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Fristot E, Cambray G, Bonnet J. LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri. ACS Synth Biol 2024; 13:951-957. [PMID: 38335132 DOI: 10.1021/acssynbio.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Lactic acid bacteria (LAB) are important for many biotechnological applications such as bioproduction and engineered probiotics for therapy. Inducible promoters are key gene expression control elements, yet those available in LAB are mainly based on bacteriocin systems and have many drawbacks, including large gene clusters, costly inducer peptides, and little portability to in vivo settings. Using Lactobacillus gasseri, a model commensal bacteria from the human gut, we report the engineering of synthetic LactoSpanks promoters (Pls), a collection of variable strength inducible promoters controlled by the LacI repressor from E. coli and induced by isopropyl β-d-1-thiogalactopyranoside (IPTG). We first show that the Phyper-spank promoter from Bacillus subtilis is functional in L. gasseri, albeit with substantial leakage. We then construct and screen a semirational library of Phyper-spank variants to select a set of four IPTG-inducible promoters that span a range of expression levels and exhibit reduced leakages and operational dynamic ranges (from ca. 9 to 28 fold-change). With their low genetic footprint and simplicity of use, LactoSpanks will support many applications in L. gasseri, and potentially other lactic acid and Gram-positive bacteria.
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Affiliation(s)
- Elsa Fristot
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), University of Montpellier, INRAE UMR1333, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
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Xu JM, Wu ZS, Zhao KJ, Xi ZJ, Wang LY, Cheng F, Xue YP, Zheng YG. IPTG-induced high protein expression for whole-cell biosynthesis of L-phosphinothricin. Biotechnol J 2023; 18:e2300027. [PMID: 37265188 DOI: 10.1002/biot.202300027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Biocatalytic production of L-phosphinothricin (L-PPT) is currently the most promising method. In this work, we use an Escherichia coli strain coexpressing of D-amino acid oxidase and catalase (E. coli DAAO-CAT) to oxidation biocatalytic D-PPT to PPO, then use the second E. coli strain coexpressing glutamate dehydrogenase and formate dehydrogenase (E. coli GluDH-FDH) to reduce biocatalytic PPO to L-PPT. MAIN METHODS AND MAJOR RESULTS We compared the effects of different concentrations of IPTG or lactose on protein expression and enzyme activity in 5 L fermenter. The best induction conditions for E. coli DAAO-CAT were 0.05 mM IPTG, induction for 18 h at 28°C. The specific enzyme activities of DAAO and CAT were 153.20 U g-1 and 896.23 U g-1 , respectively. The optimal induction conditions for E. coli GluDH-FDH were 0.2 mM IPTG, induction for 19 h at 28°C. The specific enzyme activities of GluDH and FDH were 41.72 U g-1 and 109.70 U g-1 , respectively. The 200 mM D-PPT was biocatalyzed by E. coli DAAO-CAT for 4 h with space-time yield of 9.0 g·L-1 ·h-1 and conversion rate of over 99.0%. Then 220 mM PPO was converted to L-PPT by E. coli GluDH-FDH for 3 h with space-time yield of 14.5 g·L-1 ·h-1 and conversion rate of over 99.0%. To our knowledge, this is the most efficient biocatalytic reaction for L-PPT production. CONCLUSIONS AND IMPLICATIONS We found that IPTG has advantages compared with lactose in the enzyme activity and biomass of E. coli DAAO-CAT and E. coli GluDH-FDH, and IPTG is more environmentally friendly. Our data implicated that IPTG can replace lactose in terms of economic feasibility and effectiveness for scaled-up industrial fermentations.
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Affiliation(s)
- Jian-Miao Xu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhou-Sheng Wu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ke-Ji Zhao
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhi-Jie Xi
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Liu-Yu Wang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Ping Xue
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
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Li W, Xu Y, Zhang Y, Li P, Zhu X, Feng C. Cell-Free Biosensing Genetic Circuit Coupled with Ribozyme Cleavage Reaction for Rapid and Sensitive Detection of Small Molecules. ACS Synth Biol 2023; 12:1657-1666. [PMID: 37196142 DOI: 10.1021/acssynbio.3c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Synthetic biological systems have been utilized to develop a wide range of genetic circuits and components that enhance the performance of biosensing systems. Among them, cell-free systems are emerging as important platforms for synthetic biology applications. Genetic circuits play an essential role in cell-free systems, mainly consisting of sensing modules, regulation modules, and signal output modules. Currently, fluorescent proteins and aptamers are commonly used as signal outputs. However, these signal output modes cannot simultaneously achieve faster signal output, more accurate and reliable performance, and signal amplification. Ribozyme is a highly structured and catalytic RNA molecule that can specifically recognize and cut specific substrate sequences. Here, by adopting ribozyme as the signal output, we developed a cell-free biosensing genetic circuit coupled with the ribozyme cleavage reaction, enabling rapid and sensitive detection of small molecules. More importantly, we have also successfully constructed a 3D-printed sensor array and thereby achieved high-throughput analysis of an inhibitory drug. Furthermore, our method will help expand the application range of ribozyme in the field of synthetic biology and also optimize the signal output system of cell-free biosensing, thus promoting the development of cell-free synthetic biology in biomedical research, clinical diagnosis, environmental monitoring, and food inspection.
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Affiliation(s)
- Wenxing Li
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yiming Xu
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yue Zhang
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Pengfei Li
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
- Shaoxing Institute of Shanghai University, Shaoxing 312071, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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Simas RG, Pessoa Junior A, Long PF. Mechanistic aspects of IPTG (isopropylthio-β-galactoside) transport across the cytoplasmic membrane of Escherichia coli-a rate limiting step in the induction of recombinant protein expression. J Ind Microbiol Biotechnol 2023; 50:kuad034. [PMID: 37849239 PMCID: PMC10639102 DOI: 10.1093/jimb/kuad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
Coupling transcription of a cloned gene to the lac operon with induction by isopropylthio-β-galactoside (IPTG) has been a favoured approach for recombinant protein expression using Escherichia coli as a heterologous host for more than six decades. Despite a wealth of experimental data gleaned over this period, a quantitative relationship between extracellular IPTG concentration and consequent levels of recombinant protein expression remains surprisingly elusive across a broad spectrum of experimental conditions. This is because gene expression under lac operon regulation is tightly correlated with intracellular IPTG concentration due to allosteric regulation of the lac repressor protein (lacY). An in-silico mathematical model established that uptake of IPTG across the cytoplasmic membrane of E. coli by simple diffusion was negligible. Conversely, lacY mediated active transport was a rapid process, taking only some seconds for internal and external IPTG concentrations to equalize. Optimizing kcat and KM parameters by targeted mutation of the galactoside binding site in lacY could be a future strategy to improve the performance of recombinant protein expression. For example, if kcat were reduced whilst KM was increased, active transport of IPTG across the cytoplasmic membrane would be reduced, thereby lessening the metabolic burden on the cell and expediating accumulation of recombinant protein. The computational model described herein is made freely available and is amenable to optimize recombinant protein expression in other heterologous hosts. ONE-SENTENCE SUMMARY A computational model made freely available to optimize recombinant protein expression in Escherichia coli other heterologous hosts.
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Affiliation(s)
- Rodrigo G Simas
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Adalberto Pessoa Junior
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Paul F Long
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
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Delgado-Martín J, Velasco L. An efficient dsRNA constitutive expression system in Escherichia coli. Appl Microbiol Biotechnol 2021; 105:6381-6393. [PMID: 34415390 DOI: 10.1007/s00253-021-11494-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Synthetic dsRNA are valuable tools for reverse genetics research and virus silencing applications. Its synthesis can be performed both in vivo or in vitro. Whilst the latter presents the drawback of high production cost, the former has the advantage of being less expensive and suitable for scalable production. In general, dsRNAs are obtained in vivo from Escherichia coli heterologous systems that require the gene for the T7 RNA polymerase inducible by IPTG. The (ds)RNAs for gene of interest are then synthesized under the T7 promoter. In this work, we present a reliable vector system that includes the insulated promoter proD for the constitutive expression of dsRNA in E. coli that does not require any inducer and that renders elevated dsRNA yield. In tandem, the T7 and proD promoters render the highest dsRNA yield. The accumulation of dsRNA in this system entails a high metabolic cost for the cell. Bacterial RNA extractions that included dsRNAs homologous to the m5GFPer gene and derived from both the synthetic and constitutive promoters induce silencing of GFP expression in Nicotiana benthamiana 16c.Key points• A vector system that includes a constitutive promoter and a T7 promoter in tandem for maximizing dsRNA synthesis.• The metabolic cost for bacteria is maximum when the two promoters are operating simultaneously and results from the accumulation of dsRNA.• Bacterial RNA extractions from both the induced and constitutive systems that include a mGFP5er-derived dsRNA are capable of silencing the GFP expression in Nicotiana benthamiana 16c plants.
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Affiliation(s)
- Josemaría Delgado-Martín
- Plant Protection, Centro de Málaga, Instituto Andaluz de Investigación Y Formación Agraria (IFAPA), Churriana, 29140, Málaga, Spain
- Universidad de Málaga, Málaga, Spain
| | - Leonardo Velasco
- Plant Protection, Centro de Málaga, Instituto Andaluz de Investigación Y Formación Agraria (IFAPA), Churriana, 29140, Málaga, Spain.
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Barros T, Brumano L, Freitas M, Pessoa A, Parachin N, Magalhães PO. Development of Processes for Recombinant L-Asparaginase II Production by Escherichia coli Bl21 (De3): From Shaker to Bioreactors. Pharmaceutics 2020; 13:E14. [PMID: 33374100 PMCID: PMC7823503 DOI: 10.3390/pharmaceutics13010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 11/21/2022] Open
Abstract
Since 1961, L-asparaginase has been used to treat patients with acute lymphocytic leukemia. It rapidly depletes the plasma asparagine and deprives the blood cells of this circulating amino acid, essential for the metabolic cycles of cells. In the search for viable alternatives to produce L-asparaginase, this work aimed to produce this enzyme from Escherichia coli in a shaker and in a 3 L bioreactor. Three culture media were tested: defined, semi-defined and complex medium. L-asparaginase activity was quantified using the β-hydroxamate aspartic acid method. The defined medium provided the highest L-asparaginase activity. In induction studies, two inducers, lactose and its analog IPTG, were compared. Lactose was chosen as an inducer for the experiments conducted in the bioreactor due to its natural source, lower cost and lower toxicity. Batch and fed-batch cultures were carried out to reach high cell density and then start the induction. Batch cultivation provided a final cell concentration of 11 g L-1 and fed-batch cultivation produced 69.90 g L-1 of cells, which produced a volumetric activity of 43,954.79 U L-1 after lactose induction. L-asparaginase was produced in a shaker and scaled up to a bioreactor, increasing 23-fold the cell concentration and thus, the enzyme productivity.
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Affiliation(s)
- Thaís Barros
- Department of Pharmacy, Health Sciences School, University of Brasília, Brasília 70910-900, Brazil; (T.B.); (M.F.)
| | - Larissa Brumano
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo 05508-000, Brazil; (L.B.); (A.P.J.)
| | - Marcela Freitas
- Department of Pharmacy, Health Sciences School, University of Brasília, Brasília 70910-900, Brazil; (T.B.); (M.F.)
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo 05508-000, Brazil; (L.B.); (A.P.J.)
| | - Nádia Parachin
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil;
| | - Pérola O. Magalhães
- Department of Pharmacy, Health Sciences School, University of Brasília, Brasília 70910-900, Brazil; (T.B.); (M.F.)
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Colarusso A, Lauro C, Calvanese M, Parrilli E, Tutino ML. Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering. Microorganisms 2020; 8:microorganisms8101466. [PMID: 32987756 PMCID: PMC7598627 DOI: 10.3390/microorganisms8101466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Our group has used the marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) as a platform for the successful recombinant production of “difficult” proteins, including eukaryotic proteins, at low temperatures. However, there is still room for improvement both in the refinement of PhTAC125 expression plasmids and in the bacterium’s intrinsic ability to accumulate and handle heterologous products. Here, we present an integrated approach of plasmid design and strain engineering finalized to increment the recombinant expression and optimize the inducer uptake in PhTAC125. To this aim, we developed the IPTG-inducible plasmid pP79 and an engineered PhTAC125 strain called KrPL LacY+. This mutant was designed to express the E. coli lactose permease and to produce only a truncated version of the endogenous Lon protease through an integration-deletion strategy. In the wild-type strain, pP79 assured a significantly better production of two reporters in comparison to the most recent expression vector employed in PhTAC125. Nevertheless, the use of KrPL LacY+ was crucial to achieving satisfying production levels using reasonable IPTG concentrations, even at 0 °C. Both the wild-type and the mutant recombinant strains are characterized by an average graded response upon IPTG induction and they will find different future applications depending on the desired levels of expression.
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Khani MH, Bagheri M. Skimmed milk as an alternative for IPTG in induction of recombinant protein expression. Protein Expr Purif 2020; 170:105593. [PMID: 32032772 DOI: 10.1016/j.pep.2020.105593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 01/20/2023]
Abstract
Cost-effectiveness is an important issue in biotechnological manufacturing industry and using alternative cheap materials with the same benefits has been noticed in most literatures. Isopropyl β-d-1-thiogalactopyranoside (IPTG), a well-known chemical element for induction of protein expression, has several disadvantages such as high expense and toxicity. In this study, we aimed to introduce skimmed milk as an alternative material for protein expression by induction of lac operon. In this way, Escherichia coli BL21 (DE3) bacteria were induced using 1 mM IPTG or 1.0% (w/v) skimmed milk. Protein purification was performed using Ni-NTA (nickel-nitrilotriacetic acid) for His-tagged recombinant proteins and protein purity was evaluated by SDS-PAGE. Results showed high level of recombinant protein expression using skimmed milk, and interestingly, the growth rate of bacteria improved. Our findings suggested that skimmed milk can be a suitable alternative for induction of recombinant protein expression, which has advantages such as more availability and affordability, in comparison to IPTG supplementation.
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Gomes L, Monteiro G, Mergulhão F. The Impact of IPTG Induction on Plasmid Stability and Heterologous Protein Expression by Escherichia coli Biofilms. Int J Mol Sci 2020; 21:ijms21020576. [PMID: 31963160 PMCID: PMC7013871 DOI: 10.3390/ijms21020576] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
Abstract
This work assesses the effect of chemical induction with isopropyl β-D-1-thiogalactopyranoside (IPTG) on the expression of enhanced green fluorescent protein (eGFP) by planktonic and biofilm cells of Escherichia coli JM109(DE3) transformed with a plasmid containing a T7 promoter. It was shown that induction negatively affected the growth and viability of planktonic cultures, and eGFP production did not increase. Heterologous protein production was not limited by gene dosage or by transcriptional activity. Results suggest that plasmid maintenance at high copy number imposes a metabolic burden that precludes high level expression of the heterologous protein. In biofilm cells, the inducer avoided the overall decrease in the amount of expressed eGFP, although this was not correlated with the gene dosage. Higher specific production levels were always attained with biofilm cells and it seems that while induction of biofilm cells shifts their metabolism towards the maintenance of heterologous protein concentration, in planktonic cells the cellular resources are directed towards plasmid replication and growth.
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Affiliation(s)
- Luciana Gomes
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
| | - Gabriel Monteiro
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Filipe Mergulhão
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
- Correspondence: ; Tel.: +351-225081668
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Abstract
Bacillus subtilis is the leading model Gram-positive bacterium, and a widely used chassis for industrial protein production. However, B. subtilis research is limited by a lack of inducible promoter systems with low leakiness and high dynamic range. Here, we engineer an inducible promoter system based on the T7 RNA Polymerase (T7 RNAP), the lactose repressor LacI, and the chimeric promoter PT7lac, integrated as a single copy in the B. subtilis genome. In the absence of IPTG, LacI strongly represses T7 RNAP and PT7lac and minimizes leakiness. Addition of IPTG derepresses PT7lac and simultaneously induces expression of T7RNAP, which results in very high output expression. Using green fluorescent and β-galactosidase reporter proteins, we estimate that this LacI-T7 system can regulate expression with a dynamic range of over 10 000, by far the largest reported for an inducible B. subtilis promoter system. Furthermore, LacI-T7 responds to similar IPTG concentrations and with similar kinetics as the widely used Phy-spank IPTG-inducible system, which we show has a dynamic range of at most 300 in a similar genetic context. Due to its superior performance, our LacI-T7 system should have broad applications in fundamental B. subtilis biology studies and biotechnology.
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Affiliation(s)
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77004, United States
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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Vasconcelos LTCDP, Oliveira Filho MA, Ribeiro VT, Araújo JSD, de Sousa Junior FC, Martins DRA, Dos Santos ES. Optimization of the 503 antigen induction strategy of Leishmania infantum chagasi expressed in Escherichia coli M15. Prep Biochem Biotechnol 2018; 48:968-976. [PMID: 30489218 DOI: 10.1080/10826068.2018.1525563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Leishmaniosis is a complex of diseases that can be fatal, if not given proper attention. Despite its relevance in the public health system, there is no vaccine capable of preventing the disease in humans so far and its treatment is expensive and aggressive to human health. The present study aims to optimize the induction parameters of the 503 Leishmania i. chagasi antigen expressed in recombinant Escherichia coli M15. The induction at different cell densities was evaluated in order to analyze the influence of the induction time on the yield of the protein of interest. In this segment, lactose and isopropyl-β-d-thiogalactopyranoside (IPTG) were used as inducer molecules, using various concentrations: 0.1 g/L, 1.0 g/L, and 10 g/L for lactose and 20 μM, 100 μM, 500 μM, and 1000 μM for IPTG. The results presented that the concentration of IPTG that obtained the higher antigen levels was that of 100 μM (0.087 g/L), a 10-fold lower concentration than was being previously used in this type of system and for lactose, it was 1 g/L (0.016 g/L). Thus, the induction with 100 μM allowed obtaining the antigen with a concentration 5.6 times higher than the lactose induction maximum concentration.
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Affiliation(s)
- Luan Tales Costa de Paiva Vasconcelos
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Marcos Antônio Oliveira Filho
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Vitor Troccoli Ribeiro
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Jaciara Silva de Araújo
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
| | - Francisco Canindé de Sousa Junior
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
| | | | - Everaldo Silvino Dos Santos
- a Biochemical Engineering Laboratory Chemical Engineering Postgraduate Studies Department , Federal University of Rio Grande do Norte , Natal , Brazil
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Hausjell J, Weissensteiner J, Molitor C, Halbwirth H, Spadiut O. E. coli HMS174(DE3) is a sustainable alternative to BL21(DE3). Microb Cell Fact 2018; 17:169. [PMID: 30376846 PMCID: PMC6206895 DOI: 10.1186/s12934-018-1016-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
Background Escherichia coli is one of the most widely used hosts for recombinant protein production in academia and industry. Strain BL21(DE3) is frequently employed due to its advantageous feature of lacking proteases which avoids degradation of target protein. Usually it is used in combination with the T7-pET system where induction is performed by one point addition of IPTG. We recently published a few studies regarding lactose induction in BL21(DE3) strains. BL21(DE3) can only take up the glucose-part of the disaccharide when fed with lactose. However, initially additional glucose has to be supplied as otherwise the ATP-related lactose uptake barely happens. Yet, as lactose is an inexpensive compound compared to glucose and IPTG, a new induction strategy by a lactose-only feed during induction seems attractive. Thus, we investigated this idea in the galactose metabolizing strain HMS174(DE3). Results We show that strain HMS174(DE3) can be cultivated on lactose as sole carbon source during induction. We demonstrate that strain HMS174(DE3) exhibits higher product and biomass yields compared to BL21(DE3) when cultivated in a lactose fed-batch. More importantly, HMS174(DE3) cultivated on lactose even expresses more product than BL21(DE3) in a standard IPTG induced glucose fed-batch at the same growth rate. Finally, we demonstrate that productivity in HMS174(DE3) lactose-fed batch cultivations can easily be influenced by the specific lactose uptake rate (qs,lac). This is shown for two model proteins, one expressed in soluble form and one as inclusion body. Conclusions As strain HMS174(DE3) expresses even slightly higher amounts of target protein in a lactose fed-batch than BL21(DE3) in a standard cultivation, it seems a striking alternative for recombinant protein production. Especially for large scale production of industrial enzymes cheap substrates are essential. Besides cost factors, the strategy allows straight forward adjustment of specific product titers by variation of the lactose feed rate. Electronic supplementary material The online version of this article (10.1186/s12934-018-1016-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna Hausjell
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Julia Weissensteiner
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Molitor
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Heidi Halbwirth
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
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Naorem SS, Han J, Zhang SY, Zhang J, Graham LB, Song A, Smith CV, Rashid F, Guo H. Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid. BMC Microbiol 2018; 18:158. [PMID: 30355324 PMCID: PMC6201506 DOI: 10.1186/s12866-018-1319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species. Results We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~ 108, which is ~ 2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported. Conclusion We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research. Electronic supplementary material The online version of this article (10.1186/s12866-018-1319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Stephanie Y Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Junyi Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Lindsey B Graham
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Angelou Song
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Cameron V Smith
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Fariha Rashid
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.
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Ihling N, Bittner N, Diederichs S, Schelden M, Korona A, Höfler GT, Fulton A, Jaeger KE, Honda K, Ohtake H, Büchs J. Online measurement of the respiratory activity in shake flasks enables the identification of cultivation phases and patterns indicating recombinant protein production in various Escherichia coli host strains. Biotechnol Prog 2018; 34:315-327. [PMID: 29314728 DOI: 10.1002/btpr.2600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/12/2017] [Indexed: 12/21/2022]
Abstract
Escherichia coli is commonly used for recombinant protein production with many available host strains. Screening experiments are often performed in batch mode using shake flasks and evaluating only the final product concentration. This conventional approach carries the risk of missing the best strain due to limited monitoring capabilities. Thus, this study focuses on investigating the general suitability of online respiration measurement for selecting expression hosts for heterologous protein production. The oxygen transfer rate (OTR) for different T7-RNA polymerase-dependent Escherichia coli expression strains was compared under inducing and noninducing conditions. As model enzymes, a lipase A from Bacillus subtilis (BSLA) and a 3-hydroxybutyryl-CoA dehydrogenase from Thermus thermophilus (HBD) were chosen. Four strains were compared during expression of both enzymes in autoinduction medium. Additionally, four strains were compared during expression of the BSLA with IPTG induction. It was found that the metabolic burden during recombinant protein production induces a phase of constant OTR, while undisturbed cell growth with no or little product formation is indicated by an exponential increase. This pattern is independent of the host strain, expressed enzyme, and induction method. Furthermore, the OTR gives information about carbon source consumption, biomass formation, and the transition from production to noninduced second growth phase, thereby ensuring a fair comparison of different strains. In conclusion, online monitoring of the respiration activity is suited to qualitatively identify, if a recombinant protein is produced by a strain or not. Furthermore, laborious offline sampling is avoided. Thus, the technique is easier and faster compared to conventional approaches. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:315-327, 2018.
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Affiliation(s)
- Nina Ihling
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Natalie Bittner
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany
| | - Sylvia Diederichs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany
| | - Maximilian Schelden
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Anna Korona
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany
| | - Georg Theo Höfler
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich D-52426, Germany
| | - Karl-Erich Jaeger
- Bioeconomy Science Center (BioSC), Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich D-52426, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52426, Germany
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hisao Ohtake
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, Aachen D-52074, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
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15
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Taylor T, Denson JP, Esposito D. Optimizing Expression and Solubility of Proteins in E. coli Using Modified Media and Induction Parameters. Methods Mol Biol 2017; 1586:65-82. [PMID: 28470599 DOI: 10.1007/978-1-4939-6887-9_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The major goal of any protein expression experiment is to combine the maximum production per cell of soluble protein with the highest possible cell density to most efficiently obtain high yields of protein. A large number of parameters can be optimized in these experiments, but one of the most interesting parameters that have a strong effect on both per cell productivity and cell density is the cellular growth media coupled to the expression induction process. Using specialized media and testing multiple induction conditions, it is possible to significantly enhance the production of heterologous proteins from E. coli.
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16
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Abstract
Cellular senescence is a unique process of normal physiology, from embryonic development to aging, also known for its association with a broad range of pathological conditions. Therefore a reliable model of cellular senescence remains an indispensable tool for the investigation of senescence-associated changes and human disease. Here we describe a model of HT1080 fibrosarcoma cells with an inducible senescence phenotype. These cells are equipped with the lac repressor and exogenous p21 under the control of a lac repressor regulated promoter. The senescent phenotype is induced in these cells by isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible expression of senescence-associated cell cycle inhibitor p21Waf1/Cip1/Sdi1.
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17
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Abedi D, Moazen F, Akbari V, Mirzaalian F, Sadeghi HMM. Optimization of the expression of phaC2 encoding poly (3-hydroxyalkanoate) synthase from Pseudomonas aeruginosa PTCC1310 in Fad B deleted Escherichia coli. Adv Biomed Res 2016; 5:50. [PMID: 27110547 PMCID: PMC4817391 DOI: 10.4103/2277-9175.178790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Background: Poly3-hydroxyalkanoates (PHAs) are potential candidates for the industrial production of biodegradable plastics. Therefore, in the present study, expression and activity of one of the enzymes involved in the PHA synthesis, phaC2 (isolated from Pseudomonas aeruginosa PTCC1310), were investigated in Fad B deleted Escherichia coli. Materials and Methods: The inserts obtained from recombinant pTZ57R plasmids were ligated into the pGEX-5x-1 expression vector and then transformed into Fad B deleted E. coli cells using the heat shock method. This protein was then expressed using isopropyl beta-d-thiogalactoside (IPTG) as an inducer. By changing expression conditions such as IPTG and glucose concentration, time and temperature of incubation with IPTG, the expression conditions were optimized. Results: The optimum condition for the expression of this enzyme was: 1.5 mM IPTG, 1 mM glucose, incubated at 37°C for 2 hours. Conclusion: We obtained functional expression of the phaC2 gene and investigated various conditions that could influence the expression of protein to optimize production of PHA synthase enzymes. This would allow us to study PHA production in large quantities.
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Affiliation(s)
- Daryoush Abedi
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Moazen
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farnoush Mirzaalian
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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18
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Heiss S, Hörmann A, Tauer C, Sonnleitner M, Egger E, Grabherr R, Heinl S. Evaluation of novel inducible promoter/repressor systems for recombinant protein expression in Lactobacillus plantarum. Microb Cell Fact 2016; 15:50. [PMID: 26966093 PMCID: PMC4785742 DOI: 10.1186/s12934-016-0448-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/25/2016] [Indexed: 01/30/2023] Open
Abstract
Background Engineering lactic acid bacteria (LAB) is of growing importance for food and feed industry as well as for in vivo vaccination or the production of recombinant proteins in food grade organisms. Often, expression of a transgene is only desired at a certain time point or period, e.g. to minimize the metabolic burden for the host cell or to control the expression time span. For this purpose, inducible expression systems are preferred, though cost and availability of the inducing agent must be feasible. We selected the plasmid free strain Lactobacillus plantarum 3NSH for testing and characterization of novel inducible promoters/repressor systems. Their feasibility in recombinant protein production was evaluated. Expression of the reporter protein mCherry was monitored with the BioLector® micro-fermentation system. Results Reporter gene mCherry expression was compared under the control of different promoter/repressor systems: PlacA (an endogenous promoter/repressor system derived from L. plantarum 3NSH), PxylA (a promoter/repressor system derived from Bacillus megaterium DSMZ 319) and PlacSynth (synthetic promoter and codon-optimized repressor gene based on the Escherichia colilac operon). We observed that PlacA was inducible solely by lactose, but not by non-metabolizable allolactose analoga. PxylA was inducible by xylose, yet showed basal expression under non-induced conditions. Growth on galactose (as compared to exponential growth phase on glucose) reduced basal mCherry expression at non-induced conditions. PlacSynth was inducible with TMG (methyl β-D-thiogalactopyranoside) and IPTG (isopropyl β-D-1-thiogalactopyranoside), but also showed basal expression without inducer. The promoter PlacSynth was used for establishment of a dual plasmid expression system, based on T7 RNA polymerase driven expression in L. plantarum. Comparative Western blot supported BioLector® micro-fermentation measurements. Conclusively, overall expression levels were moderate (compared to a constitutive promoter). Conclusions We evaluated different inducible promoters, as well as an orthologous expression system, for controlled gene expression in L. plantarum. Furthermore, here we provide proof of concept for a T7 RNA polymerase based expression system for L. plantarum. Thereby we expanded the molecular toolbox for an industrial relevant and generally regarded as safe (GRAS) strain. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0448-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Heiss
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Angelika Hörmann
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Margot Sonnleitner
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Esther Egger
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Stefan Heinl
- Christian Doppler Laboratory for Genetically Engineered Lactic Acid Bacteria, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria.
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Bashir H, Ahmed N, Khan MA, Zafar AU, Tahir S, Khan MI, Khan F, Husnain T. Simple procedure applying lactose induction and one-step purification for high-yield production of rhCIFN. Biotechnol Appl Biochem 2015; 63:708-714. [PMID: 26256695 DOI: 10.1002/bab.1426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/26/2015] [Indexed: 11/11/2022]
Abstract
Recombinant consensus interferon (CIFN) is a therapeutic protein with molecular weight of 19.5 kDa having broad spectrum antiviral activity. Recombinant human CIFN (rhCIFN) has previously been expressed in Escherichia coli using isopropyl-β-d-thiogalactopyranoside (IPTG), a non-metabolizable and expensive compound, as inducer. For economical and commercial-scale recombinant protein production, it is greatly needed to increase the product yield in a limited time frame to reduce the processing cost. To reduce the cost of production of rhCIFN in E. coli, induction was accomplished by using lactose instead of IPTG. Lactose induction (14 g/L) in shake flask experiment resulted in higher yield as compared with 1 mM IPTG. Finally, with single-step purification on DEAE sepharose, 150 mg/L of >98% pure rhCIFN was achieved. In the present study, an attempt was made to develop a low cost process for producing quality product with high purity. Methods devised may be helpful for pilot-scale production of recombinant proteins at low cost.
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Affiliation(s)
- Hamid Bashir
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nadeem Ahmed
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Mohsin Ahmad Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Usman Zafar
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Saad Tahir
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Islam Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Faidad Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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20
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Abstract
Production of soluble protein remains a bottleneck in the biochemistry and structural biology fields. Unfortunately, there is no 'magic bullet' that solves all solubility problems. The following is a protocol to test whether a protein expressed recombinantly is soluble, and possible strategies to circumvent insolubility issues.
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21
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Avcu N, Alyürük H, Demir GK, Pekergin F, Cavas L, Güzeliş C. Determining the bistability parameter ranges of artificially induced lac operon using the root locus method. Comput Biol Med 2015; 61:75-91. [PMID: 25864166 DOI: 10.1016/j.compbiomed.2015.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/24/2022]
Abstract
This paper employs the root locus method to conduct a detailed investigation of the parameter regions that ensure bistability in a well-studied gene regulatory network namely, lac operon of Escherichia coli (E. coli). In contrast to previous works, the parametric bistability conditions observed in this study constitute a complete set of necessary and sufficient conditions. These conditions were derived by applying the root locus method to the polynomial equilibrium equation of the lac operon model to determine the parameter values yielding the multiple real roots necessary for bistability. The lac operon model used was defined as an ordinary differential equation system in a state equation form with a rational right hand side, and it was compatible with the Hill and Michaelis-Menten approaches of enzyme kinetics used to describe biochemical reactions that govern lactose metabolism. The developed root locus method can be used to study the steady-state behavior of any type of convergent biological system model based on mass action kinetics. This method provides a solution to the problem of analyzing gene regulatory networks under parameter uncertainties because the root locus method considers the model parameters as variable, rather than fixed. The obtained bistability ranges for the lac operon model parameters have the potential to elucidate the appearance of bistability for E. coli cells in in vivo experiments, and they could also be used to design robust hysteretic switches in synthetic biology.
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Malakar P, Singh VK, Karmakar R, Venkatesh KV. Effect on β-galactosidase synthesis and burden on growth of osmotic stress in Escherichia coli. Springerplus 2015; 3:748. [PMID: 25674477 PMCID: PMC4320194 DOI: 10.1186/2193-1801-3-748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/11/2014] [Indexed: 12/21/2022]
Abstract
Osmotic Shock is known to negatively affect growth rate along with an extended lag phase. The reduction in growth rate can be characterized as burden due to the osmotic stress. Studies have shown that production of unnecessary protein also burdens cellular growth. This has been demonstrated by growing Escherichia coli on glycerol in the presence of Isopropyl-β-D-1-thiogalactopyranoside (IPTG) to induce β-galactosidase synthesis which does not offer any benefit towards growth. The trade off between osmotic stress and burden on growth due to unnecessary gene expression has not been enumerated. The influence of osmotic stress on β-galactosidase synthesis and activity is not clearly understood. Here, we study the effect of salt concentration on β-galactosidase activity and burden on growth due to unnecessary gene expression in E.coli. We characterize the burden on growth in presence of varying concentrations of salt in the presence of IPTG using three strains, namely wild type, ∆lacI and ∆lacIlacZ mutant strains. We demonstrate that the salt concentrations, sensitively inhibits enzyme synthesis thereby influencing the burden on growth. In a wild type strain, addition of lactose into the medium demonstrated growth benefit at low salt concentration but not at higher concentrations. The extent of burden due to osmotic shock was higher in a lactose M9 medium than in a glycerol M9 medium. A linear relationship was observed between enzyme activity and burden on growth in various media types studied.
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Affiliation(s)
- Pushkar Malakar
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 Maharashtra India
| | - Vivek K Singh
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 Maharashtra India
| | - Richa Karmakar
- Department of Chemical Engineering, IIT Bombay, Mumbai, 400076 India
| | - Kareenhalli V Venkatesh
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 Maharashtra India ; Department of Chemical Engineering, IIT Bombay, Mumbai, 400076 India
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Zhu C, Fan Q, Wang W, Shen C, Meng X, Tang Y, Mei B, Xu Z, Song R. Characterization of a glutamine synthetase gene DvGS2 from Dunaliella viridis and biochemical identification of DvGS2-transgenic Arabidopsis thaliana. Gene 2014; 536:407-15. [PMID: 24334123 DOI: 10.1016/j.gene.2013.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/16/2013] [Accepted: 11/05/2013] [Indexed: 01/23/2023]
Abstract
The salt-tolerant green alga Dunaliella has remarkable capability to survive in some extreme environments such as nitrogen starvation, which makes Dunaliella be a proper model for mining novel genes on nitrogen uptake or assimilation. In this study, a glutamine synthetase (GS) gene DvGS2 with amino acid identity of 72% to other homologous GS proteins, was isolated and characterized from Dunaliella viridis. Phylogenetic comparison with other GSs revealed that DvGS2 occupied an independent phylogenetic position. Expressional analysis in D. viridis cells under nitrogen starvation confirmed that DvGS2 increased its mRNA level in 12h. Subcellular localization study and functional analysis in a GS-deficient Escherichia coli mutant proved that DvGS2 was a chloroplastic and functional GS enzyme. In order to investigate the potential application of DvGS2 in higher plants, the transgenic studies of DvGS2 in Arabidopsis thaliana were carried out. Results showed that the transgenic lines expressed the DvGS2 gene and demonstrated obviously enhanced root length (29%), fresh weight (40%-48% at two concentrations of nitrate supplies), stem length (21%), leaf size (39%) and silique number (44%) in contrast with the wild-type Arabidopsis. Furthermore, the transgenic lines had higher total nitrogen content (35%-43%), total GS activity (39%-45%) and soluble protein concentration (23%-24%) than the wild type. These results indicated that the overexpression of DvGS2 in A. thaliana resulted in higher biomass and the improvement of the host's nitrogen use efficiency.
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Affiliation(s)
- Chenguang Zhu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Qianlan Fan
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Chunlei Shen
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Xiangzong Meng
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Yuanping Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Bing Mei
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Zhengkai Xu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444 Shanghai, China.
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McSorley T, Ort S, Monnerjahn C, Konrad M. A designed equine herpes thymidine kinase (EHV4 TK) variant improves ganciclovir-induced cell-killing. Biochem Pharmacol 2014; 87:435-44. [PMID: 24316433 DOI: 10.1016/j.bcp.2013.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/31/2013] [Accepted: 11/19/2013] [Indexed: 11/22/2022]
Abstract
The limitations of the ganciclovir (GCV)/herpes simplex virus thymidine kinase (HSV1 TK: EC 2.7.1.21) system as a suicide gene therapy approach have been extensively studied over the years. In our study, we focused on improving the cytotoxic profile of the GCV/equine herpes virus-4 thymidine kinase (EHV4 TK: EC 2.7.1.21) system. Our approach involved the structure-guided mutagenesis of EHV4 TK in order to switch its ability to preferentially phosphorylate the natural substrate deoxythymidine (dT) to that of GCV. We performed steady-state kinetic analysis, genetic complementation in a thymidine kinase-deficient Escherichia coli strain, isothermal titration calorimetry, and analysis of GCV-induced cell killing through generation of HEK 293 stable cell-lines expressing EHV4 TK mutants and wild-type EHV4 TK. We found that the EHV4 TK S144H-GFP mutant preferentially phosphorylates GCV and confers increased GCV-induced cytotoxicity compared to wild-type EHV4 TK.
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25
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Micozzi D, Carpi FM, Pucciarelli S, Polzonetti V, Polidori P, Vilar S, Williams B, Costanzi S, Vincenzetti S. Human cytidine deaminase: a biochemical characterization of its naturally occurring variants. Int J Biol Macromol 2014; 63:64-74. [PMID: 24183806 PMCID: PMC3904506 DOI: 10.1016/j.ijbiomac.2013.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 10/19/2013] [Accepted: 10/21/2013] [Indexed: 01/10/2023]
Abstract
Human cytidine deaminase is an enzyme of the pyrimidine salvage pathways that metabolizes several cytosine nucleoside analogs used as prodrugs in chemotherapy. We carried out a characterization of the cytidine deaminase 79A>C and 208G>A Single Nucleotide Polymorphisms, in order to highlight their functional role and provide data that could help fine-tune the chemotherapic use of cytosine nucleosides in patients carrying the above mentioned SNPs. The 79A>C SNP results in a K27Q change in a protein region not involved in the catalytic event. The 208G>A SNP produces an alanine to threonine substitution (A70T) within the conserved catalytic domain. Q27 variant is endowed with a greater catalytic efficiency toward the natural substrates and the antileukemic agent cytarabine (Ara-C), when compared to K27 variant. Molecular modeling, protein stability experiments and site-directed mutagenesis suggest that K27 variant may have an increased stability with respect to Q27 due to an ionic interaction between a lysine residue at position 27 and a glutamate residue at position 24. The T70 variant has a lower catalytic efficiency toward the analyzed substrates when compared to the A70 variant, suggesting that patients carrying the 208G>A SNP may have a greater exposure to cytosine based pro drugs, with possible toxicity consequences.
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Affiliation(s)
- Daniela Micozzi
- School of Biosciences and Biotechnology, University of Camerino, via Gentile III da Varano, 62032 Camerino, MC, Italy
| | - Francesco Martino Carpi
- School of Biosciences and Biotechnology, University of Camerino, via Gentile III da Varano, 62032 Camerino, MC, Italy
| | - Stefania Pucciarelli
- School of Biosciences and Biotechnology, University of Camerino, via Gentile III da Varano, 62032 Camerino, MC, Italy
| | - Valeria Polzonetti
- School of Biosciences and Biotechnology, University of Camerino, via Gentile III da Varano, 62032 Camerino, MC, Italy
| | - Paolo Polidori
- School of Pharmacy, University of Camerino, via circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Santiago Vilar
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Brian Williams
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Stefano Costanzi
- Department of Chemistry, American University, Washington, DC 20016, USA.
| | - Silvia Vincenzetti
- School of Veterinary Medical Sciences, University of Camerino, via circonvallazione 93/95, 62024 Matelica, MC, Italy.
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26
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Abstract
CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.
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Affiliation(s)
- Benjamin L Oakes
- Department of Molecular & Cell Biology, University of California, Berkeley, California, USA
| | - Dana C Nadler
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - David F Savage
- Department of Molecular & Cell Biology, University of California, Berkeley, California, USA; Department of Chemistry, University of California, Berkeley, California, USA; Energy Biosciences Institute, University of California, Berkeley, California, USA.
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Hatty CR, Le Brun AP, Lake V, Clifton LA, Liu GJ, James M, Banati RB. Investigating the interactions of the 18kDa translocator protein and its ligand PK11195 in planar lipid bilayers. Biochim Biophys Acta 2013; 1838:1019-30. [PMID: 24374318 DOI: 10.1016/j.bbamem.2013.12.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/16/2013] [Accepted: 12/18/2013] [Indexed: 12/20/2022]
Abstract
The functional effects of a drug ligand may be due not only to an interaction with its membrane protein target, but also with the surrounding lipid membrane. We have investigated the interaction of a drug ligand, PK11195, with its primary protein target, the integral membrane 18kDa translocator protein (TSPO), and model membranes using Langmuir monolayers, quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR). We found that PK11195 is incorporated into lipid monolayers and lipid bilayers, causing a decrease in lipid area/molecule and an increase in lipid bilayer rigidity. NR revealed that PK11195 is incorporated into the lipid chain region at a volume fraction of ~10%. We reconstituted isolated mouse TSPO into a lipid bilayer and studied its interaction with PK11195 using QCM-D, which revealed a larger than expected frequency response and indicated a possible conformational change of the protein. NR measurements revealed a TSPO surface coverage of 23% when immobilised to a modified surface via its polyhistidine tag, and a thickness of 51Å for the TSPO layer. These techniques allowed us to probe both the interaction of TSPO with PK11195, and PK11195 with model membranes. It is possible that previously reported TSPO-independent effects of PK11195 are due to incorporation into the lipid bilayer and alteration of its physical properties. There are also implications for the variable binding profiles observed for TSPO ligands, as drug-membrane interactions may contribute to the apparent affinity of TSPO ligands.
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Affiliation(s)
- Claire R Hatty
- Medical Imaging & Radiation Sciences Faculty Research Group, Faculty of Health Sciences, The University of Sydney, c/o Brain & Mind Research Institute, 94 Mallett Street, Camperdown, NSW 2050, Australia
| | - Anton P Le Brun
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Vanessa Lake
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
| | - Guo Jun Liu
- Medical Imaging & Radiation Sciences Faculty Research Group, Faculty of Health Sciences, The University of Sydney, c/o Brain & Mind Research Institute, 94 Mallett Street, Camperdown, NSW 2050, Australia; Life Sciences, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Michael James
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia; School of Chemistry, University of New South Wales, Kensington NSW 2052, Australia
| | - Richard B Banati
- Medical Imaging & Radiation Sciences Faculty Research Group, Faculty of Health Sciences, The University of Sydney, c/o Brain & Mind Research Institute, 94 Mallett Street, Camperdown, NSW 2050, Australia; Life Sciences, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia.
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28
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Zhao S, Jiang QT, Ma J, Zhang XW, Zhao QZ, Wang XY, Wang CS, Cao X, Lu ZX, Zheng YL, Wei YM. Characterization and expression analysis of WOX5 genes from wheat and its relatives. Gene 2013; 537:63-9. [PMID: 24368329 DOI: 10.1016/j.gene.2013.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 01/16/2023]
Abstract
The WUSCHEL (WUS)-related homeobox (WOX) gene family plays an important role in coordinating gene transcription in the early phases of embryogenesis. In this study, we isolated and characterized WOX5 from common wheat and its relatives Triticum monococcum, Triticum urartu, Aegilops speltoides, Aegilops searsii, Aegilops sharonensis, Aegilops longissima, Aegilops bicornis, Aegilops tauschii, and Triticum turgidum. The size of the characterized WOX5 alleles ranged from 1029 to 1038 bp and encompassed the complete open reading frame (ORF) as well as 5' upstream and 3' downstream sequences. Domain prediction analysis showed that the putative primary structures of wheat WOX5 protein include the highly conserved homeodomain besides the WUS-box domain and the EAR-like domain, which is/are present in some members of the WOX protein family. The full-length ORF was subcloned into a prokaryotic expression vector pET30a, and an approximate 26-kDa protein was successfully expressed in Escherichia coli BL21 (DE3) cells with IPTG induction. The WOX5 genes from wheat-related species exhibit a similar structure to and high sequence similarity with WOX5 genes from common wheat. The degree of divergence and phylogenetic tree analysis among WOX5 alleles suggested the existence of three homoeologous copies in the A, B, or D genome of common wheat. Quantitative PCR results showed that TaWOX5 was primarily expressed in the root and calli induced by auxin and cytokinin, indicating that TaWOX5 may play a role related to root formation or development and is associated with hormone regulation in somatic embryogenesis.
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Affiliation(s)
- Shan Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiao-Wei Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Quan-Zhi Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiu-Ying Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Chang-Shui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xue Cao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Zhen-Xiang Lu
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge T1J 4B1, Canada
| | - You-Liang Zheng
- Key Laboratory of Southwestern Crop Germplasm Utilization, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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29
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Lucas SJ, Baştaş K, Budak H. Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene 2014; 536:254-64. [PMID: 24368332 DOI: 10.1016/j.gene.2013.12.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 01/15/2023]
Abstract
The present study aims to investigate small RNA interactions with putative disease response genes in the model grass species Brachypodium distachyon. The fungal pathogen Fusarium culmorum (Fusarium herein) and phytohormone salicylic acid treatment were used to induce the disease response in Brachypodium. Initially, 121 different putative disease response genes were identified using bioinformatic and homology based approaches. Computational prediction was used to identify 33 candidate new miRNA coding sequences, of which 9 were verified by analysis of small RNA sequence libraries. Putative Brachypodium miRNA target sites were identified in the disease response genes, and a subset of which were screened for expression and possible miRNA interactions in 5 different Brachypodium lines infected with Fusarium. An NBS-LRR family gene, 1g34430, was polymorphic among the lines, forming two major genotypes, one of which has its miRNA target sites deleted, resulting in altered gene expression during infection. There were siRNAs putatively involved in regulation of this gene, indicating a role of small RNAs in the B. distachyon disease response.
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30
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Morell SW, Trinh VB, Gudipati E, Friend A, Page NA, Agius MA, Richman DP, Fairclough RH. Structural characterization of the main immunogenic region of the Torpedo acetylcholine receptor. Mol Immunol 2013; 58:116-31. [PMID: 24333757 DOI: 10.1016/j.molimm.2013.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/06/2013] [Accepted: 11/07/2013] [Indexed: 11/27/2022]
Abstract
To develop antigen-specific immunotherapies for autoimmune diseases, knowledge of the molecular structure of targeted immunological hotspots will guide the production of reagents to inhibit and halt production of antigen specific attack agents. To this end we have identified three noncontiguous segments of the Torpedo nicotinic acetylcholine receptor (AChR) α-subunit that contribute to the conformationally sensitive immunological hotspot on the AChR termed the main immunogenic region (MIR): α(1-12), α(65-79), and α(110-115). This region is the target of greater than 50% of the anti-AChR Abs in serum from patients with myasthenia gravis (MG) and animals with experimental autoimmune myasthenia gravis (EAMG). Many monoclonal antibodies (mAbs) raised in one species against an electric organ AChR cross react with the neuromuscular AChR MIR in several species. Probing the Torpedo AChR α-subunit with mAb 132A, a disease inducing anti-MIR mAb raised against the Torpedo AChR, we have determined that two of the three MIR segments, α(1-12) and α(65-79), form a complex providing the signature components recognized by mAb 132A. These two segments straddle a third, α(110-115), that seems not to contribute specific side chains for 132A recognition, but is necessary for optimum antibody binding. This third segment appears to form a foundation upon which the three-dimensional 132A epitope is anchored.
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Affiliation(s)
- Stuart W Morell
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group of UC Davis, United States
| | - Vu B Trinh
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group of UC Davis, United States
| | - Eswari Gudipati
- Biochemistry, Siemens Healthcare Diagnostics, 5210 Pacific Concourse Drive, Los Angeles, CA 90045, United States
| | - Alexander Friend
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States
| | - Nelson A Page
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; Department of Physics Graduate Program, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Mark A Agius
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; VANCHCS, 10535 Hospital Way, Mather, CA 95655, United States
| | - David P Richman
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; Neurosciences Graduate Group of UC Davis, United States
| | - Robert H Fairclough
- University of California, Davis School of Medicine, Department of Neurology, One Shields Avenue, 1515 Newton Court, Room 510C, Davis, CA 95616, United States; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group of UC Davis, United States; Biophysics Graduate Group of UC Davis, United States.
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31
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Nguyen QA, Schumann W. Use of IPTG-inducible promoters for anchoring recombinant proteins on the Bacillus subtilis spore surface. Protein Expr Purif 2013; 95:67-76. [PMID: 24326192 DOI: 10.1016/j.pep.2013.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/24/2013] [Accepted: 11/27/2013] [Indexed: 02/06/2023]
Abstract
The method of surface display allows the fusion of passenger proteins to a carrier protein displayed on the outside of bioparticles such as spores. Here, we used spores of Bacillus subtilis, the outer surface proteins CotB, CotC, and CotG as carrier and the amyQ-encoded α-amylase and GFPuv as passenger proteins. The different translational fusions were fused to two different IPTG-inducible promoters, and the regulated expression level of both passenger proteins were measured in relation to the inducer concentration added to sporulating cells. It turned out that the amount of fusion protein on the outside of spores was dependent on the amount of IPTG added, but the optimal amount of inducer varied depending on the carrier and the passenger proteins. These experiments demonstrate that a regulatable expression of passenger proteins on the surface of spores is possible. This will help to adjust the amount of any passenger protein to that needed for specific purposes.
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Affiliation(s)
- Quynh Anh Nguyen
- Department of Molecular and Environmental Biotechnology, Faculty of Biology, University of Science, Vietnam National University, HCMC, Viet Nam
| | - Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany.
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32
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Gil M, Graña M, Schopfer FJ, Wagner T, Denicola A, Freeman BA, Alzari PM, Batthyány C, Durán R. Inhibition of Mycobacterium tuberculosis PknG by non-catalytic rubredoxin domain specific modification: reaction of an electrophilic nitro-fatty acid with the Fe-S center. Free Radic Biol Med 2013; 65:150-161. [PMID: 23792274 PMCID: PMC4061738 DOI: 10.1016/j.freeradbiomed.2013.06.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
Abstract
PknG from Mycobacterium tuberculosis is a Ser/Thr protein kinase that regulates key metabolic processes within the bacterial cell as well as signaling pathways from the infected host cell. This multidomain protein has a conserved canonical kinase domain with N- and C-terminal flanking regions of unclear functional roles. The N-terminus harbors a rubredoxin-like domain (Rbx), a bacterial protein module characterized by an iron ion coordinated by four cysteine residues. Disruption of the Rbx-metal binding site by simultaneous mutations of all the key cysteine residues significantly impairs PknG activity. This encouraged us to evaluate the effect of a nitro-fatty acid (9- and 10-nitro-octadeca-9-cis-enoic acid; OA-NO2) on PknG activity. Fatty acid nitroalkenes are electrophilic species produced during inflammation and metabolism that react with nucleophilic residues of target proteins (i.e., Cys and His), modulating protein function and subcellular distribution in a reversible manner. Here, we show that OA-NO2 inhibits kinase activity by covalently adducting PknG remote from the catalytic domain. Mass spectrometry-based analysis established that cysteines located at Rbx are the specific targets of the nitroalkene. Cys-nitroalkylation is a Michael addition reaction typically reverted by thiols. However, the reversible OA-NO2-mediated nitroalkylation of the kinase results in an irreversible inhibition of PknG. Cys adduction by OA-NO2 induced iron release from the Rbx domain, revealing a new strategy for the specific inhibition of PknG. These results affirm the relevance of the Rbx domain as a target for PknG inhibition and support that electrophilic lipid reactions of Rbx-Cys may represent a new drug strategy for specific PknG inhibition.
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Affiliation(s)
- Magdalena Gil
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Uruguay
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Uruguay
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tristan Wagner
- Unité de Microbiologie Structurale & CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pedro M Alzari
- Unité de Microbiologie Structurale & CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Carlos Batthyány
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay.
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Uruguay.
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33
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Hopwood EM, Ahmed D, Aitken SM. A role for glutamate-333 of Saccharomyces cerevisiae cystathionine γ-lyase as a determinant of specificity. Biochim Biophys Acta 2014; 1844:465-72. [PMID: 24291053 DOI: 10.1016/j.bbapap.2013.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/17/2013] [Accepted: 11/21/2013] [Indexed: 11/21/2022]
Abstract
Cystathionine γ-lyase (CGL) catalyzes the hydrolysis of l-cystathionine (l-Cth), producing l-cysteine (l-Cys), α-ketobutyrate and ammonia, in the second step of the reverse transsulfuration pathway, which converts l-homocysteine (l-Hcys) to l-Cys. Site-directed variants substituting residues E48 and E333 with alanine, aspartate and glutamine were characterized to probe the roles of these acidic residues, conserved in fungal and mammalian CGL sequences, in the active-site of CGL from Saccharomyces cerevisiae (yCGL). The pH optimum of variants containing the alanine or glutamine substitutions of E333 is increased by 0.4-1.2 pH units, likely due to repositioning of the cofactor and modification of the pKa of the pyridinium nitrogen. The pH profile of yCGL-E48A/E333A resembles that of Escherichia coli cystathionine β-lyase. The effect of substituting E48, E333 or both residues is the 1.3-3, 26-58 and 124-568-fold reduction, respectively, of the catalytic efficiency of l-Cth hydrolysis. The Km(l-Cth) of E333 substitution variants is increased ~17-fold, while Km(l-OAS) is within 2.5-fold of the wild-type enzyme, indicating that residue E333 interacts with the distal amine moiety of l-Cth, which is not present in the alternative substrate O-acetyl-l-serine. The catalytic efficiency of yCGL for α,γ-elimination of O-succinyl-l-homoserine (kcat/Km(l-OSHS)=7±2), which possesses a distal carboxylate, but lacks an amino group, is 300-fold lower than that of the physiological l-Cth substrate (kcat/Km(l-Cth)=2100±100) and 260-fold higher than that of l-Hcys (kcat/Km(l-Hcys)=0.027±0.005), which lacks both distal polar moieties. The results of this study suggest that the glutamate residue at position 333 is a determinant of specificity.
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34
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Peng GJ, Kuan YC, Chou HY, Fu TK, Lin JS, Hsu WH, Yang MT. Stereoselective synthesis of (R)-phenylephrine using recombinant Escherichia coli cells expressing a novel short-chain dehydrogenase/reductase gene from Serratia marcescens BCRC 10948. J Biotechnol 2013; 170:6-9. [PMID: 24291189 DOI: 10.1016/j.jbiotec.2013.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/11/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
Abstract
(R)-Phenylephrine [(R)-PE] is an α1-adrenergic receptor agonist and is widely used as a nasal decongestant to treat the common cold without the side effects of other ephedrine adrenergic drugs. We identified a short-chain dehydrogenase/reductase (SM_SDR) from Serratia marcescens BCRC 10948 that was able to convert 1-(3-hydroxyphenyl)-2-(methylamino) ethanone (HPMAE) into (R)-PE. The SM_SDR used NADPH and NADH as cofactors with specific activities of 17.35±0.71 and 5.57±0.07mU/mg protein, respectively, at 30°C and pH 7.0, thereby indicating that this enzyme could be categorized as an NADPH-preferring short-chain dehydrogenase/reductase. Escherichia coli strain BL21 (DE3) expressing SM_SDR could convert HPMAE into (R)-PE with more than 99% enantiomeric excess. The productivity and conversion yield were 0.57mmolPE/lh and 51.06%, respectively, using 10mM HPMAE. Fructose was the most effective carbon source for the conversion of HPMAE to (R)-PE.
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Affiliation(s)
- Guan-Jhih Peng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yi-Chia Kuan
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Hsiao-Yi Chou
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
| | - Tze-Kai Fu
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jia-Shin Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
| | - Wen-Hwei Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan.
| | - Ming-Te Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan.
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Huang YH, Huang CY. The N-terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self-trimerization. Biochem Biophys Res Commun 2013; 442:147-52. [PMID: 24280305 DOI: 10.1016/j.bbrc.2013.11.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 10/26/2022]
Abstract
DnaT and PriB are replication restart primosomal proteins required for re-initiating chromosomal DNA replication in bacteria. Although the interaction of DnaT with PriB has been proposed, which region of DnaT is involved in PriB binding and self-trimerization remains unknown. In this study, we identified the N-terminal domain in DnaT (aa 1-83) that is important in PriB binding and self-trimerization but not in single-stranded DNA (ssDNA) binding. DnaT and the deletion mutant DnaT42-179 protein can bind to PriB according to native polyacrylamide gel electrophoresis, Western blot analysis, and pull-down assay, whereas DnaT84-179 cannot bind to PriB. In contrast to DnaT, DnaT26-179, and DnaT42-179 proteins, which form distinct complexes with ssDNA of different lengths, DnaT84-179 forms only a single complex with ssDNA. Analysis of DnaT84-179 protein by gel filtration chromatography showed a stable monomer in solution rather than a trimer, such as DnaT, DnaT26-179, and DnaT42-179 proteins. These results constitute a pioneering study of the domain definition of DnaT. Further research can directly focus on determining how DnaT binds to the PriA-PriB-DNA tricomplex in replication restart by the hand-off mechanism.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan
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36
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Li M, Gao Z, Wang Y, Wang H, Zhang S. Identification, expression and bioactivity of hexokinase in amphioxus: insights into evolution of vertebrate hexokinase genes. Gene 2014; 535:318-26. [PMID: 24262936 DOI: 10.1016/j.gene.2013.10.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/11/2013] [Accepted: 10/27/2013] [Indexed: 11/23/2022]
Abstract
Hexokinase family includes hexokinases I, II, III and IV, that catalyze the phosphorylation of glucose to produce glucose 6-phosphate. Hexokinase IV, also known as glucokinase, is only half size of the other types of hexokinases that contain two hexokinase domains. Despite the enormous progress in the study of hexokinases, the evolutionary relationship between glucokinase and other hexokinases is still uncertain, and the molecular processes leading to the emergence of hexokinases in vertebrates remain controversial. Here we clearly demonstrated the presence of a single hexokinase-like gene in the amphioxus Branchiostoma japonicum, Bjhk, which shows a tissue-specific expression pattern, with the most abundant expression in the hepatic caecum, testis and ovary. The phylogenetic and synteny analyses both reveal that BjHK is the archetype of vertebrate hexokinases IV, i.e. glucokinases. We also found for the first time that recombinant BjHK showed functional enzyme activity resembling vertebrate hexokinases I, II, III and IV. In addition, a native glucokinase activity was detected in the hepatic caecum. Finally, glucokinase activity in the hepatic caecum was markedly reduced by fasting, whereas it was considerably increased by feeding. Altogether, these suggest that Bjhk represents the archetype of glucokinases, from which vertebrate hexokinase gene family was evolved by gene duplication, and that the hepatic caecum plays a role in the control of glucose homeostasis in amphioxus, in favor of the notion that the hepatic caecum is a tissue homologous to liver.
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Rajagopalan K, Qiu R, Mooney SM, Rao S, Shiraishi T, Sacho E, Huang H, Shapiro E, Weninger KR, Kulkarni P. The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation. Biochim Biophys Acta Mol Basis Dis 2013; 1842:154-63. [PMID: 24263171 DOI: 10.1016/j.bbadis.2013.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/26/2013] [Accepted: 11/13/2013] [Indexed: 01/18/2023]
Abstract
The Cancer/Testis Antigen (CTA), Prostate-associated Gene 4 (PAGE4), is a stress-response protein that is upregulated in prostate cancer (PCa) especially in precursor lesions that result from inflammatory stress. In cells under stress, translocation of PAGE4 to mitochondria increases while production of reactive oxygen species decreases. Furthermore, PAGE4 is also upregulated in human fetal prostate, underscoring its potential role in development. However, the proteins that interact with PAGE4 and the mechanisms underlying its pleiotropic functions in prostatic development and disease remain unknown. Here, we identified c-Jun as a PAGE4 interacting partner. We show that both PAGE4 and c-Jun are overexpressed in the human fetal prostate; and in cell-based assays, PAGE4 robustly potentiates c-Jun transactivation. Single-molecule Förster resonance energy transfer experiments indicate that upon binding to c-Jun, PAGE4 undergoes conformational changes. However, no interaction is observed in presence of BSA or unilamellar vesicles containing the mitochondrial inner membrane diphosphatidylglycerol lipid marker cardiolipin. Together, our data indicate that PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions. To our knowledge, this is the first report demonstrating crosstalk between a CTA and a proto-oncogene. Disrupting PAGE4/c-Jun interactions using small molecules may represent a novel therapeutic strategy for PCa.
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Affiliation(s)
- Krithika Rajagopalan
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Steven M Mooney
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shweta Rao
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Takumi Shiraishi
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth Sacho
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Hongying Huang
- Department of Urology, New York University School of Medicine, New York, NY 10016, USA
| | - Ellen Shapiro
- Department of Urology, New York University School of Medicine, New York, NY 10016, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
| | - Prakash Kulkarni
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Takahashi S, Yoshikawa M, Kamada A, Ohtsuki T, Uchida A, Nakayama K, Satoh H. The photoconvertible water-soluble chlorophyll-binding protein of Chenopodium album is a member of DUF538, a superfamily that distributes in Embryophyta. J Plant Physiol 2013; 170:1549-1552. [PMID: 23820553 DOI: 10.1016/j.jplph.2013.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Various plants possess hydrophilic chlorophyll (Chl) proteins known as water-soluble Chl-binding proteins (WSCPs). WSCPs exist in two forms: Class I and Class II, of which Class I alone exhibits unique photoconvertibility. Although numerous genes encoding Class II WSCPs have been identified and the molecular properties of their recombinant proteins have been well characterized, no Class I WSCP gene has been identified to date. In this study, we cloned the cDNA and a gene encoding the Class I WSCP of Chenopodium album (CaWSCP). Sequence analyses revealed that CaWSCP comprises a single exon corresponding to 585bp of an open reading frame encoding 195 amino acid residues. The CaWSCP protein sequence possesses a signature of DUF538, a protein superfamily of unknown function found almost exclusively in Embryophyta. The recombinant CaWSCP was expressed in Escherichia coli as a hexa-histidine fusion protein (CaWSCP-His) that removes Chls from the thylakoid. Under visible light illumination, the reconstituted CaWSCP-His was successfully photoconverted into a different pigment with an absorption spectrum identical to that of native CaWSCP. Interestingly, while CaWSCP-His could bind both Chl a and Chl b, photoconversion occurred only in CaWSCP-His reconstituted with Chl a.
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Affiliation(s)
- Shigekazu Takahashi
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Zazrin H, Shaked H, Chill JH. Architecture of the hepatitis C virus E1 glycoprotein transmembrane domain studied by NMR. Biochim Biophys Acta 2013; 1838:784-92. [PMID: 24192053 DOI: 10.1016/j.bbamem.2013.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
Oligomerization of hepatitis C viral envelope proteins E1 and E2 is essential to virus fusion and assembly. Although interactions within the transmembrane (TM) domains of these glycoproteins have proven contributions to the E1/E2 heterodimerization process and consequent infectivity, there is little structural information on this entry mechanism. Here, as a first step towards our long-term goal of understanding the interaction between E1 and E2 TM-domains, we have expressed, purified and characterized E1-TM using structural biomolecular NMR methods. An MBP-fusion expression system yielded sufficient quantities of pure E1-TM, which was solubilized in two membrane-mimicking environments, SDS- and LPPG-micelles, affording samples amenable to NMR studies. Triple resonance assignment experiments and relaxation measurements provided information on the secondary structure and global fold of E1-TM in these environments. In SDS micelles E1-TM adopts a helical conformation, with helical stretches at residues 354-363 and 371-379 separated by a more flexible segment of residues 364-370. In LPPG micelles a helical conformation was observed for residues 354-377 with greater flexibility in the 366-367 dyad, suggesting LPPG provides a more native environment for the peptide. Replacement of key positively charged residue K370 with an alanine did not affect the secondary structure of E1-TM but did change the relative positioning within the micelle of the two helices. These results lay the foundation for structure determination of E1-TM and a molecular understanding of how E1-TM flexibility enhances its interaction with E2-TM during heterodimerization and membrane fusion.
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Affiliation(s)
- Hadas Zazrin
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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Hatanaka R, Hagiwara-Komoda Y, Furuki T, Kanamori Y, Fujita M, Cornette R, Sakurai M, Okuda T, Kikawada T. An abundant LEA protein in the anhydrobiotic midge, PvLEA4, acts as a molecular shield by limiting growth of aggregating protein particles. Insect Biochem Mol Biol 2013; 43:1055-1067. [PMID: 23978448 DOI: 10.1016/j.ibmb.2013.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
LEA proteins are found in anhydrobiotes and are thought to be associated with the acquisition of desiccation tolerance. The sleeping chironomid Polypedilum vanderplanki, which can survive in an almost completely desiccated state throughout the larval stage, accumulates LEA proteins in response to desiccation and high salinity conditions. However, the biochemical functions of these proteins remain unclear. Here, we report the characterization of a novel chironomid LEA protein, PvLEA4, which is the most highly accumulated LEA protein in desiccated larvae. Cytoplasmic-soluble PvLEA4 showed many typical characteristics of group 3 LEA proteins (G3LEAs), such as desiccation-inducible accumulation, high hydrophilicity, folding into α-helices on drying, and the ability to reduce aggregation of dehydration-sensitive proteins. This last property of LEA proteins has been termed molecular shield function. To further investigate the molecular shield activity of PvLEA4, we introduced two distinct methods, turbidity measurement and dynamic light scattering (DLS). Turbidity measurements demonstrated that both PvLEA4, and BSA as a positive control, reduced aggregation in α-casein subjected to desiccation and rehydration. However, DLS experiments showed that a small amount of BSA relative to α-casein increased aggregate particle size, whereas PvLEA4 decreased particle size in a dose-dependent manner. Trehalose, which is the main heamolymph sugar in most insects but also a protectant as a chemical chaperone in the sleeping chironomid, has less effect on the limitation of aggregate formation. This analysis suggests that molecular shield proteins function by limiting the growth of protein aggregates during drying and that PvLEA4 counteracts protein aggregation in the desiccation-tolerant larvae of the sleeping chironomid.
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Affiliation(s)
- Rie Hatanaka
- Insect Mimetics Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
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Wu QY, Guo HY, Geng HL, Ru BM, Cao J, Chen C, Zeng LY, Wang XY, Li F, Xu KL. T273 plays an important role in the activity and structural stability of arginine kinase. Int J Biol Macromol 2013; 63:21-8. [PMID: 24157705 DOI: 10.1016/j.ijbiomac.2013.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Arginine kinase (AK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphoarginine to ADP in invertebrates. The amino acid residue C271 is involved in keeping AK's activity and constraining the orientation of the substrate arginine. However, the roles of the C271 interaction amino acid residues in AK's substrate synergism, activity and structural stability are still unclear. The crystal structure of AK implied that the amino acid residue T273 interacted with the residue C271 and might play vital roles in keeping AK's activity, substrate synergism and structural stability. The mutations T273G and T273A led to significantly loss of activity, obviously decreased of substrate synergism and structural stability. Furthermore, spectroscopic experiments indicated that mutations T273G and T273A impaired the structure of AK and led them to a partially unfolded state. The inability to fold to the functional state made the mutations prone to aggregate under environmental stresses. Moreover, the mutations T273S and T273D almost had no effects on AK's activity and structural stability. This study herein indicated that the residue T273 played key roles in AK's activity, substrate synergism and structural stability.
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Affiliation(s)
- Qing-Yun Wu
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China; Laboratory of Transplantation and Immunology, Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Hua-Yan Guo
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Hong-Li Geng
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Bian-Mei Ru
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Jiang Cao
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Chong Chen
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Ling-Yu Zeng
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China; Laboratory of Transplantation and Immunology, Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China
| | - Xiao-Yun Wang
- College of Life Sciences, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Feng Li
- Department of Neurobiology, Xuzhou Medical College, 221002 Xuzhou, People's Republic of China.
| | - Kai-Lin Xu
- Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, No. 99 West Huaihai Road, Xuzhou 221002, People's Republic of China.
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Saha S, Mukherjee T, Chowdhury S, Mishra A, Chowdhury SR, Jaisankar P, Mukhopadhyay S, Majumder HK. The lignan glycosides lyoniside and saracoside poison the unusual type IB topoisomerase of Leishmania donovani and kill the parasite both in vitro and in vivo. Biochem Pharmacol 2013; 86:1673-87. [PMID: 24134912 DOI: 10.1016/j.bcp.2013.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
Lignans are diphenyl propanoids with vast range of biological activities. The present study provides an important insight into the anti-leishmanial activities of two lignan glycosides, viz. lyoniside and saracoside. These compounds inhibit catalytic activities of topoisomerase IB (LdTopIB) of Leishmania donovani in non-competitive manner and stabilize the LdTopIB mediated cleavage complex formation both in vitro and in Leishmania promastigotes and subsequently inhibit the religation of cleaved strand. These two compounds not only poison LdTopIB but also can interact with the free enzyme LdTopIB. We have also shown that lyoniside and saracoside are cytotoxic to promastigotes and intracellular amastigotes. The protein-DNA complex formation leads to double strand breaks in DNA which ultimately triggers apoptosis-like cell death in the parasite. Along with their cytotoxicity towards sodium antimony gluconate (SAG) sensitive AG83 strain, their ability to kill SAG resistant GE1 strain makes these two compounds potential anti-leishmanial candidates. Not only they effectively kill L. donovani amastigotes inside macrophages in vitro, lyoniside and saracoside demonstrated strong anti-leishmanial efficacies in BALB/c mice model of leishmaniasis. Treatment with these lignan glycosides produce nitric oxide and reactive oxygen species which result in almost complete clearance of the liver and splenic parasite burden. These compounds do not inhibit human topoisomerase IB upto 200μM concentrations and had poor cytotoxic effect on uninfected cultured murine peritoneal macrophages upto 100μM concentrations. Taken together it can be concluded that these compounds can be developed into excellent therapeutic agent against deadly disease leishmaniasis.
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Affiliation(s)
- Sourav Saha
- Molecular Parasitology Laboratory (S.S., S.C., A.M., S.R.C., H.K.M.), Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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Underhaug J, Koldsø H, Runager K, Nielsen JT, Sørensen CS, Kristensen T, Otzen DE, Karring H, Malmendal A, Schiøtt B, Enghild JJ, Nielsen NC. Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization. Biochim Biophys Acta 2013; 1834:2812-22. [PMID: 24129074 DOI: 10.1016/j.bbapap.2013.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 10/26/2022]
Abstract
Hereditary mutations in the transforming growth factor beta induced (TGFBI) gene cause phenotypically distinct corneal dystrophies characterized by protein deposition in cornea. We show here that the Arg555Trp mutant of the fourth fasciclin 1 (FAS1-4) domain of the protein (TGFBIp/keratoepithelin/βig-h3), associated with granular corneal dystrophy type 1, is significantly less susceptible to proteolysis by thermolysin and trypsin than the WT domain. High-resolution liquid-state NMR of the WT and Arg555Trp mutant FAS1-4 domains revealed very similar structures except for the region around position 555. The Arg555Trp substitution causes Trp555 to be buried in an otherwise empty hydrophobic cavity of the FAS1-4 domain. The first thermolysin cleavage in the core of the FAS1-4 domain occurs on the N-terminal side of Leu558 adjacent to the Arg555 mutation. MD simulations indicated that the C-terminal end of helix α3' containing this cleavage site is less flexible in the mutant domain, explaining the observed proteolytic resistance. This structural change also alters the electrostatic properties, which may explain increased propensity of the mutant to aggregate in vitro with 2,2,2-trifluoroethanol. Based on our results we propose that the Arg555Trp mutation disrupts the normal degradation/turnover of corneal TGFBIp, leading to accumulation and increased propensity to aggregate through electrostatic interactions.
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Affiliation(s)
- Jarl Underhaug
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway
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Peng Y, Li Z, Li Z. GRP78 secreted by tumor cells stimulates differentiation of bone marrow mesenchymal stem cells to cancer-associated fibroblasts. Biochem Biophys Res Commun 2013; 440:558-63. [PMID: 24113381 DOI: 10.1016/j.bbrc.2013.09.108] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/09/2023]
Abstract
Cancer-associated fibroblasts (CAFs), one type of tumor-associated stromal cells, have been shown to provide a favorable environment for the malignant tumor progression. Extensive reports have demonstrated that mesenchymal stem cells (MSCs) can function as precursors for CAFs. However, the mechanisms by which tumor cells induce the transition of MSCs to CAFs have not been well established. GRP78, traditionally known as an endoplasmic reticulum (ER) chaperone, has been identified to overexpress in a variety of tumor entities and be involved in promoting survival and chemoresistance of tumor cells. Here, we interrogated the role of GRP78 in the generation of CAFs from MSCs. The results showed that GRP78 treatment induced expression of α-smooth muscle actin (α-SMA), a marker for CAFs, in human bone marrow mesenchymal stem cells (HBMSCs) as well as murine bone marrow mesenchymal stem cells (BMMSCs). This phenomenon was correlated with the stimulated phosphorylation of Smad2/3. Furthermore, the GRP78-induced α-SMA expression in HBMSCs was obviously attenuated by SB431542, a TGF-β type I receptor kinase inhibitor. Taken together, the present data suggested that tumor-derived secreted GRP78 elicited the differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) to CAFs through activating TGF-β/Smad signaling pathway, which may represent a novel mechanism for transition of BMSCs to CAFs and a hitherto unknown function of GRP78 in the tumor microenvironment.
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Affiliation(s)
- Yanan Peng
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
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Liu CL, Lin TH, Juang RS. Optimization of recombinant hexaoligochitin-producing chitinase production with response surface methodology. Int J Biol Macromol 2013; 62:518-22. [PMID: 24099937 DOI: 10.1016/j.ijbiomac.2013.09.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/23/2013] [Accepted: 09/27/2013] [Indexed: 11/27/2022]
Abstract
Hexaoligochitin produced by chitinase, ASCHI61, from Aeromonas schubertii was recently expressed. In this work, the optimal conditions for the mass production of ASCHI61 were investigated. The efficiency of recombinant protein expression in Escherichia coli was determined by various parameters, including the pH of the culture medium, induction temperature, shaking speed, inducer concentration, and induction period. The optimization experiments could be simplified through a statistical design of experiments (response surface methodology). From the fractional factorial design, the interactive effect of induction temperature and time was the most significant. The total activity of the enzyme was 32,092 U at 23.9 °C with 115 min of induction. Under those conditions, the total activity of the recombinant protein was 30,650 U in the fermentation experiments, with an error of only 4.8%. The total activity of ASCHI61 increased 1.54-fold under the optimal conditions. Based on the results, ASCHI61 can be expressed more for hexaoligochitin production.
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Affiliation(s)
- Chao-Lin Liu
- Graduate School of Biochemical Engineering and Department of Chemical Engineering, Ming Chi University of Technology, Taishan, New Taipei, Taiwan
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Wu J, Zhang C, Mei X, Li Y, Xing XH. Controllable production of low molecular weight heparins by combinations of heparinase I/II/III. Carbohydr Polym 2014; 101:484-92. [PMID: 24299802 DOI: 10.1016/j.carbpol.2013.09.052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/09/2013] [Accepted: 09/14/2013] [Indexed: 11/21/2022]
Abstract
Enzymatic depolymerization of heparin by heparinases is promising for production of low molecular weight heparins (LMWHs) as anticoagulants, due to its mild reaction conditions and high selectivity. Here, different heparinase combinations were used to depolymerize heparin. Heparinase I and heparinase II can depolymerize heparin more efficiently than heparinase III, respectively, but heparinase III was the best able to protect the anticoagulant activities of LMWHs. Heparinase III and heparinase I/II combinations were able to efficiently depolymerize heparin to LMWHs with higher anticoagulant activity than the LMWHs produced by the respective heparinase I and heparinase II. HepIII and HepI is the best combination for maintaining high anti-IIa activity (75.7 ± 4.21 IU/mg) at the same Mw value. Furthermore, considering both the changes in molecular weight and anticoagulant activity, the action patterns of heparinase I and heparinase II were found not to follow the exolytic and processive depolymerizing mechanism from the reducing end of heparin.
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Gupta AA, Chou RH, Li H, Yang LW, Yu C. Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling. Biochim Biophys Acta 2013; 1834:2606-19. [PMID: 24063890 DOI: 10.1016/j.bbapap.2013.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/06/2013] [Accepted: 09/17/2013] [Indexed: 01/11/2023]
Abstract
S100B is a calcium sensing protein belonging to the S100 protein family with intracellular and extracellular roles. It is one of the EF hand homodimeric proteins, which is known to interact with various protein targets to regulate varied biological functions. Extracellular S100B has been recently reported to interact with FGF2 in a RAGE-independent manner. However, the recognition mechanism of S100B-FGF2 interaction at the molecular level remains unclear. In this study, the critical residues on S100B-FGF2 interface were mapped by combined information derived from NMR spectroscopy and site directed mutagenesis experiments. Utilizing NMR titration data, we generated the structural models of S100B-FGF2 complex from the computational docking program, HADDOCK which were further proved stable during 15ns unrestrained molecular dynamics (MD) simulations. Isothermal titration calorimetry studies indicated S100B interaction with FGF2 is an entropically favored process implying dominant role of hydrophobic contacts at the protein-protein interface. Residue level information of S100B interaction with FGF2 was useful to understand the varied target recognition ability of S100B and further explained its role in effecting extracellular signaling diversity. Mechanistic insights into the S100B-FGF2 complex interface and cell-based assay studies involving mutants led us to conclude the novel role of S100B in FGF2 mediated FGFR1 receptor inactivation.
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Affiliation(s)
- Arun A Gupta
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
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Kumar H, Kumar S. A functional (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase exhibits diurnal regulation of expression in Stevia rebaudiana (Bertoni). Gene X 2013; 527:332-8. [PMID: 23800667 DOI: 10.1016/j.gene.2013.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
The leaves of stevia [Stevia rebaudiana (Bertoni)] are a rich source of steviol glycosides that are used as non-calorific sweetener in many countries around the world. Steviol moiety of steviol glycosides is synthesized via plastidial 2C-methyl-D-erythritol 4-phosphate pathway, where (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) is the key enzyme. HDR catalyzes the simultaneous conversion of (E)-4-hydroxy-3-methylbut-2-enyl diphosphate into five carbon isoprenoid units, isopentenyl diphosphate and dimethylallyl diphosphate. Stevia HDR (SrHDR) successfully rescued HDR lethal mutant strain MG1655 ara<>ispH upon genetic complementation, suggesting SrHDR to encode a functional protein. The gene exhibited diurnal variation in expression. To identify the possible regulatory elements, upstream region of the gene was cloned and putative cis-acting elements were detected by in silico analysis. Electrophoretic mobility shift assay, using a putative light responsive element GATA showed the binding of nuclear proteins (NP) isolated from leaves during light period of the day, but not with the NP from leaves during the dark period. Data suggested the involvement of GATA box in light mediated gene regulation of SrHDR in stevia.
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Affiliation(s)
- Hitesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India.
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Fallecker C, Tarbouriech N, Habib M, Petit MA, Drouet E. Structural and functional characterization of the single-chain Fv fragment from a unique HCV E1E2-specific monoclonal antibody. FEBS Lett 2013; 587:3335-40. [PMID: 24021643 DOI: 10.1016/j.febslet.2013.07.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 07/12/2013] [Accepted: 07/19/2013] [Indexed: 12/11/2022]
Abstract
The nucleotide sequence of the unique neutralizing monoclonal antibody D32.10 raised against a conserved conformational epitope shared between E1 and E2 on the serum-derived hepatitis C virus (HCV) envelope was determined. Subsequently, the recombinant single-chain Fv fragment (scFv) was cloned and expressed in Escherichia coli, and its molecular characterization was assessed using multi-angle laser light scattering. The scFv mimicked the antibody in binding to the native serum-derived HCV particles from patients, as well as to envelope E1E2 complexes and E1, E2 glycoproteins carrying the viral epitope. The scFv D32.10 competed with the parental IgG for binding to antigen, and therefore could be a promising candidate for therapeutics and diagnostics.
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Affiliation(s)
- Catherine Fallecker
- Univ. Grenoble Alpes, Unit for Virus Host-Cell Interactions, F-38000 Grenoble, France; CNRS, Unit for Virus Host-Cell Interactions, F-38000 Grenoble, France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France
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Heuveling J, Frochaux V, Ziomkowska J, Wawrzinek R, Wessig P, Herrmann A, Schneider E. Conformational changes of the bacterial type I ATP-binding cassette importer HisQMP2 at distinct steps of the catalytic cycle. Biochim Biophys Acta 2013; 1838:106-16. [PMID: 24021237 DOI: 10.1016/j.bbamem.2013.08.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/27/2013] [Accepted: 08/30/2013] [Indexed: 12/15/2022]
Abstract
Prokaryotic solute binding protein-dependent ATP-binding cassette import systems are divided into type I and type II and mechanistic differences in the transport process going along with this classification are under intensive investigation. Little is known about the conformational dynamics during the catalytic cycle especially concerning the transmembrane domains. The type I transporter for positively charged amino acids from Salmonella enterica serovar Typhimurium (LAO-HisQMP2) was studied by limited proteolysis in detergent solution in the absence and presence of co-factors including ATP, ADP, LAO/arginine, and Mg(2+) ions. Stable peptide fragments could be obtained and differentially susceptible cleavage sites were determined by mass spectrometry as Lys-258 in the nucleotide-binding subunit, HisP, and Arg-217/Arg-218 in the transmembrane subunit, HisQ. In contrast, transmembrane subunit HisM was gradually degraded but no stable fragment could be detected. HisP and HisQ were equally resistant under pre- and post-hydrolysis conditions in the presence of arginine-loaded solute-binding protein LAO and ATP/ADP. Some protection was also observed with LAO/arginine alone, thus reflecting binding to the transporter in the apo-state and transmembrane signaling. Comparable digestion patterns were obtained with the transporter reconstituted into proteoliposomes and nanodiscs. Fluorescence lifetime spectroscopy confirmed the change of HisQ(R218) to a more apolar microenvironment upon ATP binding and hydrolysis. Limited proteolysis was subsequently used as a tool to study the consequences of mutations on the transport cycle. Together, our data suggest similar conformational changes during the transport cycle as described for the maltose ABC transporter of Escherichia coli, despite distinct structural differences between both systems.
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Affiliation(s)
- Johanna Heuveling
- Institut für Biologie/Bakterienphysiologie, Humboldt Universität zu Berlin, Chausseestr. 117, D-10115 Berlin, Germany
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