Expression and purification of glyceraldehyde-3-phosphate dehydrogenase from psychrophilic bacterium

Organisms that thrive in cold environments are known as psychrophiles. One of the strategies for their cold adaptation is the ability to synthesize cold-adapted enzymes. Our collection of cold-tolerant microorganisms isolated· from the Antarctic region has offered a potential source for psychrophilic enzymes. Previously our group had successfully cloned the open reading frame for GAPDH gene from an Antarctical bacterium known as phi9. The ORF was cloned into a pET-14b plasmid. The full length GAPDH protein was subsequently expressed in E. coli strain BL21 (DE3), purified as His-tag protein and confirmed to be catalytically active. Results showed that IPTG concentration did not have any effect on protein expression and solubility while 3 hours of induction time at room temperature (28°C) was the best conditions for the expression and solubility of this protein. This protein was shown to be most active at 38°C and its specific activity increased by 40% from 3.6 JlmOI/min/mg to 6.1 J.UllOifmin/mg when the temperature increased from 23°C to 38°C. This work laid the foundation for further biochemical and structural characterizations of GAPDH from a psychrophilic bacterium by providing a highly purified recombinant protein sample

Highly Specific Antibodies for Co-Detection of Human Choline Kinase α1 and α2 Isoforms

BACKGROUND: Choline kinase is the first enzyme in the CDP-choline pathway that synthesizes phosphatidylcholine, the major phospholipid in eukaryotic cell membranes. In humans, choline kinase exists as three isoforms (CKα1, α2, and β). Specific inhibition of CKα has been reported to selectively kill tumoral cells. Monoclonal and polyclonal antibodies against CKα used in previous studies to detect the level of this isozyme in different cellular or biochemical contexts were able to detect either the α1 or the α2 isoform. METHODOLOGY/PRINCIPAL FINDINGS: In this study, an antiserum against CKα was produced by immunizing rabbits with denatured, purified recombinant CKα2 full-length protein. This antiserum was highly specific for CKα when tested with extracts from different cell lines, and there was no cross reactivity with purified CKβ and other related proteins like human ethanolamine kinases (EK) and yeast choline or ethanolamine kinases. The antiserum simultaneously detected both CKα1 and α2 isoforms in MCF-7 and HepG2 cell extracts, but not in HeLa, HCT-116, and mouse embryonic stem cell extracts. Subsequent protein dot blot assay of total CKα in a human normal/tumor protein array of 30 tissue samples by using the antiserum showed that CKα was not overexpressed in all tumor tissues when compared to their normal counterparts. Most striking differences between tumor and normal CKα expression levels were observed in kidney (11-fold higher in tumor) and liver (15-fold lower in tumor) samples. CONCLUSION/SIGNIFICANCE: Apart from its high sensitivity and specificity, the antiserum produced in this work, which does not require further purification, has the advantage of co-detecting both α1 and α2 isoforms in cell extracts for direct comparison of their expression levels

AP4 transcription factor binding site is a repressor element in ek2 promoter of human liver carcinoma cell line, HepG2

Ethanolamine kinase (EK) is the first enzyme in the Kennedy pathway for the biosynthesis of phosphatidylethanolamine. Although EK has been reported to be involved in phospholipid biosynthesis, carcinogenesis, cell growth, muscle development and sex determination during embryonic development, little is known about its transcriptional regulation by endogenous or exogenous signals. Human EK exists as EK1, EK2α and EK2β isoforms, encoded by two separate genes, named ek1 and ek2. Compared to ek1 gene, ek2 is expressed at a higher level in liver and EK2 isoforms also accept choline as substrate besides ethanolamine, which could contribute to liver carcinogenesis. The main aim of this study was to analyze and characterize the human ek2 promoter in cultured mammalian cells. Human ek2 (2011 bp) promoter was cloned into reporter vector, pGL4.10 [luc2] and the promoter activities were studied in human liver carcinoma (HepG2 cells). Sequence analyses showed that ek2 promoter contains numerous putative transcription factor binding sites including AP4 and it is devoid of a recognizable consensus TATA box but it contains a high number of guanine (G) and cytosine (C) nucleotides. PCR mutagenesis of three nucleotides at E-box motif of AP4 transcription binding site located between -293 and -276 of ek2 promoter was successfully performed to show that AP4 transcription factor binding site acts as a repressive element in the regulation of ek2 expression. AP4 upregulation has been implicated in bad prognosis of carcinoma, therefore the regulatory role of AP4 binding site reported in this study could be a link between ek2 and carcinogenesis. Although further studies need to be carried out to understand and to determine the repression mechanism of AP4 in ek2 promoter, the characterization and analysis of ek promoter performed in this study provide important understanding of its basal transcriptional regulation which would allow us to control ek expression levels in pathologic conditions that involve this gene

Structural Modeling and Biochemical Characterization of Recombinant KPN_02809, a Zinc-Dependent Metalloprotease from Klebsiella pneumoniae MGH 78578

Klebsiella pneumoniae is a Gram-negative, cylindrical rod shaped opportunistic pathogen that is found in the environment as well as existing as a normal flora in mammalian mucosal surfaces such as the mouth, skin, and intestines. Clinically it is the most important member of the family of Enterobacteriaceae that causes neonatal sepsis and nosocomial infections. In this work, a combination of protein sequence analysis, structural modeling and molecular docking simulation approaches were employed to provide an understanding of the possible functions and characteristics of a hypothetical protein (KPN_02809) from K. pneumoniae MGH 78578. The computational analyses showed that this protein was a metalloprotease with zinc binding motif, HEXXH. To verify this result, a ypfJ gene which encodes for this hypothetical protein was cloned from K. pneumoniae MGH 78578 and the protein was overexpressed in Escherichia coli BL21 (DE3). The purified protein was about 32 kDa and showed maximum protease activity at 30 °C and pH 8.0. The enzyme activity was inhibited by metalloprotease inhibitors such as EDTA, 1,10-phenanthroline and reducing agent, 1,4-dithiothreitol (DTT). Each molecule of KPN_02809 protein was also shown to bind one zinc ion. Hence, for the first time, we experimentally confirmed that KPN_02809 is an active enzyme with zinc metalloprotease activity

DNA methylation of human choline kinase alpha gene

Increased level of choline kinase (CK) is a common feature in cancers and inhibition of this enzyme has been applied as anticancer strategy. DNA methylation of gene promoter especially at CpG island is associated with suppression of gene expression. Despite the importance of CK especially the alpha isoform in cancer pathogenesis, epigenetic regulation of ckα expression has not been investigated. Hence, this study aimed to determine the effect of DNA methylation on ckα promoter activity and gene expression by using hypomethylating (5-aza) and methylating (budesonide) agents. The level of DNA methylation in the second CpG island of ckα promoter was determined by PCR-based method. 5-aza and budesonide increased the methylation of the selected CpG island compared to untreated control. Treatment with the drugs produced opposite effect, with 5-aza induced ckα promoter activity and gene expression while budesonide suppressed the promoter activity and mRNA level of this gene. Deletion of a region containing the second CpG island on ckα promoter resulted in significantly lower promoter activity. In conclusion, this study showed that DNA methylation could be one of the mechanisms that regulate the expression of ckα gene

Optimization of a native gel electrophoretic process for the purification of intracellular green fluorescent protein from intact Escherichia coli cells

Intracellular green fluorescent protein (GFP) can be separated and purified from intact Escherichia coli cells by a preparative native polyacrylamide gel electrophoresis (n-PAGE). The effects of operating parameters such as the volume and concentration of feedstock and the pore size and height of resolving gel on the purity and yield of GFP were studied using a 1.7 cm internal diameter gel column. The optimum conditions for this preparative n-PAGE operation were determined to be 100 μl of 15% (w/v) feedstock and a 12% (w/v) resolving gel with a gel height of 2 cm. The purity and yield of the recovered GFP were 98 and 88%, respectively. The results of scalability studies show that the ratio of feedstock volume to cross-sectional area of the column is an important consideration for scaling up the preparative n-PAGE

Quantitation of green fluorescent protein using a gel-based imaging method.

Green fluorescent protein (GFP) is a versatile reporter protein and has been widely used in biological research. However, its quantitation requires expensive equipment such as a spectrofluorometer. In the current study, a gel documentation imaging system using a native polyacrylamide gel for the quantitation of GFP was developed. The assay was evaluated for its precision, linearity, reproducibility, and sensitivity in the presence of Escherichia coli cells and was compared with the spectrofluorometric method. Using this newly established, gel-based imaging technique; the amount of GFP can be quantified accurately

MicroRNA regulation of human choline kinase gene expression

Choline kinase (CK) is the first enzyme in the CDP-choline pathway for biosynthesis of phosphatidylcholine. Increased activity of CK has been implicated in human carcinogenesis. MicroRNAs (miRNAs) are a large family of non-coding RNAs that regulate gene expression. Dysregulation of miRNA expression is common in many types of cancer and miRNA profiling has the potential applications for cancer diagnostic and prognostic. Despite the physiological and pathological importance of CK, the regulation of its expression by miRNAs has never been reported. We hypothesize that miRNAs regulate the expression of CK and affect cell cycle progression. This study aims to predict the miRNAs that bind CK mRNAs and determine the effect of the selected miRNAs on CK gene expression, cancer cell proliferation and morphology. MiRNAs binding was predicted by several online computer programs that utilize different algorithms. Potential miRNAs were selected for the synthesis of their mimics and transfected into cancer cell lines. The effect of the miRNAs on CK alpha mRNA and protein levels were determined by real-time PCR and Western detection. MTT assay was used to determine the effect of miRNAs on cancer cell viability. The effect of miRNAs on cell morphology was investigated by scanning electron microscopy. Bioinformatic predictions of miRNAs that potentially downregulate human cka gene expression have produced ten best miRNA candidates (out ofinitial 54 non-repeating miRNAs) based on the higher scores for minimum free energy for interaction, binding site features and sequence conservation among different species. Due to the relatively large number of potential miRNA candidates, this study has focused on miRNAs targeting cka only although prediction for miRNAs targeting ckfl isoform was also conducted. Out of the ten shortlisted miRNAs potentially targeting cka, three miRNAs namely miR-876-Sp, miR-646 and miR-202-Sp were selected for experimental validation based on their favorable complementarity with cka gene 3'-untranslated region and binding energy

ChoK-ing the Pathogenic Bacteria: Potential of Human Choline Kinase Inhibitors as Antimicrobial Agents

Novel antimicrobial agents are crucial to combat antibiotic resistance in pathogenic bacteria. Choline kinase (ChoK) in bacteria catalyzes the synthesis of phosphorylcholine, which is subsequently incorporated into the cell wall or outer membrane. In certain species of bacteria, phosphorylcholine is also used to synthesize membrane phosphatidylcholine. Numerous human ChoK inhibitors (ChoKIs) have been synthesized and tested for anticancer properties. Inhibition of S. pneumoniae ChoK by human ChoKIs showed a promising effect by distorting the cell wall and retarded the growth of this pathogen. Comparison of amino acid sequences at the catalytic sites of putative choline kinases from pathogenic bacteria and human enzymes revealed striking sequence conservation that supports the potential application of currently available ChoKIs for inhibiting bacterial enzymes. We also propose the combined use of ChoKIs and nanoparticles for targeted delivery to the pathogen while shielding the human host from any possible side effects of the inhibitors. More research should focus on the verification of putative bacterial ChoK activities and the characterization of ChoKIs with active enzymes. In conclusion, the presence of ChoK in a wide range of pathogenic bacteria and the distinct function of this enzyme has made it an attractive drug target. This review highlighted the possibility of “choking” bacterial ChoKs by using human ChoKIs

Sp1 and Sp3 Are the Transcription Activators of Human ek1 Promoter in TSA-Treated Human Colon Carcinoma Cells.

Ethanolamine kinase (EK) catalyzes the phosphorylation of ethanolamine, the first step in the CDP-ethanolamine pathway for the biosynthesis of phosphatidylethanolamine (PE). Human EK exists as EK1, EK2α and EK2β isoforms, encoded by two separate genes, named ek1 and ek2. EK activity is stimulated by carcinogens and oncogenes, suggesting the involvement of EK in carcinogenesis. Currently, little is known about EK transcriptional regulation by endogenous or exogenous signals, and the ek gene promoter has never been studied.In this report, we mapped the important regulatory regions in the human ek1 promoter. 5' deletion analysis and site-directed mutagenesis identified a Sp site at position (-40/-31) that was essential for the basal transcription of this gene. Treatment of HCT116 cells with trichostatin A (TSA), a histone deacetylase inhibitor, significantly upregulated the ek1 promoter activity through the Sp(-40/-31) site and increased the endogenous expression of ek1. Chromatin immunoprecipitation assay revealed that TSA increased the binding of Sp1, Sp3 and RNA polymerase II to the ek1 promoter in HCT116 cells. The effect of TSA on ek1 promoter activity was cell-line specific as TSA treatment did not affect ek1 promoter activity in HepG2 cells.In conclusion, we showed that Sp1 and Sp3 are not only essential for the basal transcription of the ek1 gene, their accessibility to the target site on the ek1 promoter is regulated by histone protein modification in a cell line dependent manner