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Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy. Int J Mol Sci 2022; 23:ijms23126781. [PMID: 35743221 PMCID: PMC9224231 DOI: 10.3390/ijms23126781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D 15N-1H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.
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2
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Ferrero DS, Falqui M, Verdaguer N. Snapshots of a Non-Canonical RdRP in Action. Viruses 2021; 13:v13071260. [PMID: 34203380 PMCID: PMC8310298 DOI: 10.3390/v13071260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.
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3
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Human G protein-coupled receptor 30 is N-glycosylated and N-terminal domain asparagine 44 is required for receptor structure and activity. Biosci Rep 2019; 39:BSR20182436. [PMID: 30760632 PMCID: PMC6390128 DOI: 10.1042/bsr20182436] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptor 30 (GPR30), or G protein-coupled estrogen receptor (GPER), is a G protein-coupled receptor (GPCR) that is currently attracting considerable attention in breast cancer and cardiometabolic regulation. The receptor was reported to be a novel membrane estrogen receptor mediating rapid non-genomic responses. However, questions remain about both the cognate ligand and the subcellular localization of receptor activity. Here, we used human embryonic kidney (HEK) 293 (HEK293) cells ectopically expressing N-terminally FLAG-tagged human GPR30 and three unique antibodies (Ab) specifically targetting the receptor N-terminal domain (N-domain) to investigate the role of N-glycosylation in receptor maturation and activity, the latter assayed by constitutive receptor-stimulated extracellular-regulated protein kinase (ERK) 1/2 (ERK1/2) activity. GPR30 expression was complex with receptor species spanning from approximately 40 kDa to higher molecular masses and localized in the endoplasmatic reticulum (ER), the plasma membrane (PM), and endocytic vesicles. The receptor contains three conserved asparagines, Asn25, Asn32, and Asn44, in consensus N-glycosylation motifs, all in the N-domain, and PNGase F treatment showed that at least one of them is N-glycosylated. Mutating Asn44 to isoleucine inactivated the receptor, yielding a unique receptor species at approximately 20 kDa that was recognized by Ab only in a denatured state. On the other hand, mutating Asn25 or Asn32 either individually or in combination, or truncating successively N-domain residues 1–42, had no significant effect either on receptor structure, maturation, or activity. Thus, Asn44 in the GPR30 N-domain is required for receptor structure and activity, whereas N-domain residues 1–42, including specifically Asn25 and Asn32, do not play any major structural or functional role(s).
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4
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Godoy AS, Pereira CS, Ramia MP, Silveira RL, Camilo CM, Kadowaki MA, Lange L, Busk PK, Nascimento AS, Skaf MS, Polikarpov I. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. Sci Rep 2018; 8:3678. [PMID: 29487297 PMCID: PMC5829257 DOI: 10.1038/s41598-018-21798-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.
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Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Caroline S Pereira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Marina Paglione Ramia
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Cesar M Camilo
- Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo, Brazil
| | - Marco A Kadowaki
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Lene Lange
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Peter K Busk
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Alessandro S Nascimento
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.
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5
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Gonzalez de Valdivia E, Broselid S, Kahn R, Olde B, Leeb-Lundberg LMF. G protein-coupled estrogen receptor 1 (GPER1)/GPR30 increases ERK1/2 activity through PDZ motif-dependent and -independent mechanisms. J Biol Chem 2017; 292:9932-9943. [PMID: 28450397 DOI: 10.1074/jbc.m116.765875] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/25/2017] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptor 30 (GPR30), also called G protein-coupled estrogen receptor 1 (GPER1), is thought to play important roles in breast cancer and cardiometabolic regulation, but many questions remain about ligand activation, effector coupling, and subcellular localization. We showed recently that GPR30 interacts through the C-terminal type I PDZ motif with SAP97 and protein kinase A (PKA)-anchoring protein (AKAP) 5, which anchor the receptor in the plasma membrane and mediate an apparently constitutive decrease in cAMP production independently of Gi/o Here, we show that GPR30 also constitutively increases ERK1/2 activity. Removing the receptor PDZ motif or knocking down specifically AKAP5 inhibited the increase, showing that this increase also requires the PDZ interaction. However, the increase was inhibited by pertussis toxin as well as by wortmannin but not by AG1478, indicating that Gi/o and phosphoinositide 3-kinase (PI3K) mediate the increase independently of epidermal growth factor receptor transactivation. FK506 and okadaic acid also inhibited the increase, implying that a protein phosphatase is involved. The proposed GPR30 agonist G-1 also increased ERK1/2 activity, but this increase was only observed at a level of receptor expression below that required for the constitutive increase. Furthermore, deleting the PDZ motif did not inhibit the G-1-stimulated increase. Based on these results, we propose that GPR30 increases ERK1/2 activity via two Gi/o-mediated mechanisms, a PDZ-dependent, apparently constitutive mechanism and a PDZ-independent G-1-stimulated mechanism.
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Affiliation(s)
| | | | | | - Björn Olde
- Cardiology, Lund University, 22184 Lund, Sweden
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6
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Godoy AS, Camilo CM, Kadowaki MA, Muniz HDS, Espirito Santo M, Murakami MT, Nascimento AS, Polikarpov I. Crystal structure of β1→6-galactosidase fromBifidobacterium bifidumS17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose. FEBS J 2016; 283:4097-4112. [DOI: 10.1111/febs.13908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/05/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022]
Affiliation(s)
| | | | | | | | | | - Mario Tyago Murakami
- Biosciences National Laboratory; National Center for Energy and Materials Research; Campinas Brazil
| | | | - Igor Polikarpov
- Departamento de Física em São Carlos; Universidade de São Paulo; Brazil
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7
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Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep 2016; 6:23473. [PMID: 27032335 PMCID: PMC4817029 DOI: 10.1038/srep23473] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/25/2016] [Indexed: 11/25/2022] Open
Abstract
Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
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8
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Camilo CM, Lima GMA, Maluf FV, Guido RVC, Polikarpov I. HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis. J Comput Biol 2015; 23:27-9. [PMID: 26540331 DOI: 10.1089/cmb.2015.0148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Following burgeoning genomic and transcriptomic sequencing data, biochemical and molecular biology groups worldwide are implementing high-throughput cloning and mutagenesis facilities in order to obtain a large number of soluble proteins for structural and functional characterization. Since manual primer design can be a time-consuming and error-generating step, particularly when working with hundreds of targets, the automation of primer design process becomes highly desirable. HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.
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Affiliation(s)
- Cesar M Camilo
- 1 Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo, Brazil
| | - Gustavo M A Lima
- 2 Laboratório de Química Medicinal e Computacional, Centro de Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo, Brazil
| | - Fernando V Maluf
- 2 Laboratório de Química Medicinal e Computacional, Centro de Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo, Brazil
| | - Rafael V C Guido
- 2 Laboratório de Química Medicinal e Computacional, Centro de Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo, Brazil
| | - Igor Polikarpov
- 1 Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo, Brazil
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9
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Rapid assembly of multiple DNA fragments through direct transformation of PCR products into E. coli and Lactobacillus. Plasmid 2014; 76:40-6. [DOI: 10.1016/j.plasmid.2014.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/12/2014] [Accepted: 09/18/2014] [Indexed: 11/22/2022]
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10
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Merwin JR, Bogar LB, Poggi SB, Fitch RM, Johnson AW, Lycan DE. Genetic analysis of the ribosome biogenesis factor Ltv1 of Saccharomyces cerevisiae. Genetics 2014; 198:1071-85. [PMID: 25213169 PMCID: PMC4224153 DOI: 10.1534/genetics.114.168294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/04/2014] [Indexed: 01/24/2023] Open
Abstract
Ribosome biogenesis has been studied extensively in the yeast Saccharomyces cerevisiae. Yeast Ltv1 is a conserved 40S-associated biogenesis factor that has been proposed to function in small subunit nuclear export. Here we show that Ltv1 has a canonical leucine-rich nuclear export signal (NES) at its extreme C terminus that is both necessary for Crm1 interaction and Ltv1 export. The C terminus of Ltv1 can substitute for the NES in the 60S-export adapter Nmd3, demonstrating that it is a functional NES. Overexpression of an Ltv1 lacking its NES (Ltv1∆C13) was strongly dominant negative and resulted in the nuclear accumulation of RpS3-GFP; however, export of the pre-40S was not affected. In addition, expression of endogenous levels of Ltv1∆C protein complemented both the slow-growth phenotype and the 40S biogenesis defect of an ltv1 deletion mutant. Thus, if Ltv1 is a nuclear export adapter for the pre-40S subunit, its function must be fully redundant with additional export factors. The dominant negative phenotype of Ltv1∆NES overexpression was suppressed by co-overexpressing RpS3 and its chaperone, Yar1, or by deletion of the RpS3-binding site in Ltv1∆NES, suggesting that titration of RpS3 by Ltv1∆NES is deleterious in yeast. The dominant-negative phenotype did not correlate with a decrease in 40S levels but rather with a reduction in the polysome-to-monosome ratio, indicating reduced rates of translation. We suggest that titration of RpS3 by excess nuclear Ltv1 interferes with 40S function or with a nonribosomal function of RpS3.
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Affiliation(s)
- Jason R Merwin
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Lucien B Bogar
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Sarah B Poggi
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Rebecca M Fitch
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Arlen W Johnson
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712
| | - Deborah E Lycan
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
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11
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Construction and application of an expression vector from the new plasmid pLAtc1 of Acidithiobacillus caldus. Appl Microbiol Biotechnol 2014; 98:4083-94. [DOI: 10.1007/s00253-014-5507-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/27/2013] [Accepted: 12/28/2013] [Indexed: 11/26/2022]
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12
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Foo JL, Leong SSJ. Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:81. [PMID: 23693002 PMCID: PMC3680313 DOI: 10.1186/1754-6834-6-81] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 05/16/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The depletion of fossil fuels and the rising need to meet global energy demands have led to a growing interest in microbial biofuel synthesis, particularly in Escherichia coli, due to its tractable characteristics. Besides engineering more efficient metabolic pathways for synthesizing biofuels, efforts to improve production yield by engineering efflux systems to overcome toxicity problems is also crucial. This study aims to enhance hydrocarbon efflux capability in E. coli by engineering a native inner membrane transporter, AcrB, using the directed evolution approach. RESULTS We developed a selection platform based on competitive growth using a toxic substrate surrogate, which allowed rapid selection of AcrB variants showing enhanced efflux of linear and cyclic fuel molecule candidates, n-octane and α-pinene. Two mutants exhibiting increased efflux efficiency for n-octane and α-pinene by up to 47% and 400%, respectively, were isolated. Single-site mutants based on the mutations found in the isolated variants were synthesized and the amino acid substitutions N189H, T678S, Q737L and M844L were identified to have conferred improvement in efflux efficiency. The locations of beneficial mutations in AcrB suggest their contributions in widening the substrate channel, altering the dynamics of substrate efflux and promoting the assembly of AcrB with the outer membrane channel protein TolC for more efficient substrate export. It is interesting to note that three of the four beneficial mutations were located relatively distant from the known substrate channels, thus exemplifying the advantage of directed evolution over rational design. CONCLUSIONS Using directed evolution, we have isolated AcrB mutants with improved efflux efficiency for n-octane and α-pinene. The utilization of such optimized native efflux pumps will increase productivity of biofuels synthesis and alleviate toxicity and difficulties in production scale-up in current microbial platforms.
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Affiliation(s)
- Jee Loon Foo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Susanna Su Jan Leong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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13
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Saito M, Kato Y, Ito E, Fujimoto J, Ishikawa K, Doi A, Kumazawa K, Matsui A, Takebe S, Ishida T, Azuma S, Mochizuki H, Kawamura Y, Yanagisawa Y, Honma R, Imai JI, Ohbayashi H, Goshima N, Semba K, Watanabe S. Expression screening of 17q12-21 amplicon reveals GRB7 as an ERBB2-dependent oncogene. FEBS Lett 2012; 586:1708-14. [PMID: 22584052 DOI: 10.1016/j.febslet.2012.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 04/30/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022]
Abstract
Gene amplification is a major genetic alteration in human cancers. Amplicons, amplified genomic regions, are believed to contain "driver" genes responsible for tumorigenesis. However, the significance of co-amplified genes has not been extensively studied. We have established an integrated analysis system of amplicons using retrovirus-mediated gene transfer coupled with a human full-length cDNA set. Applying this system to 17q12-21 amplicon observed in breast cancer, we identified GRB7 as a context-dependent oncogene, which modulates the ERBB2 signaling pathway through enhanced phosphorylation of ERBB2 and Akt. Our work provides an insight into the biological significance of gene amplification in human cancers.
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Affiliation(s)
- Makoto Saito
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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14
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Simple cloning via direct transformation of PCR product (DNA Multimer) to Escherichia coli and Bacillus subtilis. Appl Environ Microbiol 2011; 78:1593-5. [PMID: 22194286 DOI: 10.1128/aem.07105-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a general restriction enzyme-free and ligase-free method for subcloning up to three DNA fragments into any location of a plasmid. The DNA multimer generated by prolonged overlap extension PCR was directly transformed in Escherichia coli [e.g., TOP10, DH5α, JM109, and BL21(DE3)] and Bacillus subtilis for obtaining chimeric plasmids.
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15
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Saaem I, Ma S, Quan J, Tian J. Error correction of microchip synthesized genes using Surveyor nuclease. Nucleic Acids Res 2011; 40:e23. [PMID: 22127863 PMCID: PMC3273826 DOI: 10.1093/nar/gkr887] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The development of economical and high-throughput gene synthesis technology has been hampered by the high occurrence of errors in the synthesized products, which requires expensive labor and time to correct. Here, we describe an error correction reaction (ECR), which employs Surveyor, a mismatch-specific DNA endonuclease, to remove errors from synthetic genes. In ECR reactions, errors are revealed as mismatches by re-annealing of the synthetic gene products. Mismatches are recognized and excised by a combination of mismatch-specific endonuclease and 3'→5' exonuclease activities in the reaction mixture. Finally, overlap extension polymerase chain reaction (OE-PCR) re-assembles the resulting fragments into intact genes. The process can be iterated for increased fidelity. With two iterations, we were able to reduce errors in synthetic genes by >16-fold, yielding a final error rate of ∼1 in 8700 bp.
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Affiliation(s)
- Ishtiaq Saaem
- Department of Biomedical Engineering, Duke University, Durham, NC27708, USA
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16
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Zhang BZ, Zhang X, An XP, Ran DL, Zhou YS, Lu J, Tong YG. An easy-to-use site-directed mutagenesis method with a designed restriction site for convenient and reliable mutant screening. J Zhejiang Univ Sci B 2009; 10:479-82. [PMID: 19489114 DOI: 10.1631/jzus.b0820367] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Site-directed mutagenesis (SDM) has been a very important method to probe the function-structure relationship of proteins. In this study, we introduced an easy-to-use, polymerase chain reaction (PCR)-based SDM method for double-stranded plasmid DNA, with a designed restriction site to ensure simple and efficient mutant screening. The DNA sequence to be mutated was first translated into amino acid sequence and then the amino acid sequence was reversely translated into DNA sequence with degenerate codons, resulting in a large number of sequences with silent mutations, which contained various restriction endonuclease (RE) sites. Certain mutated sequence with an appropriate RE site was selected as the target DNA sequence for designing a pair of mutation primers to amplify the full-length plasmid via inverse PCR. The amplified product was 5'-phosphorylated, circularized, and transformed into an Escherichia coli host. The transformants were screened by digesting with the designed RE. This protocol uses only one pair of primers and only one PCR is conducted, without the need for hybridization with hazardous isotope for mutant screening or subcloning step.
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Affiliation(s)
- Bao-zhong Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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17
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Xiong AS, Peng RH, Zhuang J, Gao F, Li Y, Cheng ZM, Yao QH. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 2008; 32:522-40. [DOI: 10.1111/j.1574-6976.2008.00109.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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18
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Wong TS, Roccatano D, Schwaneberg U. Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries. Environ Microbiol 2007; 9:2645-59. [DOI: 10.1111/j.1462-2920.2007.01411.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Rabhi-Essafi I, Sadok A, Khalaf N, Fathallah DM. A strategy for high-level expression of soluble and functional human interferon alpha as a GST-fusion protein in E. coli. Protein Eng Des Sel 2007; 20:201-9. [PMID: 17430974 DOI: 10.1093/protein/gzm012] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Escherichia coli is the most extensively used host for the production of recombinant proteins. However, most of the eukaryotic proteins are typically obtained as insoluble, misfolded inclusion bodies that need solubilization and refolding. To achieve high-level expression of soluble recombinant human interferon alpha (rhIFNalpha) in E. coli, we have first constructed a recombinant expression plasmid (pGEX-hIFNalpha2b), in which we merged the hIFNalpha2b cDNA with the glutathione S-transferase (GST) coding sequence downstream of the tac-inducible promoter. Using this plasmid, we have achieved 70% expression of soluble rhIFNalpha2b as a GST fusion protein using E. coli BL21 strain, under optimized environmental factors such as culture growth temperature and inducer (IPTG) concentration. However, release of the IFN moiety from the fusion protein by thrombin digestion was not optimal. Therefore, we have engineered the expression cassette to optimize the amino acid sequence at the GST-IFN junction and to introduce E. coli preferred codon within the thrombin cleavage site. We have used the engineered plasmid (pGEX-Delta-hIFNalpha2b) and the modified E. coli trxB(-)/gor(-) (Origami) strain to overcome the problem of removing the GST moiety while expressing soluble rhIFNalpha2b. Our results show the production of soluble and functional rhIFNalpha2b at a yield of 100 mg/l, without optimization of any step of the process. The specific biological activity of the purified soluble rhIFNalpha2b was equal to 2.0 x 10(8) IU/mg when compared with the WHO IFNalpha standard. Our data are the first to show that high yield production of soluble and functional rhIFNalpha2b tagged with GST can be achieved in E. coli.
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Zerria K, Jerbi E, Hammami S, Maaroufi A, Boubaker S, Xiong JP, Arnaout MA, Fathallah DM. Recombinant integrin CD11b A-domain blocks polymorphonuclear cells recruitment and protects against skeletal muscle inflammatory injury in the rat. Immunology 2006; 119:431-40. [PMID: 17026721 PMCID: PMC2265825 DOI: 10.1111/j.1365-2567.2006.02454.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The beta2 integrin CD11b/CD18 (CR3) is a major adhesion receptor of neutrophils, normally utilized to fend off infections. This receptor contributes, however, to multiple forms of non-infectious inflammatory injury when dysregulated as shown in gene knock-outs and through the use of blocking monoclonal antibodies. The major ligand recognition site of CR3 has been mapped to the A-domain in the CD11b subunit (CD11bA). The recombinant form of this domain exhibits a ligand binding profile similar to that of the holoreceptor. To assess the potential anti-inflammatory activity of CD11bA as a competitive antagonist of CR3 in vivo, we assessed its effects on a developed animal model of traumatic skeletal muscle injury in the rat. Recombinant soluble rat CD11bA-domain fused to glutathione-S-transferase (GST) was administered intravenously in a single dose at 1 mg/kg to nine groups of Wistar rats, five in each group, 30 min before inducing traumatic skeletal muscle injury. Control animals received either a function-blocking anti-CD11b/CD18 monoclonal antibody (1 mg/kg), non-functional mutant forms of the CD11bA (D140GS/AGA, T209/A, D242/A), recombinant GST or buffer alone. In control animals, the wounded muscle showed oedema, erythrocyte extravasation and myonecrosis both within and outside the immediate wounded area (5-10 mm zone) and influx of neutrophils was detected 30 min post-wound, followed by a second wave 3 hr later. Wild-type CD11bA- or anti-CD11b monoclonal antibody (mAb)-treated rats showed a comparable and significant decrease in the number of infiltrating PMN (78 + 4%, n = 70 and 86 +/- 2%, n = 50, respectively) and preservation of the muscular fibres outside the immediate zone of necrosis (75 + 4%, n = 70, 84 +/- 1%, n = 50, respectively), compared to controls. These data demonstrate that CD11bA can be an effective tissue-preserving agent in acute inflammatory muscular injury.
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MESH Headings
- Amino Acid Sequence
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/immunology
- Anti-Inflammatory Agents, Non-Steroidal/therapeutic use
- Antibodies, Monoclonal/immunology
- CD11b Antigen/immunology
- CD11b Antigen/therapeutic use
- Disease Models, Animal
- Female
- Molecular Sequence Data
- Muscle Fibers, Skeletal/immunology
- Muscle Fibers, Skeletal/pathology
- Muscle, Skeletal/immunology
- Muscle, Skeletal/injuries
- Muscle, Skeletal/pathology
- Myositis/immunology
- Myositis/prevention & control
- Neutrophil Infiltration/immunology
- Rats
- Rats, Wistar
- Recombinant Proteins/therapeutic use
- Sequence Alignment
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Affiliation(s)
- K Zerria
- Molecular Biotechnology Group, Institute Pasteur, Tunis, Tunisia
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An Y, Ji J, Wu W, Lv A, Huang R, Wei Y. A rapid and efficient method for multiple-site mutagenesis with a modified overlap extension PCR. Appl Microbiol Biotechnol 2005; 68:774-8. [PMID: 16249879 DOI: 10.1007/s00253-005-1948-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Revised: 02/20/2005] [Accepted: 02/22/2005] [Indexed: 11/25/2022]
Abstract
A rapid and efficient method to perform site-directed mutagenesis based on an improved version of overlap extension by polymerase chain reaction (OE-PCR) is demonstrated in this paper. For this method, which we name modified (M)OE-PCR, there are five steps: (1) synthesis of individual DNA fragments of interest (with average 20-bp overlap between adjacent fragments) by PCR with high-fidelity pfu DNA polymerase, (2) double-mixing (every two adjacent fragments are mixed to implement OE-PCR without primers), (3) pre-extension (the teams above are mixed to obtain full-length reassembled DNA by OE-PCR without primers), (4) synthesis of the entire DNA of interest by PCR with outermost primers and template DNA from step 3, (5) post-extension (ten cycles of PCR at 72 degrees C for annealing and extension are implemented). The method is rapid, simple and error-free. It provides an efficient choice, especially for multiple-site mutagenesis of DNAs; and it can theoretically be applied to the modification of any DNA fragment. Using the MOE-PCR method, we have successfully obtained a modified sam1 gene with eight rare codons optimized simultaneously.
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Affiliation(s)
- Yingfeng An
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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