for degradation of RNA to nucleosides and inorganic phosphate. Further investigations are being carried on to define the biochemical properties of castor bean RN-ase.     

Bacterial Synthesis of Nucleotides

5′-Phosphoribosyl 5-amino-4-imidazole carboxamide was prepared by incubating 5-amino-4-imidazole carboxamide riboside and a phosphate compound with the bacteria characterized to phosphorylate at C_5′ via the phosphoryl transfer reaction. Aromatic phosphate compounds and 5′-nucleotides were able to act as the phosphate donor. This material was isolated chromatographically and its properties were studied. The other bacteria characterized to phosphorylate at C_{3′ (or 2′)} also phosphorylated a little probably at C_{3′ (or 2′)} of 5-amino-4-imidazole carboxamide riboside.

The phosphoryl interconversion between nucleotides and nucleosides was studied to be carried out via the phosphoryl transfer reaction observed in bacteria. The phosphotransferase activity of Ps. trifolii mediated reversibly the phosphoryl transfer between 5′-nucleotides and nucleosides, and its optimal pH was at around 8.5, whereas that of Prot. mirabilis did transfer the phosphoryl radical from 2′- and 3′-nucleotide to nucleoside at its optimal pH, around 5.0.

These donor- and product-isomer specificities of both bacteria were evident to be invariable, regardless of reaction pH and cultural conditions. These reactions, especially using the bacteria characterized to phosphorylate at C_5′ of nucleoside, were demonstrated to catalyze the phosphoryl interconversion between 5′-purine nucleotides and pyrimidine nucleosides or vice versa.     

Degradation of Nucleic Acids and their Related Compounds by Microbial Enzymes

The distribution in microorganisms of extracellular enzymes which degrade RNA into 5′-mononucleotides was studied. The degradation products of RNA were determined by using 5′-nucleotidase and adenosine deaminase.

It was found that the enzymes were produced by various microorganisms belonging to Streptomyces, Bacillus, Fungi imperfecta such as Fusarium, Helminthosporium, etc., and Ascomycetes such as Neurospora, Glomerella, Aspergillus, etc.     

Degradation of Nucleic Acids and Related Compounds by Microbial Enzymes

The culture filtrate of a strain of Bacillus subtilis decomposed ribonucleic acid into 5′-nucleotides and into other intermediates which released orthophosphate by an arsenate-resistant phosphatase. Under the best conditions examined in these experiments, about 50 per cent of ribonucleic acid was converted into 5′-nucleotides.

The culture filtrate of a strain of Bacillus brevis showed slight activities of ribonuclease and/or phosphodiesterase which produced 5′-nucleotides from ribonucleic acid, but showed predominant activity of 5′-adenylic acid degrading phosphatase.     

Constituents of Plant Leaf Wax Contained in Rice Callus Tissues

Two enzyme preparations having both nuclease and 3′-nucleotidase activities were partially purified from an extract of tea leaves. They resemble each other in most enzymatic properties, but are separated by DEAE-cellulose column chromatography.

The enzyme activities for RNA, native DNA, heat-denatured DNA and 3′-AMP of each preparation showed a high degree of similarity with respect to the following properties: pH stability, thermal stability and response to EDTA. Both enzymes were shown to be endonucleases (EC 3.1.30.2) which liberated 5′-mononucleotides and oligonucleotides from both RNA and DNA with the following relative rate of hydrolysis: RNA > native DNA = heat-denatured DNA.     

Purification and Some Properties of Nucleases from Shii-take,Lentinus edodes

Three kinds of nuclease preparations, each of which having both endonuclease activity that formed 5′-mononucleotides and 3′-nucleotidase activity, were separated and partially purified from Shii-take, Lentinus edodes. Both enzyme activities of each preparation showed a similar thermostability and electrophoretic mobility on Polyacrylamide gel, and a competitive relationship was observed between RNA and 3′-AMP in their enzyme reactions. From these results, it is concluded that both enzyme activities of these three preparations reside in a single protein, respectively. They resemble one another in substrate specificity, cleavage pattern of RNA and thermostability, but are distinguishable from one another by molecular weight, electrophoretic mobility and optimum pH for degradation of RNA.     

Hydrolysis of RNA to 5′-nucleotide by seed sprouts,particularly malt sprouts

Conditions for the efficient conversion of commercial RNA to nucleoside 5′-monophosphate by means of a phosphodiesterase in malt sprouts have been determined. A comparison of the enzyme content of the rootlets, stems, and kernels of various plant seedlings, including barley, rye, oat, wheat, rice, and beans shows maximum amounts in the rootlets, and minimum quantities in the ungerminated kernels. Of all the seedlings tested, (mung bean, soy bean, oat, wheat, rice, barley) barley gave the highest conversion of RNA to 5′-nucleotides. Commercial malt sprouts prepared from 6 different malted barleys including 2-rowed and 6-rowed samples all showed about the same amount of phosphodiesterase content. Besides phosphodiesterase, other enzymes capable of hydrolyzing RNA and 5′-nucleotides were found in sprouts. These included 3′-phosphodiesterases, 5′-nucleotidases, and nucleosidases. By carefully pretreating both extracts and the solid sprouts at elevated temperatures for a limited time and by the addition of minimum amounts of Zn⁺², the action of these undesirable enzymes was either effectively destroyed or minimized so that the production of 5′-nucleotides was maximized. It was found that suspensions of appropriately washed and treated barley malt rootlets are substantially more effective than aqueous extracts for converting RNA to 5′-nucleotides.     

Degradation of RNA during the autolysis of Saccharomyces cerevisiae produces predominantly ribonucleotides

Autolytic degradation of yeast RNA occurs in many foods and beverages and can impact on the sensory quality of the product, but the resulting complex mixture of nucleotides, nucleosides and nucleobases has not been properly characterised. In this study, yeast autolysis was induced by incubating cell suspensions of Saccharomyces cerevisiae at 30–60 °C (pH 7.0), and at pH 4.0–7.0 (40 °C) for 10–14 days, and the RNA degradation products formed during the process were determined by reversed-phase HPLC. Up to 95% of cell RNA was degraded, with consequent leakage into the extracellular environment of mainly 3′-, 5′- and 2′-ribonucleotides, and lesser amounts of polynucleotides, ribonucleosides and nucleobases. The rate of RNA degradation and the composition of the breakdown products varied with temperature and pH. RNA degradation was fastest at 50 °C (pH 7.0). Autolysis at lower temperatures (30 °C and 40 °C) and at pH 5.0 and 6.0 favoured the formation of 3′-nucleotides, whereas autolysis at 40 °C and 50 °C (pH 7.0) favoured 5′- and 2′-nucleotides. The best conditions for the formation of the two flavour-enhancing nucleotides, 5′-AMP and 5′-GMP, were 50 °C (pH 7.0) and pH 4.0 (40 °C), respectively.     

Studies on Metabolic Pathway of NAD in Yeast

The properties of yeast 5′-nucleotidase, one of NAD-metabolic system in yeast, were studied.

1) The enzyme has optimum pH at 5.8~6.1 for its activity and is most stable at pH 6. It is inactivated completely at 55°C for 6 min, pH 7, but never at 40°C for 6 min. 2) The enzyme hydrolyzes only 5′-nucleotides of guanine, adenine, hypoxanthine, uracil and cytosine, but never splits nicotinamide mononucleotide, thiamine monophosphate, ribose 5-monophosphate and flavin mononucleotide. 3) The enzyme seems to have specially high affinity for 5′-AMP. 4) The enzyme activity is accelerated by addition of Co⁺⁺ and Ni⁺⁺, but inhibited by Ag⁺, Cu⁺⁺, EDTA, I₂ and N-bromosuccimide. Mg⁺⁺, KCN, NaF and thiol reagents except p-chloromercuribenzoate have no effects. 5) Nucleosides have inhibitory effects, among which adenosine is most effective inhibitor. 6) The activity is reduced up to 30% by dialysis against 1 mm EDTA solution, and the reduced activity is completely reactivated by addition of Co⁺⁺ or Ni⁺⁺, but not by Mn⁺⁺ or Mg⁺⁺.     

Differences in biochemical properties of two 5′-nucleotidases from deep- and shallow-sea Shewanella species under various harsh conditions

Deep-sea Shewanella violacea 5′-nucleotidase (SVNTase) activity exhibited higher NaCl tolerance than that of a shallow-sea Shewanella amazonensis homologue (SANTase), the sequence identity between them being 70.4%. Here, SVNTase exhibited higher activity than SANTase with various inorganic salts, similar to the difference in their NaCl tolerance. In contrast, SVNTase activity decreased with various organic solvents, while SANTase activity was retained with the same concentrations of the solvents. Therefore, SVNTase is more robust than SANTase with inorganic salts, but more vulnerable with organic solvents. As to protein stability, SANTase was more stable against organic solvents and heat than SVNTase, which correlated with the differences in their enzymatic activities. We also found that SANTase retained higher activity for three weeks than SVNTase did in the presence of glycerol. These findings will facilitate further application of these enzymes as appropriate biological catalysts under various harsh conditions.

Abbreviations: NTase: 5′-nucleotidase; SANTase: Shewanella amazonensis 5′-nucleotidase; SVNTase: Shewanella violacea 5′-nucleotidase; CD: circular dichroism     

The Incorporation of Leucine-U-14C into Ipomeamarone

1. It was demonstrated by silica gel thin layer chromatography that leucine-U-¹⁴C was incorporated into furanoterpenes, e. g. ipomeamarone, in sweet potato root tissue infected by Ceratocystis fimbriata.

2. Further proof for ipomeamarone synthesis from leucine-U-¹⁴C was obtained by the constancy of the specific radioactivity of ipomeamarone semicarbazone through repetitive crystallization.

3. The synthetic pathway of ipomeamarone from leucine was found to be connected with the synthetic pathway from acetate at least at some steps.

4. Leucine-U-¹⁴C was incorporated into both saponifiable and non-saponifiable materials in the same way as acetate-2-¹⁴C.     

Substrate Properties of Adenosine- and Uridine- 3′, 5′-bisphenylphosphonates for 3′-Nucleotidase/Nucleases

Abstract

3′, 5′-Bisphenylphosphonate and 5′-phenylphosphonate esters of adenosine and uridine were synthesized to investigate the substrate properties of the 3′, 5′-bisphenylphosphonates for 3′-nucleotidase/nucleases. The V _max/apparent K _m, values of the enzymes for them were found to be 9 to 21-fold higher than those for the corresponding nucleoside 3′-phenylphosphonates.     

S1 nuclease of Aspergillus oryzae: a glycoprotein with an associated nucleotidase activity

S₁ nuclease (EC 3.1.30.1) of Aspergillus oryzae has been purified 1600-fold by a procedure designed to remove traces of contaminating phosphatases. The nearly homogeneous enzyme was found to be a glycoprotein with a carbohydrate content of 18%. At pH 4.5 the enzyme preparation hydrolyzed single-stranded DNA, RNA, 3′-AMP, and 2′-AMP at relative rates of 100, 52, 13, and 0.05, respectively. The 3′-nucleotidase activity of this single-strand specific nuclease is inhibited by single-stranded DNA but not by double-stranded DNA. Three forms of the enzyme, with isoelectric points of 3.35, 3.53, and 3.67, were observed on electrofocusing, and each form exhibited the same relative activity on single-stranded DNA and 3′-AMP. Enzymatic hydrolysis of nucleotides occurred over a broad range of pH, with maximal activity at pH 6–7. Ribonucleotides were hydrolyzed approximately 100-fold more rapidly than deoxyribonucleotides. A high degree of base specificity was not observed. The 3′-nucleotidase activity was stimulated by Zn²⁺, but not by other divalent cations tested.     

Conformations of cyclic 2,3-nucleotides and 2,3-Cyclic-5-diphosphates. Interrelation between the phase angle of pseudorotation of the sugar and the torsions about the glycosyl C(1)-N and the backbone C(4)-C(5) bonds

Semiempirical potential energy calculations have been carried out for cyclic 2′,3′-nucleotides and their 5′-phosphorylated derivatives, which are the intermediates in the hydrolysis of RNA. Calculations have been performed for both purine and pyrimidine bases for the observed O(1′)-endo, O(1′)-exo and the unpuckered planar sugar ring conformations. It is found that the mode of sugar pucker largely determines the preferred conformations of these molecules. For cyclic 2′,3′-nucleotides themselves, the O(1′)-endo sugars show a preference for the syn glycosyl conformation while the O(1′)-exo sugars exclusively favor the anti conformation regardless of whether the base is a purine or pyrimidine. For the unpuckered planar sugar, the syn conformation is favored for purines and anti for pyrimidines. Both the gauche (+) (60°) and trans (180°) conformations about the C(4′)? C(5′) bond are favored for O(1′)-endo sugars, while the gauche (?) (300°) and trans (180°) are favored for O(1′)-exo sugars. On the contrary, the 5′-phosphorylated cyclic 2′,3′-nucleotides of both purines and pyrimidines show a preference for the anti-gauche (+) conformational combination about the glycosyl and C(4′)? C(5′) bonds for the O(1′)-endo sugars and the anti-trans combination for the O(1′)-exo sugars. The correlation between the phase angle of the sugar ring and the favored torsions about the glycosyl and the backbone C(4′)? C(5′) bonds as one traverses along the pseudorotational pathway of the sugar ring is examined.     

Substrate Properties of Adenosine- and Uridine- 3′- Phenylphosphonates for 3′-Nucleotidase/Nucleases

Abstract

Adenosine- and uridine- 3′-phenylphosphonates have been synthesized and evaluated as substrates of 3′-nucleotidase/nucleases. No other nucleases hydrolyzed these compounds. Since V_max values for the adenosine derivative were comparable to those for 3 -AMP and the apparent K_m were 1.4–2.6 mM, it may be a useful substrate.