Molecular cloning and characterization of NAD+ dependent isocitrate dehydrogenase enzyme from Shewanella putrefaciens

2021 ◽  
Vol 16 (10) ◽  
pp. 78-86
Author(s):  
Fahri Akbas ◽  
Metin Demirel ◽  
Ahmet Ozaydin ◽  
Sahabettin Selek

Isocitrate dehydrogenase (IDH) is a fundamental enzyme for carbon metabolism in the Krebs cycle. This enzyme is required for oxidation-reduction reactions in both eukaryotic and prokaryotic cells and plays a critical role in their growth and pathogenesis. In this study, we cloned the gene encoding NAD+ dependent isocitrate dehydrogenase from Shewanella putrefaciens. The expression of recombinant protein was induced with 0.5 mM of IPTG. His-tagged IDH overexpressed in E. coli was purified and characterized. The expressed IDH enzyme was purified in an active soluble form. The molecular weight of the enzyme was confirmed with Western blotting. High sequence homology was observed with IDH sequences of other Shewanella strains and remarkable sequence homology was found with other bacteria reported in the database. The open reading frame of the gene encoding IDH of S. putrefaciens was 1069 bp in length, which codes a polypeptide composed of 356 amino acids and with a 38 KDa molecular weight. The optimum enzyme activity was obtained at pH 8. We cloned, purified and characterized Shewanella putrefaciens isocitrate dehydrogenase enzyme (SpIDH). The recombinant enzyme demonstrated a specific activity of Vmax 4.6±0.3 μM/min and Km 334 μM using NAD+ as a cofactor.

2020 ◽  
Author(s):  
Alei Zhang ◽  
Xiaofang Mo ◽  
Ning Zhou ◽  
Yingying Wang ◽  
Guoguang Wei ◽  
...  

Abstract Background: N-acetyl glucosamine (GlcNAc) and N-acetyl chitooligosaccharides (N-acetyl COSs) exhibit antitumor and antimicrobial activities, and have been widely used in the pharmaceutical, agriculture, food, and chemical industries. Thus, it is crucial to discover a NAGase that can both synthesize GlcNAc and N-acetyl COSs. Results: The gene encoding the novel β-N-acetyl glucosaminidase, designated CmNAGase, was cloned from Chitinolyticbacter meiyuanensis SYBC-H1. The deduced amino acid sequence of CmNAGase contains a glycoside hydrolase family 20 catalytic module that shows low identity with the corresponding domain of the well-characterized NAGases. CmNAGase gene was highly expressed with soluble form in Escherichia coli BL21 (DE3) cells, whereupon it had a specific activity of 4,878.6 U/mg of protein toward p-nitrophenyl-N-acetyl glucosaminide. CmNAGase had a molecular mass of 92 kDa, and its optimum activity was at pH 5.4 and 40ºC. The Vmax, Km, and Kcat of CmNAGase were 833.33 μmol·L-1 ·min-1, 10.9 mmol, and 6.37 ´ 108 mM·mg-1, respectively. Analysis of the hydrolysis products of N-acetyl chitooligosaccharides and colloidal chitin revealed that CmNAGase exhibits exo-acting activities. Particularly, it possesses transglycosylation activity, which can synthesize (GlcNAc)n+1 from (GlcNAc)n (n=1−6), respectively. In addition, CmNAGase also can catalyze GlcNAc to its dimers with various linked forms. Conclusions: The observations recorded in this study that CmNAGase is an exo NAGase with unique transglycosylation activity, suggests a possible application in the production of long-chain N-acetyl CHOs. This is first report of a bacterial NAGase, which can produce long-chain N-acetyl COSs via transglycosylation activity.


1984 ◽  
Vol 4 (12) ◽  
pp. 2865-2875
Author(s):  
E White ◽  
S H Blose ◽  
B W Stillman

The adenovirus early-region 1B 19,000-molecular-weight tumor antigen is required for oncogenic transformation of cells by adenovirus. We have demonstrated that this tumor antigen is located in the nuclear envelope of infected and transformed cells and that a fraction of the protein within the nuclear envelope is associated with the nuclear lamina. During cell division in the transformed cells, the nuclear envelope containing the tumor antigen dissociates at metaphase and then reforms around the separated daughter chromosomes at telophase. Adenovirus mutants carrying lesions in the gene encoding this tumor antigen cause degradation of host cell chromosomal DNA, and in these mutants, the intracellular localization of the 19,000-dalton protein is altered. These results demonstrate that components of the nuclear envelope function in the organization of chromatin in infected and transformed cells and that a virus-encoded protein plays a critical role in this process.


1984 ◽  
Vol 4 (12) ◽  
pp. 2865-2875 ◽  
Author(s):  
E White ◽  
S H Blose ◽  
B W Stillman

The adenovirus early-region 1B 19,000-molecular-weight tumor antigen is required for oncogenic transformation of cells by adenovirus. We have demonstrated that this tumor antigen is located in the nuclear envelope of infected and transformed cells and that a fraction of the protein within the nuclear envelope is associated with the nuclear lamina. During cell division in the transformed cells, the nuclear envelope containing the tumor antigen dissociates at metaphase and then reforms around the separated daughter chromosomes at telophase. Adenovirus mutants carrying lesions in the gene encoding this tumor antigen cause degradation of host cell chromosomal DNA, and in these mutants, the intracellular localization of the 19,000-dalton protein is altered. These results demonstrate that components of the nuclear envelope function in the organization of chromatin in infected and transformed cells and that a virus-encoded protein plays a critical role in this process.


1970 ◽  
Vol 24 (03/04) ◽  
pp. 325-333 ◽  
Author(s):  
G. H Tishkoff ◽  
L. C Williams ◽  
D. M Brown

SummaryAs a corollary to our previous studies with bovine prothrombin, we have initiated a study of human prothrombin complex. This product has been isolated in crystalline form as a barium glycoprotein interaction product. Product yields were reduced compared to bovine product due to the increased solubility of the barium glycoprotein interaction product. On occasion the crystalline complex exhibited good yields. The specific activity of the crystalline complex was 1851 Iowa u/mg. Further purification of human prothrombin complex was made by removal of barium and by chromatography on Sephadex G-100 gels. The final product evidenced multiple procoagulant activities (II, VII, IX and X). The monomeric molecular weight determined by sedimentation equilibrium in a solvent of 6 M guanidine-HCl and 0.5% mercaptoethanol was 70,191 ± 3,057 and was homogeneous with respect to molecular weight. This product was characterized in regard to physical constants and chemical composition. In general, the molecular properties of human prothrombin complex are very similar to the comparable bovine product. In some preparations a reversible proteolytic enzyme inhibitor (p-aminophenylarsonic acid) was employed in the ultrafiltration step of the purification scheme to inhibit protein degradation.


1992 ◽  
Vol 12 (1) ◽  
pp. 15-21
Author(s):  
S. Kojima ◽  
K. Nara ◽  
Y. Inada ◽  
S. Hirose ◽  
Y. Saito

Platelet aggregation activity due to platelet-activating factor (PAF) was detected at high molecular weight (HMW) and low molecular weight fractions after gel-filtration chromatography of cell lysate of endothelial cells. [3H]PAF added to the cell lysate was similarly distributed after chromatography. The radioactivity associated with HMW fraction was not reduced by digesting the lysate with trypsin, suggesting that PAF was not making complexes with proteins but was included in lipid vesicles in cell lysate. Further evidence showed that an unknown specific factor(s) was needed to form these PAF-containing lipid vesicles. Radioactivity was not found in HMW fraction when [3H]PAF was mixed with cell lysate of vascular smooth muscle cells. When monomeric PAF was added to endothelial cell lysate, the specific activity of aggregation decreased to the level exerted by endogenous PAF-containing lipid vesicles due to incorporation into lipid vesicles. PAF in the form of lipid vesicles was more stable in plasma than monomeric form.


2000 ◽  
Vol 279 (6) ◽  
pp. R2329-R2335 ◽  
Author(s):  
Paul Trayhurn ◽  
Jacqueline S. Duncan ◽  
Anne M. Wood ◽  
John H. Beattie

White adipose tissue (WAT) has been examined to determine whether the gene encoding metallothionein (MT), a low-molecular-weight stress response protein, is expressed in the tissue and whether MT may be a secretory product of adipocytes. The MT-1 gene was expressed in epididymal WAT, with MT-1 mRNA levels being similar in lean and obese ( ob/ ob) mice. MT-1 mRNA was found in each of the main adipose tissue sites (epididymal, perirenal, omental, subcutaneous), and there was no major difference between depots. Separation of adipocytes from the stromal-vascular fraction of WAT indicated that the MT gene (MT-1 and MT-2) was expressed in adipocytes themselves. Treatment of mice with zinc had no effect on MT-1 mRNA levels in WAT, despite strong induction of MT-1 expression in the liver. MT-1 gene expression in WAT was also unaltered by fasting or norepinephrine. However, administration of a β3-adrenoceptor agonist, BRL-35153A, led to a significant increase in MT-1 mRNA. On differentiation of fibroblastic preadipocytes to adipocytes in primary culture, MT was detected in the medium, suggesting that the protein may be secreted from WAT. It is concluded that WAT may be a significant site of MT production; within adipocytes, MT could play an antioxidant role in protecting fatty acids from damage.


1938 ◽  
Vol 21 (3) ◽  
pp. 335-366 ◽  
Author(s):  
John H. Northrop

1. A method for isolating a nucleoprotein from lysed staphylococci culture is described. 2. It is homogeneous in the ultracentrifuge and has a sedimentation constant of 650 x 10–13 cm. dyne–1 sec.–1, corresponding to a molecular weight of about 300,000,000. 3. The diffusion coefficient varies from about 0.001 cm.2/day in solutions containing more than 0.1 mg. protein/ml. to 0.02 in solutions containing less than 0.001 mg. protein/ml. The rate of sedimentation also decreases as the concentration decreases. It is suggested, therefore, that this protein exists in various sized molecules of from 500,000–300,000,000 molecular weight, the proportion of small molecules increasing as the concentration decreases. 4. This protein is very unstable and is denatured by acidity greater than pH 5.0, by temperature over 50°C. for 5 minutes. It is digested by chymo-trypsin but not by trypsin. 5. The loss in activity by heat, acid, and chymo-trypsin digestion is roughly proportional to the amount of denatured protein formed under these conditions. 6. The rate of diffusion of the protein is the same as that of the active agent. 7. The rate of sedimentation of the protein is the same as that of the active agent. 8. The loss in activity when susceptible living or dead bacteria are added to a solution of the protein is proportional to the loss in protein from the solution. Non-susceptible bacteria remove neither protein nor activity. 9. The relative ultraviolet light absorption, as determined directly, agrees with that calculated from Gates' inactivation experiments in the range of 2500–3000 Å. u. but is somewhat greater in the range of 2000–2500 Å. u. 10. Solubility determinations showed that most of the preparations contained at least two proteins, one being probably the denatured form of the other. Two preparations were obtained, however, which had about twice the specific activity of the earlier ones and which gave a solubility curve approximating that of a pure substance. 11. It is suggested that the formation of phage may be more simply explained by analogy with the autocatalytic formation of pepsin and trypsin than by analogy with the far more complicated system of living organisms.


Some of the constituent amino-acids of fibroin (degummed silk) are determined. Special attention is directed to histidine, owing to its use in the calculation of the molecular weight of fibroin. A value of 0⋅45% has been found by methods in which the histidine is isolated as nitranilate or di-(3:4-dichlorobenzenesulphonate). Other values obtained are serine 12⋅6%, threonine 1⋅5%, tyrosine 10⋅6%, and proline 1⋅5%. Hydroxyproline appears to be absent, but the presence of small amounts of some hydroxyamino-acid other than serine and threonine is indicated. The mean residue weight of fibroin is determined by three methods, one of which is a new method based on analysis of the complex formed between fibroin and cupri-ethylenediamine. This method gives a Cu:fibroin-N ratio of 1:1⋅92 and, if allowance is made for co-ordination with the tyrosine hydroxy1 group, an equivalence of 1⋅964 atoms of peptide-nitrogen to 1 atom of copper is obtained. The three methods give an average value of 78⋅0 for the mean residue weight of fibroin. This value, together with the most acceptable data for amino-acid constituents, indicate that the unidentified anhydro-residues (about 20%) have a mean residue weight of about 107. Evidence is presented that fibroin contains no amide-nitrogen. Methods for the determination of amide-nitrogen at present in use, which indicate a content of 1 to 2%, are considered to be unreliable. Fibroin dissolved in cupri-ethylenediamine gives, on neutralization and dialysis of the resulting solution, a water-soluble protein. The production of this water-soluble protein is attended by little or no degradation of the original fibroin as shown by determinations of fluidity, amino-nitrogen, and acid- and alkali-combining power. The water-soluble protein is precipitated by the normal protein-precipitating reagents, but in every instance examined the precipitated material exhibits an insolubility comparable with that of the original fibroin. Factors responsible for the solubilization process are investigated and data for molecular weight, titration values, ultra-violet absorption spectra, reducing activity, optical rotation, tryptic hydrolysis, and viscosity for both soluble and dispersed fibroin are given. Soluble fibroin has [ α ] D 15 — 53⋅1° and dispersed fibroin [ α ] D 15 — 58⋅9°, both in aqueous media. The preparation and properties of films and filaments of fibroin are described. Films of fibroin can be prepared that are water-soluble. On stretching, these films show strain-birefringence, acquire considerable tensile strength, and become insoluble in water, but X-ray examination gives the β -keratin pattern for both the stretched and unstretched films. Reasons are advanced for considering the water-soluble form of fibroin to be the native or renatured protein and the original protein to be the denatured form. The denaturation of fibroin is discussed on the basis that denaturation is essentially an unfolding of a coiled long-chain molecule. The subsequent aggregation of the uncoiled molecules to give an insoluble product is considered to be a secondary process. Some aspects of protein and polypeptide chains as macro-molecules are also discussed.


1990 ◽  
Vol 68 (7-8) ◽  
pp. 1037-1044 ◽  
Author(s):  
Peter C. Loewen ◽  
Jacek Switala ◽  
Mark Smolenski ◽  
Barbara L. Triggs-Raine

Hydroperoxidase I (HPI) of Escherichia coli is a bifunctional enzyme exhibiting both catalase and peroxidase activities. Mutants lacking appreciable HPI have been generated using nitrosoguanidine and the gene encoding HPI, katG, has been cloned from three of these mutants using either classical probing methods or polymerase chain reaction amplification. The mutant genes were sequenced and the changes from wild-type sequence identified. Two mutants contained G to A changes in the coding strand, resulting in glycine to aspartate changes at residues 119 (katG15) and 314 (katG16) in the deduced amino acid sequence of the protein. A third mutant contained a C to T change resulting in a leucine to phenylalanine change at residue 139 (katG14). The Phe139-, Asp119-, and Asp314-containing mutants exhibited 13, < 1, and 18%, respectively, of the wild-type catalase specific activity and 43, 4, and 45% of the wild-type peroxidase specific activity. All mutant enzymes bound less protoheme IX than the wild-type enzyme. The sensitivities of the mutant enzymes to the inhibitors hydroxylamine, azide, and cyanide and the activators imidazole and Tris were similar to those of the wild-type enzyme. The mutant enzymes were more sensitive to high temperature and to β-mercaptoethanol than the wild-type enzyme. The pH profiles of the mutant catalases were unchanged from the wild-type enzyme.Key words: catalase, hydroperoxidase I, mutants, sequence analysis.


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