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211.
212.
Chandanapurath Shiny Nagampalli S.A. Krushna Bairavasundaram Archana Begum Farzana Rangarajan B. Narayanan 《Microbiology and immunology》2009,53(12):685-693
Wolbachia surface protein (WSP), which is the most abundantly expressed protein of Wolbachia from the human filarial parasite Brugia malayi, was chosen for the present study. B‐cell epitope prediction of the WSP protein sequence indicates a high antigenicity, surface probability and hydrophilicity by DNA STAR software analysis. ProPred analysis suggests the presence of HLA class II binding regions in the WSP protein that contribute to T‐cell responses and isotype reactivity. In order to validate these findings, the gene coding for endosymbiont WSP was PCR‐amplified from the genomic DNA of the human filarial parasite Brugia malayi and cloned in T‐7 expression vector pRSET‐A. Western blot and ELISA at the total IgG level with recombiant WSP indicated a significantly elevated reactivity in CP compared to MF, EN and NEN individuals. Isotype ELISA also suggested an elevated reactivity in CP patients at the IgG1 level. In contrast, WSP‐specific IgG4 levels were found to be elevated in MF patients compared to CP and EN. Besides this, WSP‐specific IgE levels indicated an elevated reactivity in CP and MF patients compared to normals. Observations from ELISA supported the in silico predictions that indicate the presence of B‐ and T‐cell epitopes. Hence, a combinatorial approach of in silico predictions and wet‐lab studies provides interesting insights into the role of Wolbachia proteins in filarial pathogenesis. 相似文献
213.
Nagampalli S. A. Krushna Chandanpurath Shiny Srinivasan Dharanya Arivazhagan Sindhu Sridharan Aishwarya Rangarajan B. Narayanan 《Microbiology and immunology》2009,53(3):173-183
cDNA coding for Brugia malayi pepsin inhibitor homolog (Bm-33) from the human filarial parasite was cloned in pRSET for large-scale expression and functional characterization. The pRSET-B cloned gene did not yield recombinant protein expression and the reason was attributed to the presence of an N-terminal signal peptide. The gene was subcloned in pRSET-A without a signal peptide and the 33 kDa histidine-tagged recombinant protein was purified by IMAC. All individuals from an endemic area generated IgG responses against Bm-33 in the order MF>CP>EN. Isotype analysis indicated an elevated IgG4 reactivity in the order MF>EN>CP. Bm-33-specific IgE levels were elevated in MF, CP and EN compared to non-endemic normals with no significant differences among the groups. Paraffin-embedded sections of Setaria digitata (cattle filarial parasite) stained with mouse anti-Bm-33 antibodies exhibited the hypodermal nature of Bm-33. These findings suggest that Bm-33 is an immunodominant antigen and contributes to filarial pathogenesis. 相似文献
214.
Narayanan Sriram 《Chemico-biological interactions》2009,180(2):271-104
Pulmonary fibrosis is characterized by excessive deposition of extracellular matrix components in the alveolar space, which hampers normal respiration process. Pathophysiological enzymes, glycoprotein moieties and matrix degrading lysosomal hydrolases are key markers and play a crucial role in the progression of fibrosis. Bleomycin is an anti-neoplastic drug, used for the treatment of various types of cancers and induces pulmonary fibrosis due its deleterious side effect. Tea catechin epigallocatechin-3-gallate (EGCG) is known for its wide array of beneficial effects. The present study was intended to evaluate the beneficial efficacy of EGCG against bleomycin-induced glycoconjugates, lysosomal hydrolases and ultrastructural changes in the lungs of Wistar rats. Intratracheal instillation of bleomycin (6.5 U/kg body weight) to rats increased the activities of pathophysiological enzymes such as aspartate transaminase, alanine transaminase, lactate dehydrogenase and alkaline phosphatase, which were attenuated upon EGCG treatment. The increased level of hydroxyproline and histopathological parameters in bleomycin-induced rats were decreased upon EGCG treatment. Bleomycin-induced increase in the level of glycoconjugates was restored closer to normal levels on EGCG treatment. Furthermore, the increased activities of matrix degrading lysosomal enzymes in bleomycin-induced rats were reduced upon EGCG supplementation. Treatment with EGCG also attenuated bleomycin-induced ultrastructural changes as observed from transmission electron microscopy studies. The results of the present study put-forward EGCG as a potential anti-fibrotic agent due to its attenuating effect on potential fibrotic markers. 相似文献
215.
Ranjani Narayanan 《Journal of molecular biology》2009,390(3):538-15338
Because the rate of a diffusional process such as protein folding is controlled by friction encountered along the reaction pathway, the speed of folding is readily tunable through adjustment of solvent viscosity. The precise relationship between solvent viscosity and the rate of diffusion is complex and even conformation-dependent, however, because both solvent friction and protein internal friction contribute to the total reaction friction. The heterogeneity of the reaction friction along the folding pathway may have subtle consequences. For proteins that fold on a multidimensional free-energy surface, an increase in solvent friction may drive a qualitative change in folding trajectory. Our time-resolved experiments on the rapidly and heterogeneously folding β-hairpin TZ2 show a shift in the folding pathway as viscosity increases, even though the energetics of folding is unaltered. We also observe a nonlinear or saturating behavior of the folding relaxation time with rising solvent viscosity, potentially an experimental signature of the shifting pathway for unfolding. Our results show that manipulations of solvent viscosity in folding experiments and simulations may have subtle and unexpected consequences on the folding dynamics being studied. 相似文献
216.
Two amino acids, Leu149 and Val223, were identified as proteolytically sensitive when Pseudozyma antarctica lipase (PalB) was heterologously expressed in Escherichia coli. The functional expression was enhanced using the double mutant for cultivation. However, the recombinant protein production was still limited by PalB misfolding, which was resolved by DsbA coexpression.Though Escherichia coli retains popularity as a host for recombinant protein production, it has technical limitations for expressing eukaryotic proteins. Host/protein incompatibility is critical, since eukaryotic proteins heterologously expressed in E. coli are recognized as a foreign object that can induce heat shock responses and drive protease-mediated degradation. E. coli contains several proteases situated in various intracellular compartments, including the cytoplasm, periplasm, inner membrane, and outer membrane (7, 9). While these proteases play a pivotal role in maintaining cell physiology by clearing up abnormal proteins (4), they can potentially degrade recombinant proteins (6). Nevertheless, the mechanisms associated with protein degradation and protein substrate specificity are incompletely understood.Since the proteolysis of recombinant proteins is a common issue, approaches to overcome this limitation have been extensively explored. These include using protease-deficient mutants as an expression host (10, 18), lowering the cultivation temperature (3), coexpressing folding factors (19, 20), applying protein fusion technology (2, 8), eliminating protease cleavage sites (5, 15), and modifying target protein hydrophobicity (11). While genetic elimination of proteolytically sensitive sequences without impacting the target protein''s bioactivity appears to be technically attractive, there is no effective prediction or identification of potential protease cleavage sites. Proteolytically sensitive sequences might not be specific to certain proteases. Various factors affecting the folding, solubility, steric hindrance, and binding of the substrate protein, e.g., neighboring domains or amino acids, can contribute to the sensitivity of proteolytic sites, making sequence manipulation for proteolysis alleviation more difficult.Herein, the recombinant protein''s sensitivity toward intracellular proteolysis was genetically alleviated to enhance the functional expression of PalB, an industrial enzyme with justified applications (1), in E. coli and to understand the relationship between proteolytic specificity and substrate protein sequence. Since there are three intramolecular disulfide bonds whose formation can potentially affect PalB structure and bioactivity, PalB expression in the oxidative periplasm of E. coli was explored (20, 22). However, the expressed PalB protein was extremely sensitive to intracellular proteolysis, resulting in complete degradation. To overcome this problem, PalB mutant variants that were stable against proteolysis were derived (Table (Table11).
Open in a separate windowaFor oligonucleotides, italic indicates mutated nucleotides, underlining indicates restriction site (silent mutation), and bold indicates a mutation codon.bSDM, site-directed mutagenesis.The results for functional expression of various PalB variants are summarized in Table Table22 and Fig. Fig.1.1. Neither PalB activity nor PalB-related polypeptide was detectable for the BL21(DE3)(pETG) culture sample, suggesting that the expressed gene product was degraded. Error-prone PCR (ep-PCR) was conducted using pETG as the template and LB-P10/LB-P11 as the primers. Potential mutants were screened on tributyrin agar plates. A colony developed a large halo, and the harboring plasmid (i.e., pETGM-2) was purified for sequencing. Two mutations, Leu149Val and Val223Ile, were identified in the expressed PalB mutant (i.e., M-2). High PalB activity was obtained for the BL21(DE3) (pETGM-2) culture sample. However, a PalB-related polypeptide was detected in both the soluble and insoluble fractions, implying potential protein misfolding. It was previously reported that the functional expression of PalB could be limited by disulfide bond formation associated with folding (21). It was intriguing to observe the structural effect of these two simple mutations on improving PalB stabilization and functional expression.Open in a separate windowFIG. 1.Western blotting analysis of the culture samples for the expression of various PalB mutants. Both soluble and insoluble fractions are shown. The number (n = 2 to 12) represents the PalB mutant (M-n) with the use of BL21(DE3) harboring the expression plasmid pETGM-n, summarized in Tables Tables11 and and2.2. “G” represents the control experiment using BL21(DE3) harboring pETG. “C” and “I” represent the cultures without and with IPTG induction, respectively.
Open in a separate windowaBL21(DE3) was used as an expression host to harbor various plasmids. PalB enzyme assay was conducted at 37°C and pH 8.0 using a pH stat with olive oil as a substrate. One unit of enzyme activity is defined as the amount of enzyme required to liberate one μmole of fatty acid per min.bOD600, optical density at 600 nm; w/o and w/IPTG, without and with isopropyl-β-d-thiogalactopyranoside, respectively.cThese activities represent IPTG-induced cultures. No activity was detected for all control cultures without IPTG induction. ND, not detected.Site-directed mutagenesis was conducted to introduce various single mutations of Leu149 and Val223 for a further understanding of the structural effect. Note that only hydrophobic amino acid residues were selected for the replacement to avoid any major structural disturbances. Among the five single mutations on Leu149, only Leu149Val and Leu149Ile were associated with a slight improvement in functional expression, and Leu149Val was more effective than Leu149Ile, whereas the others behaved similarly to the wild type. Among the five single mutations at Val223, only Val223Phe, Val223Gly, and Val223Ile showed a slight improvement in functional expression, with Val223Ile as the most effective one, whereas the others showed no improvement. The results suggest that Leu149 and Val223 are two amino acids critically affecting the proteolytic susceptibility of PalB in E. coli, with a synergistic effect on PalB stabilization from Leu149Val and Val223Ile mutations.Several amino acids were identified as being involved in the catalytic mechanism (17), such as Ser107-Asp189-His226, forming the catalytic triad, and Thr42 and Gly108, acting as the hydrogen bond donors in the oxyanion hole of the active site. However, Leu149 is located at the entrance of the partially formed lid of the protein structure, whereas Val223 is situated near one of the catalytic triad residues, His226, in the active site. The substitutions at Leu149 and/or Val223 with a PalB stabilization effect potentially convert the overall protein conformation into a less proteolytically sensitive form without changing the enzyme kinetics or activity. It was interesting to observe a similarly positive effect upon replacing Val223 with either a bulky Phe or a small Gly, implying that the molecular size of this amino acid residue was not critical for alleviation of the proteolytic sensitivity. Note that PalB-related polypeptide was present in the insoluble fraction for all the PalB mutants with improved functional expression, suggesting another expression hurdle of protein misfolding.To overcome the protein misfolding, coexpression of two periplasmic folding factors, DsbA and DsbC, was explored, and the cultivation results are summarized in Fig. Fig.2.2. DsbA coexpression significantly boosted functional expression, with specific PalB activity of more than twofold that of the control culture and a slight reduction of insoluble PalB. However, the improving effect associated with DsbC coexpression was minimal. The results suggest that the initiation but not isomerization for disulfide bond formation in the periplasm became limiting. The chaperone activity associated with DsbA could assist the folding of the expressed PalB double mutant.Open in a separate windowFIG. 2.Effect of DsbA or DsbC coexpression on the functional expression of the PalB double mutant. Cultivations were performed in a bioreactor containing 1 liter LB medium and operated at pH 7.0, 28°C, and 650 rpm. The cultures were induced with 0.1 mM isopropyl-β-d-thiogalactopyranoside and/or 0.2 g/liter arabinose at a ∼0.5 optical density at 600 nm (OD600) cell density. (A) Time profiles of cell density; (B) time profiles of the specific PalB activity [note that there was no detectable activity for BL21(DE3) (pETG) culture samples]; (C) Western blotting analysis of the final samples of the four cultures. Both soluble and insoluble fractions are shown. Lanes 1 and 5, BL21(DE3) (pETG); lanes 2 and 6, BL21(DE3) (pETGM-2); lane 3 and 7, BL21(DE3) (pETGM-2, pARDsbC); lanes 4 and 8, BL21(DE3) (pETGM-2, pARDsbA).While many studies based on rational mutagenesis, directed evolution, and gene shuffling are conducted to derive PalB mutants with improved enzyme properties, such as thermostability, bioactivity, or enantioselectivity (12-14, 16), this is an approach to improve protein manufacturing by deriving the variants with less proteolytic susceptibility. Though it has been perceived that the proteolytic specificity can be intrinsically determined by the protein substrate sequence, experimental demonstration of this is rarely reported. This study complements the lack of such experimental demonstration by showing the proteolytic specificity and sensitivity of PalB heterologously expressed in E. coli can be drastically altered by simple amino acid substitutions. It also demonstrates the application of molecular manipulation to enhance recombinant protein production in E. coli. 相似文献
TABLE 1.
Strains, plasmids, and oligonucleotidesStrain, plasmid, or oligonucleotide | Relevant genotype or DNA sequencea |
---|---|
Strain | |
BL21(DE3) | F−ompT dcm lon hsdSB (rB− mB−) gal λ(DE3[lacIind1sam7 nin5 lacUV5-T7 gene 1]) |
Plasmids | |
pARDsbA (20) | ParaB::dsbA, Ori (pACYC184), Cmr |
pARDsbC (20) | ParaB::dsbA, Ori (pACYC184), Cmr |
pETG (20) | PT7-pelB::palB, Ori (pBR322), Apr |
pETGM-2 | pETG derivative containing two mutations of Leu149Val and Val223Ile in palB (by ep-PCR with pETG and LB-P10/LB-P11) |
pETGM-3 | pETG derivative containing mutation of Leu149Gly in palB (by SDMb with pETG and P104/P114) |
pETGM-4 | pETG derivative containing mutation of Leu149Val in palB (by SDM with pETG and P103/P113) |
pETGM-5 | pETG derivative containing mutation of Leu149Ala in palB (by SDM with pETG and P105/P115) |
pETGM-6 | pETG derivative containing mutation of Leu149Met in palB (by SDM with pETG and P106/P116) |
pETGM-7 | pETG derivative containing mutation of Leu149Ile in palB (by SDM with pETG and P107/P117) |
pETGM-8 | pETG derivative containing mutation of Val223Phe in palB (by SDM with pETG and P112/P122) |
pETGM-9 | pETG derivative containing mutation of Val223Met in palB (by SDM with pETG and P111/P121) |
pETGM-10 | pETG derivative containing mutation of Val223Ala in palB (by SDM with pETG and P110/P120) |
pETGM-11 | pETG derivative containing mutation of Val223Gly in palB (by SDM with pETG and P109/P119) |
pETGM-12 | pETG derivative containing mutation of Val223Ile in palB (by SDM with pETGM-2 and P136/P137, i.e., by reverting the mutation of Val149 to Leu in pETGM-2) |
Oligonucleotides | |
LB-P10 | 5′-GGCCATGGGTCTACCTTCCGGTTCGG-3′ |
LB-P11 | 5′-CTGAATTCTCAGGGGGTGACGATGCCGGAGCAGG-3′ |
P103 | 5′-CCTCTCGATGCAGTCGCGGTTAGTGCACCC-3′ |
P113 | 5′-GGGTGCACTAACCGCGACTGCATCGAGAGG-3′ |
P104 | 5′-CCTCTCGATGCAGGCGCCGTTAGTGCACCC-3′ |
P114 | 5′-GGGTGCACTAACGGCGCCTGCATCGAGAGG-3′ |
P105 | 5′-CCTCTCGATGCAGCCGCGGTTAGTGCACCC-3′ |
P115 | 5′-GGGTGCACTAACCGCGGCTGCATCGAGAGG-3′ |
P106 | 5′-CCTCTCGATGCCATGGCGGTTAGTGCACCC-3′ |
P116 | 5′-GGGTGCACTAACCGCCATGGCATCGAGAGG-3′ |
P107 | 5′-CCTCTCGATGCGATCGCGGTTAGTGCACCC-3′ |
P117 | 5′-GGGTGCACTAACCGCGATCGCATCGAGAGG-3′ |
P109 | 5′-GGGCCGCTGTTCGGGATCGACCATGCAGGC-3′ |
P119 | 5′-GCCTGCATGGTCGATCCCGAACAGCGGCCC-3′ |
P110 | 5′-GGGCCGCTGTTCGCGATCGACCATGCAGGC-3′ |
P120 | 5′-GCCTGCATGGTCGATCGCGAACAGCGGCCC-3′ |
P111 | 5′-GGGCCGCTGTTCATGATCGACCATGCAGGC-3′ |
P121 | 5′-GCCTGCATGGTCGATCATGAACAGCGGCCC-3′ |
P112 | 5′-GGGCCGCTGTTCTTTATCGACCATGCAGGC-3′ |
P122 | 5′-GCCTGCATGGTCGATAAAGAACAGCGGCCC-3′ |
P136 | 5′-CCTCTCGATGCACTGGCGGTTAGTGCACCC-3′ |
P137 | 5′-GGGTGCACTAACCGCCAGTGCATCGAGAGG-3′ |
TABLE 2.
Cultivation performance for production of PalB mutant variantsaPlasmid | Cell density (OD600)b
| Activity (U/liter/OD600)c | Mutation in PalB | |
---|---|---|---|---|
w/o IPTG | w/IPTG | |||
pETG | 3.1 ± 0.0 | 3.3 ± 0.1 | ND | None |
pETGM-2 | 3.4 ± 0.1 | 3.3 ± 0.0 | 155 | Leu149Val, Val223Ile |
pETGM-3 | 3.2 ± 0.1 | 3.3 ± 0.0 | ND | Leu149Gly |
pETGM-4 | 3.4 ± 0.1 | 3.6 ± 0.1 | 60 | Leu149Val |
pETGM-5 | 3.3 ± 0.1 | 3.5 ± 0.1 | ND | Leu149Ala |
pETGM-6 | 2.7 ± 0.1 | 3.0 ± 0.1 | ND | Leu149Met |
pETGM-7 | 3.5 ± 0.0 | 3.2 ± 0.0 | 38 | Leu149Ile |
pETGM-8 | 3.0 ± 0.0 | 3.6 ± 0.0 | 50 | Val223Phe |
pETGM-9 | 2.9 ± 0.1 | 2.8 ± 0.0 | ND | Val223Met |
pETGM-10 | 3.4 ± 0.1 | 3.3 ± 0.1 | ND | Val223Ala |
pETGM-11 | 3.5 ± 0.0 | 3.5 ± 0.1 | 30 | Val223Gly |
pETGM-12 | 3.6 ± 0.1 | 3.5 ± 0.1 | 57 | Val223Ile |
217.
Fusobacterium necrophorum: a ruminal bacterium that invades liver to cause abscesses in cattle 总被引:1,自引:0,他引:1
Fusobacterium necrophorum, a Gram-negative, rod-shaped, and an aerotolerant anaerobe, is a normal inhabitant of the rumen of cattle. The organism is in ruminal contents and adherent to the ruminal wall. Its role in ruminal fermentation is to metabolize lactic acid and degrade feed and epithelial proteins. The ruminal concentration is higher in grain-fed than forage-fed cattle. From the rumen, the organism gains entry into the portal circulation and is trapped in the liver to cause abscesses. The organism is an opportunistic pathogen and a primary causative agent of liver abscesses, an economically important disease of grain-fed cattle. Liver abscesses are often secondary to ruminal acidosis and rumenitis in grain-fed cattle. Two subspecies of F. necrophorum, subsp. necrophorum (biotype A) and subsp. funduliforme (biotype B), are recognized that can be differentiated based on morphological, biochemical, biological and molecular characteristics. The subsp. necrophorum is more virulent and is isolated more frequently from infections than the subsp. funduliforme. Several toxins or secreted products have been implicated as virulence factors. The major factors contributing to ruminal colonization and invasion into the liver are hemagglutinin, endotoxin and leukotoxin, of which leukotoxin is the protective antigen. In some conditions, the organism synergistically interacts with Arcanobacterium pyogenes, a facultative anaerobic organism and a secondary etiologic agent, to cause liver abscesses. 相似文献
218.
The regulation of intracellular calcium by the endoplasmic reticulum (ER) plays a critical role in neuronal function. While the consequences associated with depleting calcium from the ER have been studied in multiple systems, it is not known whether the intrinsic properties of a neuron change in response to such perturbations. In this study, we demonstrate that the depletion of calcium from the ER of hippocampal CA1 pyramidal neurons induces a persistent, perisomatic increase in the density of functional h channels resulting in a reduction in intrinsic excitability and an increase in the optimal response frequency. This form of intrinsic plasticity is dependent on the elevation of cytoplasmic calcium, inositol triphosphate receptors, store-operated calcium channels, and the protein kinase A pathway. We postulate that this form of depletion-induced intrinsic plasticity is a neuroprotective mechanism that reduces excitability after depletion of calcium stores triggered through altered network activity during pathological conditions. 相似文献
219.
Real-time fluorescence loop mediated isothermal amplification for the diagnosis of malaria 总被引:2,自引:0,他引:2
Lucchi NW Demas A Narayanan J Sumari D Kabanywanyi A Kachur SP Barnwell JW Udhayakumar V 《PloS one》2010,5(10):e13733
BACKGROUND: Molecular diagnostic methods can complement existing tools to improve the diagnosis of malaria. However, they require good laboratory infrastructure thereby restricting their use to reference laboratories and research studies. Therefore, adopting molecular tools for routine use in malaria endemic countries will require simpler molecular platforms. The recently developed loop-mediated isothermal amplification (LAMP) method is relatively simple and can be improved for better use in endemic countries. In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. We refer to this as the RealAmp method. METHODOLOGY AND SIGNIFICANT FINDINGS: Published genus-specific primers were used to test the utility of this method. DNA derived from different species of malaria parasites was used for the initial characterization. Clinical samples of P. falciparum were used to determine the sensitivity and specificity of this system compared to microscopy and a nested PCR method. Additionally, directly boiled parasite preparations were compared with a conventional DNA isolation method. The RealAmp method was found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was generally less than 60 minutes. All human-infecting Plasmodium species were detected. The sensitivity and specificity of RealAmp in detecting P. falciparum was 96.7% and 91.7% respectively, compared to microscopy and 98.9% and 100% respectively, compared to a standard nested PCR method. In addition, this method consistently detected P. falciparum from directly boiled blood samples. CONCLUSION: This RealAmp method has great potential as a field usable molecular tool for diagnosis of malaria. This tool can provide an alternative to conventional PCR based diagnostic methods for field use in clinical and operational programs. 相似文献