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1.
J Biotechnol ; 351: 99-108, 2022 Jun 10.
Article in English | MEDLINE | ID: mdl-35500701

ABSTRACT

Over expression of recombinant proteins triggers a cellular stress response (CSR) that down-regulates numerous genes that have a key role in sustaining expression. Instead of trying to individually up-regulate these genes we hypothesized that a superior strategy would be to modulate the expression of global regulators that control the expression of many such downstream genes. Transcriptomic profiling of post induction cultures expressing recombinant asparaginase in Escherichia coli showed the down-regulation of several critical genes many of which were under the control of the global regulator lrp which is known to have a significant impact on both amino acid metabolism and protein translation. Therefore, to ameliorate the deleterious effects of the CSR we decided to supplement the activity of lrp using plasmid-based co-expression. We observed that the test culture containing an additional plasmid expressing lrp under the arabinose promoter gave a 50% higher yield of recombinant L-Asparaginase after 32 h in batch culture compared to the control, which had only one plasmid expressing the recombinant protein. This approach helped us design a better performing strain, which could sustain expression rates for a significantly longer time period. This work illustrates that modifying the expression of regulatory genes could serve as a better strategy to prevent the reprogramming of the cellular machinery which is the hallmark of the CSR and help in the design better hosts for recombinant protein expression.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Asparaginase/genetics , Bacterial Proteins/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Gene Expression Regulation, Bacterial , Leucine/metabolism , Leucine-Responsive Regulatory Protein/genetics , Leucine-Responsive Regulatory Protein/metabolism , Recombinant Proteins/metabolism
2.
Microb Cell Fact ; 19(1): 227, 2020 Dec 11.
Article in English | MEDLINE | ID: mdl-33308214

ABSTRACT

BACKGROUND: A cellular stress response (CSR) is triggered upon recombinant protein synthesis which acts as a global feedback regulator of protein expression. To remove this key regulatory bottleneck, we had previously proposed that genes that are up-regulated post induction could be part of the signaling pathways which activate the CSR. Knocking out some of these genes which were non-essential and belonged to the bottom of the E. coli regulatory network had provided higher expression of GFP and L-asparaginase. RESULTS: We chose the best performing double knockout E. coli BW25113ΔelaAΔcysW and demonstrated its ability to enhance the expression of the toxic Rubella E1 glycoprotein by 2.5-fold by tagging it with sfGFP at the C-terminal end to better quantify expression levels. Transcriptomic analysis of this hyper-expressing mutant showed that a significantly lower proportion of genes got down-regulated post induction, which included genes for transcription, translation, protein folding and sorting, ribosome biogenesis, carbon metabolism, amino acid and ATP synthesis. This down-regulation which is a typical feature of the CSR was clearly blocked in the double knockout strain leading to its enhanced expression capability. Finally, we supplemented the expression of substrate uptake genes glpK and glpD whose down-regulation was not prevented in the double knockout, thus ameliorating almost all the negative effects of the CSR and obtained a further doubling in recombinant protein yields. CONCLUSION: The study validated the hypothesis that these up-regulated genes act as signaling messengers which activate the CSR and thus, despite having no casual connection with recombinant protein synthesis, can improve cellular health and protein expression capabilities. Combining gene knockouts with supplementing the expression of key down-regulated genes can counter the harmful effects of CSR and help in the design of a truly superior host platform for recombinant protein expression.


Subject(s)
Escherichia coli/genetics , Escherichia coli/metabolism , Metabolic Engineering , Recombinant Fusion Proteins/biosynthesis , Asparaginase/genetics , Asparaginase/metabolism , Down-Regulation , Gene Expression Profiling , Gene Expression Regulation, Bacterial , Gene Knockout Techniques , Genes, Bacterial , Glycerol Kinase/genetics , Glycerol Kinase/metabolism , Glycerolphosphate Dehydrogenase/genetics , Glycerolphosphate Dehydrogenase/metabolism , Signal Transduction , Stress, Physiological , Up-Regulation , Viral Envelope Proteins/biosynthesis , Viral Envelope Proteins/genetics
3.
Sci Rep ; 10(1): 10850, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32616741

ABSTRACT

Isobutanol, in spite of its significant superiority over ethanol as a biofuel, remains commercially non-viable due to the non-availability of a suitable chassis which can handle the solvent toxicity associated with its production. To meet this challenge, we chose Lactococcus lactis which is known for its ability to handle environmental stress and carried out Adaptive laboratory evolution (ALE) in a continuous stirred tank reactor (CSTR) to evolve an isobutanol tolerant strain. The strain was grown for more than 60 days (> 250 generations) while gradually increasing the selection pressure, i.e. isobutanol concentration, in the feed. This led to the evolution of a strain that had an exceptionally high tolerance of up to 40 g/l of isobutanol even though a scanning electron microscope (SEM) study as well as analysis of membrane potential revealed only minor changes in cellular morphology. Whole genome sequencing which was done to confirm the strain integrity also showed comparatively few mutations in the evolved strain. However, the criticality of these mutations was reflected in major changes that occurred in the transcriptome, where gene expression levels from a wide range of categories that involved membrane transport, amino acid metabolism, sugar uptake and cell wall synthesis were significantly altered. Analysing the synergistic effect of these changes that lead to the complex phenotype of isobutanol tolerance can help in the construction of better host platforms for isobutanol production.


Subject(s)
Bacterial Proteins/metabolism , Butanols/pharmacology , Drug Tolerance/genetics , Genomics/methods , Laboratories/statistics & numerical data , Lactococcus lactis/genetics , Transcriptome/drug effects , Bacterial Proteins/genetics , Lactococcus lactis/drug effects , Lactococcus lactis/growth & development
4.
Microb Cell Fact ; 19(1): 148, 2020 Jul 23.
Article in English | MEDLINE | ID: mdl-32703203

ABSTRACT

BACKGROUND: The expression of recombinant proteins triggers a stress response which downregulates key metabolic pathway genes leading to a decline in cellular health and feedback inhibition of both growth and protein expression. Instead of individually upregulating these downregulated genes or improving transcription rates by better vector design, an innovative strategy would be to block this stress response thereby ensuring a sustained level of protein expression. RESULTS: We postulated that the genes which are commonly up-regulated post induction may play the role of signalling messengers in mounting the cellular stress response. We identified those genes which have no known downstream regulatees and created knock outs which were then tested for GFP expression. Many of these knock outs showed significantly higher expression levels which was also sustained for longer periods. The highest product yield (Yp/x) was observed in a BW25113ΔcysJ knock out (Yp/x 0.57) and BW25113ΔelaA (Yp/x 0.49), whereas the Yp/x of the control W3110 strain was 0.08 and BW25113 was 0.16. Double knock out combinations were then created from the ten best performing single knock outs leading to a further enhancement in expression levels. Out of 45 double knock outs created, BW25113ΔelaAΔyhbC (Yp/x 0.7) and BW25113ΔcysJΔyhbC (Yp/x 0.64) showed the highest increase in product yield compared to the single gene mutant strains. We confirmed the improved performance of these knock outs by testing and obtaining higher levels of recombinant asparaginase expression, a system better suited for analysing sustained expression since it gets exported to the extracellular medium. CONCLUSION: Creating key knock outs to block the CSR and enhance expression is a radically different strategy that can be synergistically combined with traditional methods of improving protein yields thus helping in the design of superior host platforms for protein expression.


Subject(s)
Asparaginase/biosynthesis , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Knockout Techniques/methods , Asparaginase/genetics , Escherichia coli Proteins/genetics , Fermentation , Gene Expression Regulation, Bacterial , Genes, Bacterial , Green Fluorescent Proteins/biosynthesis , Metabolic Networks and Pathways/genetics , Recombinant Proteins/biosynthesis , Signal Transduction/genetics , Stress, Physiological , Up-Regulation
5.
Prep Biochem Biotechnol ; 48(8): 671-682, 2018.
Article in English | MEDLINE | ID: mdl-30015557

ABSTRACT

L-Tyrosine which is one of the terminal metabolites of highly regulated aromatic amino-acid biosynthesis pathway in Escherichia coli is a precursor for synthesis of L-Dopa. In this study, we report over production of L-Dopa by enhancing expression of rate limiting isoenzyme of shikimate kinase (aroL), chorismate synthase (aroC), aromatic-amino-acid aminotransferase (tyrB) and 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) form a plasmid module harboring five enzymes under two inducible promoters converting shikimate to tyrosine. 4-hydroxyphenylacetate-3-hydrolase (hpaBC) which converts L-Tyrosine to L-Dopa was expressed constitutively from a separate plasmid module. Feedback deregulated expression of 3-Deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) synthase (aroG*) replacing wild type aroG under its natural promoter led to enhancement of L-Dopa production. Deletion of transcriptional repressor tyrR and links to other competing pathways improved titers of L-Dopa. We focused on having a balanced flux by constitutive expression of pathway enzymes from plasmid constructs rather than achieving higher amounts of catalytic protein by induction. We observed glycerol when used as a carbon source for the final strain led to low acid production. The best performing strain led to decoupling of acid production and product formation in bioreactor. Fed batch analysis of the final strain led to 12.5 g/L of L-Dopa produced in bioreactor.


Subject(s)
Escherichia coli , Genome, Bacterial , Glycerol/metabolism , Levodopa/biosynthesis , Metabolic Engineering , Microorganisms, Genetically-Modified , Plasmids , Escherichia coli/genetics , Escherichia coli/metabolism , Levodopa/genetics , Microorganisms, Genetically-Modified/genetics , Microorganisms, Genetically-Modified/metabolism
6.
Biotechnol J ; 13(5): e1700571, 2018 May.
Article in English | MEDLINE | ID: mdl-29266768

ABSTRACT

The authors show that quiescent (Q-Cell) Escherichia coli cultures can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater specific productivity of a model metabolite, 3-hydroxybutyrate (3HB), than a control. Q-cells can be created by using the proton ionophore indole to halt cell division of an hns mutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks because less metabolic effort is diverted to surplus biomass production. However, the reason for the increased productivity of cells in the quiescent state was previously unknown. In this study, proteome expression patterns between wild-type and Q-cell cultures show that Q-cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Metabolomic data reveal the accumulation of acetyl-coenzyme A and phosphoenolpyruvate: excellent starting points for high-value chemical production. We demonstrate the exploitation of these accumulated metabolites by engineering a simple pathway for 3HB production from acetyl-coenzyme A. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g L-1 of 3HB compared to 18.6 g L-1 in the control. Q-cells therefore have great potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals.


Subject(s)
3-Hydroxybutyric Acid/metabolism , Bioelectric Energy Sources/microbiology , Escherichia coli , Indoles/pharmacology , Proteome , 3-Hydroxybutyric Acid/analysis , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli/metabolism , Glycolysis , Metabolic Engineering/methods , Metabolome/drug effects , Proteome/drug effects , Proteome/metabolism
7.
Microb Cell Fact ; 16(1): 133, 2017 Jul 28.
Article in English | MEDLINE | ID: mdl-28754100

ABSTRACT

BACKGROUND: A cellular stress response is triggered upon induction of recombinant protein expression which feedback inhibits both growth as well as protein synthesis. In order to separate these two effects, it was decided to study "quiescent cultures" which continue to be metabolically active and express recombinant proteins even after growth cessation. The idea was to identify and up-regulate genes which are responsible for protein synthesis in the absence of growth. This would ensure that, even if growth were adversely affected post induction, there would be no attendant reduction in the protein expression capability of the cells. This strategy allowed us to design host strains, which did not grow better post induction but had significantly higher levels of protein expression. RESULTS: A quiescent Escherichia coli culture, which is able to sustain recombinant protein expression in the absence of growth, was analyzed by transcriptomic and proteomic profiling. Many genes involved in carbon utilization, biosynthesis of building blocks and stress protection were found to be up-regulated in the quiescent phase. Analysis of the global regulators showed that fis, which tends to get down-regulated as the cells enter stationary phase, remained up-regulated throughout the non-growing quiescent phase. The downstream genes regulated by fis like carB, fadB, nrfA, narH and queA were also up-regulated in the quiescent phase which could be the reason behind the higher metabolic activity and protein expression ability of these non-growing cells. To test this hypothesis, we co-expressed fis in a control culture expressing recombinant L-asparaginase and observed a significantly higher buildup of L-asparaginase in the culture medium. CONCLUSIONS: This work represents an important breakthrough in the design of a superior host platform where a gene not directly associated with protein synthesis was used to generate a phenotype having higher protein expression capability. Many alternative gene targets were also identified which may have beneficial effects on expression ability.


Subject(s)
Escherichia coli/metabolism , Proteomics , Asparaginase/genetics , Asparaginase/metabolism , Aspartic Acid/metabolism , Down-Regulation , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Gene Expression Profiling , Plasmids/genetics , Plasmids/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Transcriptome , Up-Regulation
8.
Prep Biochem Biotechnol ; 47(8): 754-760, 2017 Sep 14.
Article in English | MEDLINE | ID: mdl-28430025

ABSTRACT

L-Dopa and dopamine are important pathway intermediates toward the synthesis of catecholamine such as epinephrine and norepinephrine from amino acid L-tyrosine. Dopamine, secreted from dopaminergic nerve cells, serves as an important neurotransmitter. We report the synthesis of dopamine by extending the aromatic amino acid pathway of Escherichia coli DH5α by the expression of 4-hydroxyphenylacetate-3-hydrolase (HpaBC) from E. coli and an engineered dopa decarboxylase (DDC) from pig kidney cell. The activity of HpaBC and DDC require 200 µM iron supplementation and 50 µM vitamin B6, respectively as additives to the growth media. The maximum concentration of L-dopa and dopamine obtained from the broth was around 26 and 27 mg/L after 24 hr of separate shake flask studies. We observed that in the presence of dopamine synthesized in vivo host growth was remarkably enhanced. These observations lead us to an interesting finding about the role of these catecholamines on bacterial growth. It is clear that synthesis of dopamine in vivo actually promotes growth much efficiently as compared to when dopamine is added to the system from outside. From HPLC and GC-MS data it was further observed that L-dopa was stable within the observable time of experiments whereas dopamine actually was subjected to degradation via oxidation and host consumption.


Subject(s)
Dopamine/metabolism , Escherichia coli/metabolism , Animals , Dopa Decarboxylase/genetics , Dopa Decarboxylase/metabolism , Dopamine/genetics , Escherichia coli/genetics , Escherichia coli/growth & development , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Industrial Microbiology , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/metabolism , Protein Engineering/methods , Swine
9.
Mol Biotechnol ; 59(4-5): 168-178, 2017 May.
Article in English | MEDLINE | ID: mdl-28374116

ABSTRACT

The phenylalanine pathway flux is controlled by two types of regulators, those that are specific to the pathway, as well as by global regulators. In order to demonstrate the importance of these global regulators, we first removed the pathway-specific regulators using all possible combinations of gene knockouts and knockins. We found that genes like aroG fbr performed best individually as well as in combination with other genes, while other genes like tyrA and tyrR worked only in combination with other modifications. Knocking in the tktA gene under a tyrR promoter and knocking out pykF further increased phenylalanine production demonstrating that the supply of precursor via PEP and E4P is also a rate-limiting step. Finally, we tested the role of global regulators on this deregulated pathway and found that Fis overexpression helps in both enhancing and sustaining the flux through this pathway. This work opens up the possibility of using global regulators in synergy with pathway-specific modifications to enhance product yields.


Subject(s)
Escherichia coli/genetics , Escherichia coli/metabolism , Genetic Enhancement/methods , Metabolic Engineering/methods , Models, Biological , Phenylalanine/biosynthesis , Computer Simulation , Metabolic Flux Analysis/methods , Metabolic Networks and Pathways/physiology , Phenylalanine/isolation & purification , Up-Regulation/genetics
10.
J Obstet Gynaecol India ; 65(4): 246-50, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26243991

ABSTRACT

OBJECTIVE: To identify an effective misoprostol-only regimen for termination of pregnancy between 12 and 20 weeks of gestation, a prospective randomized study comparing sublingual, vaginal, and oral routes of administration of misoprostol was done. METHODS: One hundred and fifty women (12-20 weeks gestation) were randomly divided into three groups and given 400 mcg misoprostol sublingually, vaginally, and orally every 4 h up to a maximum of four doses. Primary outcome was the success rate at 24 h. Secondary outcomes were failure rate, induction-abortion interval, and need for surgical intervention. Various side effects and patients' subjective assessment of comfort with the route of administration were also studied. RESULTS: Success rate at 24 h of sublingual (86 %) group was higher compared to oral (64 %) group (P = 0.011). Complete abortion rate of sublingual (76 %) group was higher than that of oral (48 %) group (P = 0.004). There was no significant difference in the failure rate and need for surgical intervention in the three groups. Induction-abortion interval in sublingual (9.8 ± 3.6 h) and vaginal (10.6 ± 2.9 h) groups was shorter than that in oral group (14.3 ± 3.3). Diarrhea occurred significantly more in the oral group (28 %) and sublingual (22 %) compared to vaginal group (6 %). Fever was significantly higher in vaginal (36 %) than that in the oral group (12 %). Oral route of administration was most comfortable. CONCLUSION: Sublingual route results in significantly higher abortion rate compared to oral route. Vaginal route has efficacy similar to sublingual route.

11.
Biotechnol J ; 10(4): 636-46, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25594833

ABSTRACT

An inherent problem with bacterial cell factories used to produce recombinant proteins or metabolites is that resources are channeled into unwanted biomass as well as product. Over several years, attempts have been made to increase efficiency by unlinking biomass and product generation. One example was the quiescent cell (Q-Cell) expression system that generated non-growing but metabolically active Escherichia coli by over-expressing a regulatory RNA (Rcd) in a defined genetic background. Although effective at increasing the efficiency with which resources are converted to product, the technical complexity of the Rcd-based Q-Cell system limited its use. We describe here an alternative method for generating Q-Cells by the direct addition of indole, or related indole derivatives, to the culture medium of an E. coli strain carrying defined mutations in the hns gene. This simple and effective approach is shown to be functional in both shake-flask and fermenter culture. The cells remain metabolically active and analysis of their performance in the fermenter suggests that they may be particularly suitable for the production of cellular metabolites.


Subject(s)
Bioreactors/microbiology , Escherichia coli/drug effects , Escherichia coli/metabolism , Indoles/pharmacology , Recombinant Proteins/metabolism , Escherichia coli/genetics , Fermentation , Recombinant Proteins/genetics
12.
Microb Cell Fact ; 13: 177, 2014 Dec 19.
Article in English | MEDLINE | ID: mdl-25523647

ABSTRACT

A metabolic engineering perspective which views recombinant protein expression as a multistep pathway allows us to move beyond vector design and identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level and the supply of precursors in the form of energy, amino acids and nucleotides. Further recombinant protein production triggers a global cellular stress response which feedback inhibits both growth and product formation. Countering this requires a system level analysis followed by a rational host cell engineering to sustain expression for longer time periods. Another strategy to increase protein yields could be to divert the metabolic flux away from biomass formation and towards recombinant protein production. This would require a growth stoppage mechanism which does not affect the metabolic activity of the cell or the transcriptional or translational efficiencies. Finally cells have to be designed for efficient export to prevent buildup of proteins inside the cytoplasm and also simplify downstream processing. The rational and the high throughput strategies that can be used for the construction of such improved host cell platforms for recombinant protein expression is the focus of this review.


Subject(s)
Escherichia coli , Gene Expression , Genetic Engineering/methods , Genome, Bacterial , Recombinant Proteins , Escherichia coli/genetics , Escherichia coli/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics
13.
J Biosci Bioeng ; 115(3): 291-7, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23098681

ABSTRACT

The kinetics of recombinant human granulocyte-macrophage colony-stimulating factor (hGM-CSF) expression was studied under the strong T7 promoter in continuous culture of Escherichia coli using complex medium to design an optimum feeding strategy for high cell density cultivation. Continuous culture studies were done at different dilution rates and the growth and product formation profiles were monitored post-induction. Recombinant protein expression was in the form of inclusion bodies with a maximum specific product formation rate (q(p)) of 63.5 mg g(-1) DCW h(-1) at a dilution rate (D) of 0.3 h(-1). The maximum volumetric product concentration achieved at this dilution rate was 474 mg l(-1), which translated a ~1.4 and ~1.75 folds increase than the values obtained at dilution rates of 0.2 h(-1) and 0.4 h(-1) respectively. The specific product yield (Y(P/x)) peaked at 138 mg g(-1) DCW, demonstrating a ~1.6 folds increase in the values obtained at other dilution rates. A drop in q(p) was observed within 5-6 h of induction at all the dilution rates, possibly due to protein toxicity and metabolic stress associated with protein expression. The data from the continuous culture studies allowed us to design an optimal feeding strategy and induction time in fed-batch cultures which resulted in a maximum product concentration of 3.95 g l(-1) with a specific hGM-CSF yield (Y(P/x)) of 107 mg g(-1) DCW.


Subject(s)
Escherichia coli/metabolism , Granulocyte-Macrophage Colony-Stimulating Factor/biosynthesis , Batch Cell Culture Techniques , Escherichia coli/genetics , Escherichia coli/growth & development , Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Humans , Inclusion Bodies/metabolism , Kinetics , Models, Biological , Recombinant Proteins/biosynthesis
14.
Mol Biotechnol ; 54(2): 692-702, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23180218

ABSTRACT

Over-expression of recombinant proteins in Escherichia coli triggers a metabolic stress response which causes a sharp decline in both growth and product formation rates post induction. We identified a key down-regulated substrate utilization gene, glycerol kinase (glpK), whose up-regulation could help alleviate this stress response. In a proof of principal study conducted in shake flask cultures, the glpK gene under the "ara" promoter in a pPROLar.A122 vector was co-transformed along with the recombinant interferon-ß (rhIFN-ß) gene in a pET22b vector into E. coli BL-21(DE3) cells. Co-expression of glpK improved the expression levels of rhIFN-ß in glycerol containing medium, while no such gain was observed in medium without glycerol. This study was extended to high cell density fed-batch cultures where exponential feeding of complex substrates was done to increase biomass and hence product titers. For this we first constructed a modified E. coli strain BL-21(glpK (+)) where the glpK gene was inserted downstream of the ibpA promoter in the host chromosome. There was a significant improvement in growth as well as expression levels of rhIFN-ß in this modified strain when the feed medium contained high glycerol. A final product concentration of 4.8 g/l of rhIFN-ß was obtained with the modified strain which was 35 % higher than the control.


Subject(s)
Escherichia coli Proteins/genetics , Escherichia coli/growth & development , Escherichia coli/genetics , Interferon-beta/genetics , Batch Cell Culture Techniques/methods , Cell Count , Cloning, Molecular/methods , Culture Media , Down-Regulation , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Glycerol Kinase/genetics , Glycerol Kinase/metabolism , Interferon-beta/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Up-Regulation
15.
Microb Cell Fact ; 11: 93, 2012 Jul 03.
Article in English | MEDLINE | ID: mdl-22759404

ABSTRACT

BACKGROUND: A useful goal for metabolic engineering would be to generate non-growing but metabolically active quiescent cells which would divert the metabolic fluxes towards product formation rather than growth. However, for products like recombinant proteins, which are intricately coupled to the growth process it is difficult to identify the genes that need to be knocked-out/knocked-in to get this desired phenotype. To circumvent this we adopted an inverse metabolic engineering strategy which would screen for the desired phenotype and thus help in the identification of genetic targets which need to be modified to get overproducers of recombinant protein. Such quiescent cells would obviate the need for high cell density cultures and increase the operational life span of bioprocesses. RESULTS: A novel strategy for generating a library, consisting of randomly down regulated metabolic pathways in E. coli was designed by cloning small genomic DNA fragments in expression vectors. Some of these DNA fragments got inserted in the reverse orientation thereby generating anti-sense RNA upon induction. These anti-sense fragments would hybridize to the sense mRNA of specific genes leading to gene 'silencing'. This library was first screened for slow growth phenotype and subsequently for enhanced over-expression ability. Using Green Fluorescent Protein (GFP) as a reporter protein on second plasmid, we were able to identify metabolic blocks which led to significant increase in expression levels. Thus down-regulating the ribB gene (3, 4 dihydroxy-2-butanone-4-phosphate synthase) led to a 7 fold increase in specific product yields while down regulating the gene kdpD (histidine kinase) led to 3.2 fold increase in specific yields. CONCLUSION: We have designed a high throughput screening approach which is a useful tool in the repertoire of reverse metabolic engineering strategies for the generation of improved hosts for recombinant protein expression.


Subject(s)
Escherichia coli/metabolism , Metabolic Engineering , Recombinant Proteins/biosynthesis , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Heat-Shock Proteins/genetics , Heat-Shock Proteins/metabolism , Intramolecular Transferases/genetics , Intramolecular Transferases/metabolism , Protein Kinases/genetics , Protein Kinases/metabolism , RNA, Antisense/genetics , RNA, Antisense/metabolism , RNA, Messenger/metabolism , Recombinant Proteins/genetics
16.
Mol Biosyst ; 8(2): 615-28, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22134216

ABSTRACT

Fed batch cultures expressing recombinant interferon beta under the T7 promoter were run with different exponential feeding rates of a complex substrate and induced at varying cell densities. Post-induction profiles of the specific product formation rates showed a strong dependence on the specific growth rate with the maximum product yield obtained at 0.2 h(-1). A study of the relative transcriptomic profiles as a function of pre-induction µ was therefore done to provide insight into the role of cellular physiology in enhancing recombinant protein expression. Hierarchical clustering analysis of the significantly regulated genes allowed us to identify biologically important groups of genes which fall under specific master regulators. The groups were: rpoH, ArcB, CreB, Lrp, RelA, Fis and Hfq. The response of these regulators, which exert a feedback control on the growth and product formation rates correlated well with the expression levels obtained. Thus at the optimum pre-induction µ, the alternative sigma factors and ribosomal machinery genes did not get depressed till the 6th hour post-induction unlike at other specific growth rates, demonstrating a critical role for the genes in sustaining recombinant protein expression.


Subject(s)
Escherichia coli/genetics , Escherichia coli/metabolism , Interferon-beta/biosynthesis , Bacterial Outer Membrane Proteins/metabolism , Bioreactors , Escherichia coli/growth & development , Escherichia coli Proteins/metabolism , Humans , Ligases/metabolism , Membrane Proteins/metabolism , Protein Kinases/metabolism , Recombinant Proteins/biosynthesis , Repressor Proteins/metabolism , Stress, Physiological , Transcriptome
17.
AMB Express ; 1(1): 33, 2011 Oct 22.
Article in English | MEDLINE | ID: mdl-22018139

ABSTRACT

There is a need to elucidate the product specific features of the metabolic stress response of the host cell to the induction of recombinant protein synthesis. For this, the method of choice is transcriptomic profiling which provides a better insight into the changes taking place in complex global metabolic networks. The transcriptomic profiles of three fed-batch cultures expressing different proteins viz. recombinant human interferon-beta (rhIFN-ß), Xylanase and Green Fluorescence Protein (GFP) were compared post induction. We observed a depression in the nutrient uptake and utilization pathways, which was common for all the three expressed proteins. Thus glycerol transporters and genes involved in ATP synthesis as well as aerobic respiration were severely down-regulated. On the other hand the amino acid uptake and biosynthesis genes were significantly repressed only when soluble proteins were expressed under different promoters, but not when the product was expressed as an inclusion body (IB). High level expression under the T7 promoter (rhIFN-ß and xylanase) triggered the cellular degradation machinery like the osmoprotectants, proteases and mRNA degradation genes which were highly up-regulated, while this trend was not true with GFP expression under the comparatively weaker ara promoter. The design of a better host platform for recombinant protein production thus needs to take into account the specific nature of the cellular response to protein expression.

18.
Bioprocess Biosyst Eng ; 30(5): 305-12, 2007 Sep.
Article in English | MEDLINE | ID: mdl-17453257

ABSTRACT

Granulocyte-macrophage colony stimulating factor (GM-CSF) is a hematopoietic growth factor, which has been used as a therapeutic agent in clinical cases like neutropenia. In this study, we report the production of recombinant human GM-CSF in the methylotrophic yeast Pichia pastoris through secretory expression using the inducible AOX1 promoter. Recombinant P. pastoris GS115 cells were grown in fed batch cultures to obtain a biomass density of 55.6 gDCW L(-1) and a high volumetric activity of 131 mg L(-1) of GM-CSF. The protein migrated as a diffuse band on SDS-PAGE at the range of 28-35 kDa indicating differential glycosylation. The secreted protein was purified to 95% in two steps using cation exchange and size exclusion chromatography.


Subject(s)
Biotechnology/methods , Granulocyte-Macrophage Colony-Stimulating Factor/chemistry , Pichia/metabolism , Biomass , Bioreactors , Cations , Chromatography, Ion Exchange/methods , Genetic Vectors , Glycosylation , Hematopoietic System/embryology , Humans , Plasmids/metabolism , Promoter Regions, Genetic , Recombinant Proteins/chemistry , Reproducibility of Results
19.
Food Nutr Bull ; 27(4): 311-5, 2006 Dec.
Article in English | MEDLINE | ID: mdl-17209473

ABSTRACT

BACKGROUND: Nutritional anemia is one of India's major public health problems. The prevalence of anemia ranges from 33% to 89% among pregnant women and is more than 60% among adolescent girls. Under the anemia prevention and control program of the Government of India, iron and folic acid tablets are distributed to pregnant women, but no such program exists for adolescent girls. OBJECTIVE: To assess the status of anemia among pregnant women and adolescent girls from 16 districts of 11 states of India. METHODS: A two-stage random sampling method was used to select 30 clusters on the basis of probability proportional to size. Anemia was diagnosed by estimating the hemoglobin concentration in the blood with the use of the indirect cyanmethemoglobin method. RESULTS: The survey data showed that 84.9% of pregnant women (n = 6,923) were anemic (hemoglobin < 110 g/L); 13.1% had severe anemia (hemoglobin < 70 g/L), and 60.1% had moderate anemia (hemoglobin > or = 70 to 100 g/L). Among adolescent girls (n = 4,337)from 16 districts, the overall prevalence of anemia (defined as hemoglobin < 120 g/L) was 90.1%, with 7.1% having severe anemia (hemoglobin < 70 g/L). CONCLUSIONS: Any intervention strategy for this population must address not only the problem of iron deficiency, but also deficiencies of other micronutrients, such as B12 and folic acid and other possible causal factors.


Subject(s)
Anemia, Iron-Deficiency/epidemiology , Anemia/epidemiology , Hemoglobins/analysis , Iron/therapeutic use , Nutritional Status , Pregnancy Complications/epidemiology , Adolescent , Adolescent Nutritional Physiological Phenomena , Adult , Anemia/prevention & control , Anemia, Iron-Deficiency/prevention & control , Cluster Analysis , Female , Folic Acid/therapeutic use , Folic Acid Deficiency/epidemiology , Folic Acid Deficiency/prevention & control , Humans , India/epidemiology , Pregnancy , Pregnancy Complications/prevention & control , Prevalence , Vitamin B 12 Deficiency/epidemiology , Vitamin B 12 Deficiency/prevention & control
20.
Mol Biotechnol ; 30(2): 103-16, 2005 Jun.
Article in English | MEDLINE | ID: mdl-15920280

ABSTRACT

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a hematopoietic growth factor, that has been used as a therapeutic agent in facilitating bone marrow and stem cell transplantation and in other clinical cases like neutropenia. Although biologically active recombinant GM-CSF has been successfully produced in Escherichia coli, the reported levels are extremely poor. In this study we looked into the possible reasons for poor expression and found that protein toxicity coupled with protease-based degradation was the principal reason for low productivity. To overcome this problem we attached a signal sequence, as well as an amino-terminal His-tag fusion to the GM-CSF gene. This combination had a dramatic effect on expression levels, which increased from 0.8 microg/mL in the control to 40 microg/mL. When a larger fusion partner, such as the Maltose-binding protein (MBP-tag), was used the expression levels increased further to 69.5 microg/mL, which along with the MBP-tag represented approx 12% of the total cellular protein.


Subject(s)
Escherichia coli/genetics , Granulocyte-Macrophage Colony-Stimulating Factor/biosynthesis , Protein Sorting Signals , Carrier Proteins/genetics , Codon/genetics , Escherichia coli/metabolism , Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Humans , Industrial Microbiology , Maltose-Binding Proteins , Periplasm/chemistry , Periplasm/metabolism , Plasmids/genetics , RNA Stability , RNA, Messenger/metabolism , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/genetics , Recombinant Proteins
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