51
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Ma XX, Ma P, Chang QY, Liu ZB, Zhang D, Zhou XK, Ma ZR, Cao X. Adaptation ofBorrelia burgdorferito its natural hosts by synonymous codon and amino acid usage. J Basic Microbiol 2018. [DOI: 10.1002/jobm.201700652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiao-Xia Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Peng Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Qiu-Yan Chang
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Zhen-Bin Liu
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Derong Zhang
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Xiao-Kai Zhou
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Zhong-Ren Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Xin Cao
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
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52
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Tang Y, Zhang G, Wang Z, Liu D, Zhang L, Zhou Y, Huang J, Yu F, Yang Z, Ding G. Efficient synthesis of a (S)-fluoxetine intermediate using carbonyl reductase coupled with glucose dehydrogenase. BIORESOURCE TECHNOLOGY 2018; 250:457-463. [PMID: 29197272 DOI: 10.1016/j.biortech.2017.10.097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
(S)-3-chloro-1-phenyl-1-propanol ((S)-CPPO) is an important chiral intermediate predominantly used in the synthesis of the chiral side chain of (S)-fluoxetine. In this study, carbonyl reductase (CBR) from Novosphingobium aromaticivorans was successfully expressed in recombinant E. coli. The enzymatic activity of the recombinant CBR was significantly increased to 1875 U/mL in the fed-batch fermentation in a 10 L fermenter and recombinant CBR was then purified and characterized. By regenerating NADH with glucose dehydrogenase, 100 g/L 3-chloro-1-phenyl-1-propanone (3-CPP) was successfully converted to (S)-CPPO with a conversion of 100% and ee value of 99.6% after 12 h at 30 °C in PBS buffer (pH 7.0), which are the highest reported to date for the bio-production of (S)-CPPO and presented great potential for green production of (S)-CPPO at industrial scale.
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Affiliation(s)
- Yunping Tang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Guomei Zhang
- Institute of Health Food of Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Zheng Wang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Dan Liu
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Linglu Zhang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yafeng Zhou
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ju Huang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Fangmiao Yu
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zuisu Yang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Guofang Ding
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China.
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53
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Evaluation of rice tetraticopeptide domain-containing thioredoxin as a novel solubility-enhancing fusion tag in Escherichia coli. J Biosci Bioeng 2018; 125:160-167. [DOI: 10.1016/j.jbiosc.2017.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023]
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54
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Brown SD. Multivalent Display Using Hybrid Virus Nanoparticles. Methods Mol Biol 2018; 1798:119-140. [PMID: 29868956 DOI: 10.1007/978-1-4939-7893-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many important biological interactions are multivalent and often sensitive to spatial organization. Nonenveloped viruses are a natural source of scaffolds for building multivalent ligands to probe these types of interactions which avoid complex synthetic schemes required for other types of scaffolds. The coat protein (CP) of bacteriophage Qβ can be fused to protein domains and coexpressed with the unfused CP to produce hybrid nanoparticles with high exterior loading of xenogenic protein domains. These hybrid nanoparticles are simple to produce in large quantity. Starting from cDNAs for the virus CP and a codon-optimized ligand domain of interest, bulk purification can be completed in as little as 3 weeks. Major phases of the work involve the cloning of cDNAs into plasmid vectors, test expressions for hybrid nanoparticle formation, and purification by selective precipitation and ultracentrifugation. For uncomplicated protein domains, laboratory culture yields as high as 50 mg/L and 30 protein domains per particle have been routinely achieved.
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Affiliation(s)
- Steven D Brown
- Department of Gastroenterology, University of California-San Diego, La Jolla, CA, USA.
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55
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Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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56
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Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017; 9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.
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Affiliation(s)
- Mónica Marín
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Tamara Fernández-Calero
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Ricardo Ehrlich
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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57
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Ma XX, Chang QY, Ma P, Li LJ, Zhou XK, Zhang DR, Li MS, Cao X, Ma ZR. Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus. Gene 2017; 637:115-123. [PMID: 28947301 DOI: 10.1016/j.gene.2017.09.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/03/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
Abstract
Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.
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Affiliation(s)
- Xiao-Xia Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Qiu-Yan Chang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Peng Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Lin-Jie Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xiao-Kai Zhou
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - De-Rong Zhang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Ming-Sheng Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xin Cao
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
| | - Zhong-Ren Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
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58
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Wang W, Sun J, Xiao W, Jiang L, Wang R, Fan J. Change of the N-terminal codon bias combined with tRNA supplementation outperforms the selected fusion tags for production of human d-amino acid oxidase as active inclusion bodies. Biotechnol Lett 2017; 39:1733-1740. [DOI: 10.1007/s10529-017-2413-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/18/2017] [Indexed: 11/29/2022]
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Villada JC, Brustolini OJB, Batista da Silveira W. Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. DNA Res 2017; 24:419-434. [PMID: 28449100 PMCID: PMC5737324 DOI: 10.1093/dnares/dsx014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 01/21/2023] Open
Abstract
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis. We designed a codon quantification method for assessing CUB as a function of position within genes with a novel constraint: the relativity of position-dependent codon usage shaped by coding sequence length. Thus, we propose a new way of identifying the enrichment, depletion and non-uniform positional distribution of codons in different regions of yeast genes. We clustered codons that shared attributes of frequency and optimality. The cluster of non-optimal codons with rare occurrence displayed two remarkable characteristics: higher codon decoding time than frequent-non-optimal cluster and enrichment at the 5'-end region, where optimal codons with the highest frequency are depleted. Interestingly, frequent codons with non-optimal adaptation to tRNAs are uniformly distributed in the Saccharomyces cerevisiae genes, suggesting their determinant role as a speed regulator in protein elongation.
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Affiliation(s)
- Juan C. Villada
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
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60
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Doud DFR, Holmes EC, Richter H, Molitor B, Jander G, Angenent LT. Metabolic engineering of Rhodopseudomonas palustris for the obligate reduction of n-butyrate to n-butanol. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:178. [PMID: 28702083 PMCID: PMC5504763 DOI: 10.1186/s13068-017-0864-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/28/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Rhodopseudomonas palustris is a versatile microbe that encounters an innate redox imbalance while growing photoheterotrophically with reduced substrates. The resulting excess in reducing equivalents, together with ATP from photosynthesis, could be utilized to drive a wide range of bioconversions. The objective of this study was to genetically modify R. palustris to provide a pathway to reduce n-butyrate into n-butanol for maintaining redox balance. RESULTS Here, we constructed and expressed a plasmid-based pathway for n-butanol production from Clostridium acetobutylicum ATCC 824 in R. palustris. We maintained the environmental conditions in such a way that this pathway functioned as the obligate route to re-oxidize excess reducing equivalents, resulting in an innate selection pressure. The engineered strain of R. palustris grew under otherwise restrictive redox conditions and achieved concentrations of 1.5 mM n-butanol at a production rate of 0.03 g L-1 day-1 and a selectivity (i.e., products compared to the consumed substrate) of close to 40%. Since the theoretical maximum selectivity is 45%, the engineered strain converted close to its maximum selectivity. CONCLUSIONS The innate redox imbalance of R. palustris can be used to drive the reduction of n-butyrate into n-butanol after expression of a plasmid-based enzyme from a butanol-producing Clostridium strain.
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Affiliation(s)
- Devin F. R. Doud
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Eric C. Holmes
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Hanno Richter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Bastian Molitor
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
- Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853 USA
| | - Largus T. Angenent
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
- Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853 USA
- Center for Applied Geosciences, University of Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
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61
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Cripwell RA, Rose SH, van Zyl WH. Expression and comparison of codon optimised Aspergillus tubingensis amylase variants in Saccharomyces cerevisiae. FEMS Yeast Res 2017. [DOI: 10.1093/femsyr/fox040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Bhattacharya S, Reddy D, Reddy R, Sharda A, Bose K, Gupta S. Incorporation of a tag helps to overcome expression variability in a recombinant host. ACTA ACUST UNITED AC 2017; 11:62-69. [PMID: 28352541 PMCID: PMC5042304 DOI: 10.1016/j.btre.2016.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/08/2016] [Accepted: 06/27/2016] [Indexed: 11/03/2022]
Abstract
Reason for the lack of recombinant protein expression in E. coli is indefinite. Recombinant histone expression does not correlate with rare codon content. Translational variability may lead to lack of expression or degradation of protein. Expression variability could be averted by incorporating a tag.
Epigenetics have witnessed a renewed interest over the past decade and assays with recombinant histones has become an important tool for uncovering various aspects of histone biology. However, at times absence of recombinant histone accumulation in bacteria is encountered which is also commonly observed for many eukaryotic proteins in general. In this study, we have investigated the effect of multiple parameters on heterologous expression of proteins. We show that there is marked variability in the accumulation of H2A.2, H2B.1, H3.2 and H4 in the recombinant host, possibly owing to translational variability and degradation by the host proteases. We found that the variability could be overcome by incorporation of the commonly used purification tags, like GST or MBP, of appropriate size and position. Our results provide compelling evidence that transcript parameters like rare codon and GC content, mRNA secondary structure etc. together modulate translation kinetics and govern recombinant protein accumulation.
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Key Words
- CAI, codon adaptation indexes
- DUSP1, dual specificity phosphatase 1
- GAPDH, glyceraldehyde phosphate dehydrogenase
- GST, glutathione-S-transferase
- HAX-1, human protein HCLS-1 associated protein X-1
- Histones
- IPTG, Isopropyl β-d-1-thiogalactopyranoside
- MALDI, matrix-assisted laser desorption/ionization
- MBP, maltose binding protein
- Misfolding
- NAP1, nucleosome assemble protein 1
- PP1, protein phosphatase 1
- RBS, ribosome-binding site
- RT-PCR, reverse transcriptase polymerase chain reaction
- Rare codons
- TMAO, trimethylamine oxide
- Translation
- Truncated GST
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Affiliation(s)
| | - Divya Reddy
- Epigenetics and Chromatin Biology Group, Gupta Lab, India
| | - Raja Reddy
- Integrated Biophysics and Structural Biology Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Asmita Sharda
- Epigenetics and Chromatin Biology Group, Gupta Lab, India
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, India
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Tuan-Anh T, Ly LT, Viet NQ, Bao PT. Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. BMC Bioinformatics 2017; 18:100. [PMID: 28187713 PMCID: PMC5303253 DOI: 10.1186/s12859-017-1517-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Background Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host’s expression system, so the yields can fall down significantly. Hence, we propose novel methods for gene optimization based on neural network, Bayesian theory, and Euclidian distance. Result The correlation coefficients of our neural network are 0.86, 0.73, and 0.90 in training, validation, and testing process. In addition, genes optimized by our methods seem to associate with highly expressed genes and give reasonable codon adaptation index values. Furthermore, genes optimized by the proposed methods are highly matched with the previous experimental data. Conclusion The proposed methods have high potential for gene optimization and further researches in gene expression. We built a demonstrative program using Matlab R2014a under Mac OS X. The program was published in both standalone executable program and Matlab function files. The developed program can be accessed from http://www.math.hcmus.edu.vn/~ptbao/paper_soft/GeneOptProg/.
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Affiliation(s)
- Tran Tuan-Anh
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Le Thi Ly
- School of Biotechnology, VNUHCM-International University, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Ngo Quoc Viet
- Faculty of Information Technology, Ho Chi Minh City University of Pedagogy, 280 An Duong Vuong Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam.
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Cui Y, Meng Y, Zhang J, Cheng B, Yin H, Gao C, Xu P, Yang C. Efficient secretory expression of recombinant proteins in Escherichia coli with a novel actinomycete signal peptide. Protein Expr Purif 2017; 129:69-74. [DOI: 10.1016/j.pep.2016.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/04/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
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65
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Assessment of the Fusion Tags on Increasing Soluble Production of the Active TEV Protease Variant and Other Target Proteins in E. coli. Appl Biochem Biotechnol 2016; 182:769-781. [DOI: 10.1007/s12010-016-2360-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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66
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3'-UTR engineering to improve soluble expression and fine-tuning of activity of cascade enzymes in Escherichia coli. Sci Rep 2016; 6:29406. [PMID: 27406241 PMCID: PMC4942690 DOI: 10.1038/srep29406] [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: 02/01/2016] [Accepted: 06/20/2016] [Indexed: 02/06/2023] Open
Abstract
3′-Untranslated region (3′UTR) engineering was investigated to improve solubility of heterologous proteins (e.g., Baeyer-Villiger monooxygenases (BVMOs)) in Escherichia coli. Insertion of gene fragments containing putative RNase E recognition sites into the 3′UTR of the BVMO genes led to the reduction of mRNA levels in E. coli. Importantly, the amounts of soluble BVMOs were remarkably enhanced resulting in a proportional increase of in vivo catalytic activities. Notably, this increase in biocatalytic activity correlated to the number of putative RNase E endonucleolytic cleavage sites in the 3′UTR. For instance, the biotransformation activity of the BVMO BmoF1 (from Pseudomonas fluorescens DSM50106) in E. coli was linear to the number of RNase E cleavage sites in the 3′UTR. In summary, 3′UTR engineering can be used to improve the soluble expression of heterologous enzymes, thereby fine-tuning the enzyme activity in microbial cells.
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Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA. Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Mol Cell 2016; 61:341-351. [PMID: 26849192 DOI: 10.1016/j.molcel.2016.01.008] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/12/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022]
Abstract
In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Förster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell.
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Affiliation(s)
- Florian Buhr
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Sujata Jha
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA
| | - Michael Thommen
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Joerg Mittelstaet
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Felicitas Kutz
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA.,Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
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69
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Nouri HR, Karkhah A, Varasteh A, Sankian M. Expression of a Chimeric Allergen with High Rare Codons Content in Codon Bias-Adjusted Escherichia coli: Escherichia coli BL21 (DE3)-Codon Plus RIL as an Efficient Host. Curr Microbiol 2016; 73:91-8. [DOI: 10.1007/s00284-016-1027-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/06/2016] [Indexed: 11/28/2022]
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70
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Agashe D, Sane M, Phalnikar K, Diwan GD, Habibullah A, Martinez-Gomez NC, Sahasrabuddhe V, Polachek W, Wang J, Chubiz LM, Marx CJ. Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium. Mol Biol Evol 2016; 33:1542-53. [PMID: 26908584 PMCID: PMC4868122 DOI: 10.1093/molbev/msw035] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae. These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.
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Affiliation(s)
- Deepa Agashe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India Department of Organismic and Evolutionary Biology, Harvard University
| | - Mrudula Sane
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - Kruttika Phalnikar
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - Gaurav D Diwan
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India SASTRA University, Thanjavur, India
| | - Alefiyah Habibullah
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | | | - Vinaya Sahasrabuddhe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - William Polachek
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Jue Wang
- Department of Organismic and Evolutionary Biology, Harvard University Systems Biology Graduate Program, Harvard University
| | - Lon M Chubiz
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Christopher J Marx
- Department of Organismic and Evolutionary Biology, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Harvard University Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies, University of Idaho
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71
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Production of recombinant proteins from Plasmodium falciparum in Escherichia coli. BIOMEDICA 2016; 36:97-108. [PMID: 27622630 DOI: 10.7705/biomedica.v36i3.3011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/16/2015] [Indexed: 01/30/2023]
Abstract
INTRODUCTION The production of recombinant proteins is essential for the characterization and functional study of proteins from Plasmodium falciparum. However, the proteins of P. falciparum are among the most challenging to express, and when expression is achieved, the recombinant proteins usually fold incorrectly and lead to the formation of inclusion bodies. OBJECTIVE To obtain and purify four recombinant proteins and to use them as antigens to produce polyclonal antibodies. The production efficiency and solubility were evaluated as the proteins were expressed in two genetically modified strains of Escherichia coli to favor the production of heterologous proteins (BL21-CodonPlus (DE3)-RIL and BL21-pG-KJE8). MATERIALS AND METHODS The four recombinant P. falciparum proteins corresponding to partial sequences of PfMyoA (Myosin A) and PfGAP50 (gliding associated protein 50), and the complete sequences of PfMTIP (myosin tail interacting protein) and PfGAP45 (gliding associated protein 45), were produced as glutathione S-transferase-fusion proteins, purified and used for immunizing mice. RESULTS The protein expression was much more efficient in BL21-CodonPlus, the strain that contains tRNAs that are rare in wild-type E. coli, compared to the expression in BL21-pG-KJE8. In spite of the fact that BL21-pG-KJE8 overexpresses chaperones, this strain did not minimize the formation of inclusion bodies. CONCLUSION The use of genetically modified strains of E. coli was essential to achieve high expression levels of the four evaluated P. falciparum proteins and lead to improved solubility of two of them. The approach used here allowed us to obtain and purify four P. falciparum proteins in enough quantity to produce polyclonal antibodies in mice, and a fair amount of two pure and soluble recombinant proteins for future assays.
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72
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Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? Life (Basel) 2016; 6:life6010009. [PMID: 26901226 PMCID: PMC4810240 DOI: 10.3390/life6010009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.
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73
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Overproduction of PIB-Type ATPases. Methods Mol Biol 2016; 1377:29-36. [PMID: 26695020 DOI: 10.1007/978-1-4939-3179-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Understanding of the functions and mechanisms of fundamental processes in the cell requires structural information. Structural studies of membrane proteins typically necessitate large amounts of purified and preferably homogenous target protein. Here, we describe a rapid overproduction and purification strategy of a bacterial PIB-type ATPase for isolation of milligrams of target protein per liter Escherichia coli cell culture, with a final quality of the sample which is sufficient for generating high-resolution crystals.
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74
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Whisper mutations: cryptic messages within the genetic code. Oncogene 2015; 35:3753-9. [PMID: 26657150 DOI: 10.1038/onc.2015.454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
Abstract
Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.
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75
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Imsoonthornruksa S, Pruksananonda K, Parnpai R, Rungsiwiwut R, Ketudat-Cairns M. Expression and Purification of Recombinant Human Basic Fibroblast Growth Factor Fusion Proteins and Their Uses in Human Stem Cell Culture. J Mol Microbiol Biotechnol 2015; 25:372-80. [DOI: 10.1159/000441453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022] Open
Abstract
To reduce the cost of cytokines and growth factors in stem cell research, a simple method for the production of soluble and biological active human basic fibroblast growth factor (hbFGF) fusion protein in <i>Escherichia coli</i> was established. Under optimal conditions, approximately 60-80 mg of >95% pure hbFGF fusion proteins (Trx-6xHis-hbFGF and 6xHis-hbFGF) were obtained from 1 liter of culture broth. The purified hbFGF proteins, both with and without the fusion tags, were biologically active, which was confirmed by their ability to stimulate proliferation of NIH3T3 cells. The fusion proteins also have the ability to support several culture passages of undifferentiated human embryonic stem cells and induce pluripotent stem cells. This paper describes a low-cost and uncomplicated method for the production and purification of biologically active hbFGF fusion proteins.
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76
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Rahmen N, Schlupp CD, Mitsunaga H, Fulton A, Aryani T, Esch L, Schaffrath U, Fukuzaki E, Jaeger KE, Büchs J. A particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity. Microb Cell Fact 2015; 14:156. [PMID: 26438243 PMCID: PMC4595056 DOI: 10.1186/s12934-015-0348-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombinant protein production using Escherichia coli as expression host is highly efficient, however, it also induces strong host cell metabolic burden. Energy and biomass precursors are withdrawn from the host's metabolism as they are required for plasmid replication, heterologous gene expression and protein production. Rare codons in a heterologous gene may be a further drawback. This study aims to investigate the influence of particular silent codon exchanges within a heterologous gene on host cell metabolic activity. Silent mutations were introduced into the coding sequence of a model protein to introduce all synonymous arginine or leucine codons at two randomly defined positions, as well as substitutions leading to identical amino acid exchanges with different synonymous codons. The respective E. coli clones were compared during cultivation in a mineral autoinduction medium using specialized online and offline measuring techniques to quantitatively analyze effects on respiration, biomass and protein production, as well as on carbon source consumption, plasmid copy number, intracellular nucleobases and mRNA content of each clone. RESULTS Host stain metabolic burden correlates with recombinant protein production. Upon heterologous gene expression, tremendous differences in respiration, biomass and protein production were observed. According to their different respiration activity the E. coli clones could be classified into two groups, Type A and Type B. Type A clones tended to higher product formation, Type B clones showed stronger biomass formation. Whereas codon usage and intracellular nucleobases had no influence on the Type-A-Type-B-behavior, plasmid copy number, mRNA content and carbon source consumption strongly differed between the two groups. CONCLUSIONS Particular silent codon exchanges in a heterologous gene sequence led to differences in initial growth of Type A and Type B clones. Thus, the biomass concentration at the time point of induction varied. In consequence, not only plasmid copy number and expression levels differed between the two groups, but also the kinetics of lactose and glycerol consumption. Even though the underlying molecular mechanisms are not yet identified we observed the astonishing phenomenon that particular silent codon exchanges within a heterologous gene tremendously affect host cell metabolism and recombinant protein production. This could have great impact on codon optimization of heterologous genes, screening procedures for improved variants, and biotechnological protein production processes.
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Affiliation(s)
- Natalie Rahmen
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Christian D Schlupp
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Hitoshi Mitsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan.
| | - Alexander Fulton
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
| | - Tita Aryani
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Lara Esch
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Eiichiro Fukuzaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan.
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany. .,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.
| | - Jochen Büchs
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M. ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. BMC Bioinformatics 2015; 16:303. [PMID: 26391121 PMCID: PMC4578782 DOI: 10.1186/s12859-015-0743-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/16/2015] [Indexed: 02/06/2023] Open
Abstract
Background Codon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism differ significantly, for example when a human gene is expressed in E. coli. Therefore, to enable or enhance efficient gene expression it is of great importance to identify rare codons in any given DNA sequence and subsequently mutate these to codons which are more frequently used in the expression host. Results We describe an open-source web-based application, ATGme, which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence. Conclusions This application provides a simple user-friendly interface utilizing three optimization strategies: 1. one-click optimization, 2. bulk optimization (by codon-type), 3. individualized custom (codon-by-codon) optimization. ATGme is an open-source application which is freely available at: http://atgme.org
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Affiliation(s)
- Edward Daniel
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland.
| | - Goodluck U Onwukwe
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland.
| | - Rik K Wierenga
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Structural Biochemistry, University of Oulu, Oulu, Finland.
| | - Susan E Quaggin
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Seppo J Vainio
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5A, FIN-90220, Oulu, Finland.
| | - Mirja Krause
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5A, FIN-90220, Oulu, Finland.
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78
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Bjerga GEK, Williamson AK. Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 2015; 15:78. [PMID: 26286037 PMCID: PMC4544801 DOI: 10.1186/s12896-015-0185-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background Heterologous expression of psychrophilic enzymes in E. coli is particularly challenging due to their intrinsic instability. The low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. Recombinant production presents a significant barrier to their exploitation for commercial applications in industry. Methods As part of an enzyme discovery project we have investigated the utility of a cold-shock inducible promoter for low-temperature expression of five diverse genes derived from the metagenomes of marine Arctic sediments. After evaluation of their production, we further optimized for soluble production by building a vector suite from which the environmental genes could be expressed as fusions with solubility tags. Results We found that the low-temperature optimized system produced high expression levels for all putatively cold-active proteins, as well as reducing host toxicity for several candidates. As a proof of concept, activity assays with one of the candidates, a putative chitinase, showed that functional protein was obtained using the low-temperature optimized vector suite. Conclusions We conclude that a cold-shock inducible system is advantageous for the heterologous expression of psychrophilic proteins, and may also be useful for expression of toxic mesophilic and thermophilic proteins where properties of the proteins are deleterious to the host cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0185-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gro Elin Kjæreng Bjerga
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Centre for Applied Biotechnology, Uni Research AS, Thormøhlensgt. 55, N-5008, Bergen, Norway.
| | - Adele Kim Williamson
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
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79
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Feng J, Wan R, Yi Q, He L, Yang L, Tang L. Examination of alternate codon bias solutions for expression and purification of recombinant mechano-growth factor inEscherichia coli. Biotechnol Appl Biochem 2015; 62:690-8. [PMID: 25345350 DOI: 10.1002/bab.1312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Jianguo Feng
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Rongxue Wan
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Qian Yi
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Ling He
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology; Ministry of Education; College of Bioengineering; Chongqing University; Chongqing People's Republic of China
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80
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Ihssen J, Reiss R, Luchsinger R, Thöny-Meyer L, Richter M. Biochemical properties and yields of diverse bacterial laccase-like multicopper oxidases expressed in Escherichia coli. Sci Rep 2015; 5:10465. [PMID: 26068013 PMCID: PMC4464401 DOI: 10.1038/srep10465] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 04/15/2015] [Indexed: 11/09/2022] Open
Abstract
Laccases are multi-copper oxidases that oxidize a broad range of substrates at the expense of molecular oxygen, without any need for co-factor regeneration. These enzymes bear high potential for the sustainable synthesis of fine chemicals and the modification of (bio)polymers. Here we describe cloning and expression of five novel bacterial laccase-like multi copper oxidases (LMCOs) of diverse origin which were identified by homology searches in online databases. Activity yields under different expression conditions and temperature stabilities were compared to three previously described enzymes from Bacillus subtilis, Bacillus pumilus and Bacillus clausii. In almost all cases, a switch to oxygen-limited growth conditions after induction increased volumetric activity considerably. For proteins with predicted signal peptides for secretion, recombinant expression with and without signal sequence was investigated. Bacillus CotA-type LMCOs outperformed enzymes from Streptomyces and Gram-negative bacteria with respect to activity yields in Escherichia coli and application relevant biochemical properties. The novel Bacillus coagulans LMCO combined high activity yields in E. coli with unprecedented activity at strong alkaline pH and high storage stability, making it a promising candidate for further development.
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Affiliation(s)
- Julian Ihssen
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Renate Reiss
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Ronny Luchsinger
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Linda Thöny-Meyer
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Michael Richter
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
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Hess AK, Saffert P, Liebeton K, Ignatova Z. Optimization of translation profiles enhances protein expression and solubility. PLoS One 2015; 10:e0127039. [PMID: 25965266 PMCID: PMC4428881 DOI: 10.1371/journal.pone.0127039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 12/12/2022] Open
Abstract
mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5’-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.
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Affiliation(s)
- Anne-Katrin Hess
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Paul Saffert
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (KL)
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82
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Gorochowski TE, Ignatova Z, Bovenberg RAL, Roubos JA. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 2015; 43:3022-32. [PMID: 25765653 PMCID: PMC4381083 DOI: 10.1093/nar/gkv199] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/26/2015] [Indexed: 01/28/2023] Open
Abstract
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
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Affiliation(s)
| | - Zoya Ignatova
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Johannes A Roubos
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
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mRNA secondary structure engineering of Thermobifida fusca endoglucanase (Cel6A) for enhanced expression in Escherichia coli. World J Microbiol Biotechnol 2015; 31:499-506. [PMID: 25617066 DOI: 10.1007/s11274-015-1806-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/19/2015] [Indexed: 01/21/2023]
Abstract
The sequence and structure of mRNA plays an important role in solubility and expression of the translated protein. To divulge the role of mRNA secondary structure and its thermodynamics in the expression level of the recombinant endoglucanase in Escherichia coli, 5'-end of the mRNA was thermodynamically optimized. Molecular engineering was done by introducing two silent synonymous mutations at positions +5 (UCU with UCC) and +7 (UUC with UUU) of the 5'-end of mRNA to relieve hybridization with ribosomal binding site. Two variants of glycoside hydrolase family six endoglucanase, wild type (cel6A.wt) and mutant (cel6A.mut) from Thermobifida fusca were expressed and characterized in E. coli using T7 promoter-based expression vector; pET22b(+). Enhanced expression level of engineered construct (Cel6A.mut) with ∆G = -2.7 kcal mol(-1)was observed. It showed up to ~45 % higher expression as compared to the wild type construct (Cel6A.wt) having ∆G = -7.8 kcal mol(-1) and ~25 % expression to the total cell proteins. Heterologous protein was purified by heating the recombinant E. coli BL21 (DE3) CodonPlus at 60 °C. The optimum pH for enzyme activity was six and optimum temperature was 60 °C. Maximum activity was observed 4.5 Umg(-1) on CMC. Hydrolytic activity was also observed on insoluble substrates, i.e. RAC (2.8 Umg(-1)), alkali treated bagass (1.7 Umg(-1)), filter paper (1.2 Umg(-1)) and BMCC (0.3 Umg(-1)). Metal ions affect endoglucanase activity in different ways. Only Fe(2+) exhibited 20.8 % stimulatory effects on enzyme activity. Enzyme activity was profoundly inhibited by Hg2(+) (91.8 %).
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84
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Overcoming the solubility problem in E. coli: available approaches for recombinant protein production. Methods Mol Biol 2015; 1258:27-44. [PMID: 25447857 DOI: 10.1007/978-1-4939-2205-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the importance of recombinant protein production in academy and industrial fields, many issues concerning the expression of soluble and homogeneous product are still unsolved. Although several strategies were developed to overcome these obstacles, at present there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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Fang J, Zou L, Zhou X, Cheng B, Fan J. Synonymous rare arginine codons and tRNA abundance affect protein production and quality of TEV protease variant. PLoS One 2014; 9:e112254. [PMID: 25426854 PMCID: PMC4245098 DOI: 10.1371/journal.pone.0112254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/10/2014] [Indexed: 11/27/2022] Open
Abstract
It has been identified that a TEV protease (TEVp) variant, TEVp5M, displays improved solubility. Here, we constructed fifteen TEVp5M variants with one or more of six rare arginine codons in the coding sequence replaced with abundant E. coli arginine codons. These codon variants expressed in either E. coli BL21 (DE3) or Rossetta (DE3) showed different solubility and activity. Supply of rare tRNAs increased the tendency of certain codon variants to form insoluble aggregates at early induction stage, as determined by the fused S-tag. About 32% increase in soluble protein production of M5 variant with four synonymously mutated arginine codons was identified in Rossetta (DE3) cells using GFP fusion reporter, comparable to that of TEVp5M. After purification, two other codon variants from both E. coli strains exhibited less activity than TEVp5M on cleaving the native or modified recognition sequence incorporated between GST and E. coli diaminopropionate ammonialyase by enzyme-coupled assay, whereas purified M5 variant showed activity similar to the TEVp5M. Supply of rare tRNAs caused the decrease of activity of TEVp5M and M5 by about 21%. Our results revealed that engineering of highly soluble TEVp variants can be achieved by the combined mutations of amino acid residues and optimization of specific rare codons, whereas simple augment of rare tRNAs abundance resulted in partial loss of activity.
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Affiliation(s)
- Jie Fang
- Key Laboratory of Crop Biology of Anhui Province, School of Life Science, Anhui Agricultural University, Hefei, Anhui, PR China
| | - Lingling Zou
- Key Laboratory of Crop Biology of Anhui Province, School of Life Science, Anhui Agricultural University, Hefei, Anhui, PR China
| | - Xuan Zhou
- Key Laboratory of Crop Biology of Anhui Province, School of Life Science, Anhui Agricultural University, Hefei, Anhui, PR China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui Province, School of Life Science, Anhui Agricultural University, Hefei, Anhui, PR China
| | - Jun Fan
- Key Laboratory of Crop Biology of Anhui Province, School of Life Science, Anhui Agricultural University, Hefei, Anhui, PR China
- * E-mail:
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86
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A critical analysis of codon optimization in human therapeutics. Trends Mol Med 2014; 20:604-13. [PMID: 25263172 DOI: 10.1016/j.molmed.2014.09.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 02/01/2023]
Abstract
Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications.
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87
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Fernández-Calero T, Astrada S, Alberti A, Horjales S, Arnal JF, Rovira C, Bollati-Fogolín M, Flouriot G, Marin M. The transcriptional activities and cellular localization of the human estrogen receptor alpha are affected by the synonymous Ala87 mutation. J Steroid Biochem Mol Biol 2014; 143:99-104. [PMID: 24607813 DOI: 10.1016/j.jsbmb.2014.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
Until recently, synonymous mutations (which do not change amino acids) have been much neglected. Some evidence suggests that this kind of mutations could affect mRNA secondary structure or stability, translation kinetics and protein structure. To explore deeper the role of synonymous mutations, we studied their consequence on the functional activity of the estrogen receptor alpha (ERα). The ERα is a ligand-inducible transcription factor that orchestrates pleiotropic cellular effects, at both genomic and non-genomic levels in response to estrogens. In this work we analyzed in transient transfection experiments, the activity of ERα carrying the synonymous mutation Ala87, a polymorphism involving about 5-10% of the population. In comparison to the wild type receptor, our results show that ERαA87 mutation reduces the transactivation efficiency of ERα on an ERE reporter gene while its expression level remains similar. This mutation enhances 4-OHT-induced transactivation of ERα on an AP1 reporter gene. Finally, the mutation affects the subcellular localization of ERα in a cell type specific manner. It enhances the cytoplasmic location of ERα without significant changes in non-genomic effects of E2. The functional alteration of the ERαA87 determined in this work highlights the relevance of synonymous mutations for biomedical and pharmacological points of view.
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Affiliation(s)
- Tamara Fernández-Calero
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Soledad Astrada
- Cell Biology Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Alvaro Alberti
- Cell Biology Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Sofía Horjales
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Jean Francois Arnal
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1048, Institute of Metabolic and Cardiovascular Diseases, University of Toulouse 3, Toulouse, France
| | - Carlos Rovira
- Department of Oncology and CREATE Health Strategic Centre for Clinical Cancer Research, Lund University, BMC, 221 84 Lund, Sweden
| | | | - Gilles Flouriot
- University of Rennes 1, Institut de Recherche en Santé, Environnement et Travail, IRSET, INSERM U1085, Team TREC, Biosit, Rennes, France
| | - Mónica Marin
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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88
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Rosano GL, Ceccarelli EA. Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 2014; 5:172. [PMID: 24860555 PMCID: PMC4029002 DOI: 10.3389/fmicb.2014.00172] [Citation(s) in RCA: 1322] [Impact Index Per Article: 132.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/29/2014] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli is one of the organisms of choice for the production of recombinant proteins. Its use as a cell factory is well-established and it has become the most popular expression platform. For this reason, there are many molecular tools and protocols at hand for the high-level production of heterologous proteins, such as a vast catalog of expression plasmids, a great number of engineered strains and many cultivation strategies. We review the different approaches for the synthesis of recombinant proteins in E. coli and discuss recent progress in this ever-growing field.
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Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
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89
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Ding J, Yi Y, Su Q, Qiu F, Jia Z, Bi S. High expression of small hepatitis D antigen in Escherichia coli and ELISA for diagnosis of hepatitis D virus. J Virol Methods 2014; 197:34-8. [DOI: 10.1016/j.jviromet.2013.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 09/29/2013] [Accepted: 10/01/2013] [Indexed: 11/30/2022]
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90
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Ramón A, Señorale-Pose M, Marín M. Inclusion bodies: not that bad…. Front Microbiol 2014; 5:56. [PMID: 24592259 PMCID: PMC3924032 DOI: 10.3389/fmicb.2014.00056] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/28/2014] [Indexed: 12/03/2022] Open
Abstract
The formation of inclusion bodies (IBs) constitute a frequent event during the production of heterologous proteins in bacterial hosts. Although the mechanisms leading to their formation are not completely understood, empirical data have been exploited trying to predict the aggregation propensity of specific proteins while a great number of strategies have been developed to avoid the generation of IBs. However, in many cases, the formation of such aggregates can be considered an advantage for basic research as for protein production. In this review, we focus on this positive side of IBs formation in bacteria. We present a compilation on recent advances on the understanding of IBs formation and their utilization as a model to understand protein aggregation and to explore strategies to control this process. We include recent information about their composition and structure, their use as an attractive approach to produce low cost proteins and other promising applications in Biomedicine.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mario Señorale-Pose
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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91
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Arbing MA, Chan S, Harris L, Kuo E, Zhou TT, Ahn CJ, Nguyen L, He Q, Lu J, Menchavez PT, Shin A, Holton T, Sawaya MR, Cascio D, Eisenberg D. Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions. PLoS One 2013; 8:e81753. [PMID: 24312350 PMCID: PMC3843698 DOI: 10.1371/journal.pone.0081753] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
The expression of heteroligomeric protein complexes for structural studies often requires a special coexpression strategy. The reason is that the solubility and proper folding of each subunit of the complex requires physical association with other subunits of the complex. The genomes of pathogenic mycobacteria encode many small protein complexes, implicated in bacterial fitness and pathogenicity, whose characterization may be further complicated by insolubility upon expression in Escherichia coli, the most common heterologous protein expression host. As protein fusions have been shown to dramatically affect the solubility of the proteins to which they are fused, we evaluated the ability of maltose binding protein fusions to produce mycobacterial Esx protein complexes. A single plasmid expression strategy using an N-terminal maltose binding protein fusion to the CFP-10 homolog proved effective in producing soluble Esx protein complexes, as determined by a small-scale expression and affinity purification screen, and coupled with intracellular proteolytic cleavage of the maltose binding protein moiety produced protein complexes of sufficient purity for structural studies. In comparison, the expression of complexes with hexahistidine affinity tags alone on the CFP-10 subunits failed to express in amounts sufficient for biochemical characterization. Using this strategy, six mycobacterial Esx complexes were expressed, purified to homogeneity, and subjected to crystallization screening and the crystal structures of the Mycobacterium abscessus EsxEF, M. smegmatis EsxGH, and M. tuberculosis EsxOP complexes were determined. Maltose binding protein fusions are thus an effective method for production of Esx complexes and this strategy may be applicable for production of other protein complexes.
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Affiliation(s)
- Mark A. Arbing
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sum Chan
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Liam Harris
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Emmeline Kuo
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tina T. Zhou
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Christine J. Ahn
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lin Nguyen
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Qixin He
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jamie Lu
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Phuong T. Menchavez
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Annie Shin
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas Holton
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael R. Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - David Eisenberg
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biological Chemistry, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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92
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Van Zyl LJ, Taylor MP, Eley K, Tuffin M, Cowan DA. Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius. Appl Microbiol Biotechnol 2013; 98:1247-59. [DOI: 10.1007/s00253-013-5380-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/30/2013] [Accepted: 11/02/2013] [Indexed: 11/25/2022]
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93
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Zhou JH, Zhang J, Sun DJ, Ma Q, Chen HT, Ma LN, Ding YZ, Liu YS. The distribution of synonymous codon choice in the translation initiation region of dengue virus. PLoS One 2013; 8:e77239. [PMID: 24204777 PMCID: PMC3808402 DOI: 10.1371/journal.pone.0077239] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/30/2013] [Indexed: 11/18/2022] Open
Abstract
Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been 'branded' on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts.
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Affiliation(s)
- Jian-hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Jie Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Dong-jie Sun
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Qi Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Hao-tai Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Li-na Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Yao-zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
| | - Yong-sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Lanzhou, Gansu, P.R. China
- * E-mail:
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94
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Kim D, Park HJ, Kim IC, Yim JH. A new approach for discovering cold-active enzymes in a cell mixture of pure-cultured bacteria. Biotechnol Lett 2013; 36:567-73. [PMID: 24158673 DOI: 10.1007/s10529-013-1384-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/08/2013] [Indexed: 12/01/2022]
Abstract
To overcome the intrinsic problems of conventional approaches, such as the unavailability of source microorganisms in metagenomic libraries and the production of inactive aggregates, a new method was tested for discovering new enzymes (e.g. cold-active chitinase). A metagenome-like library was constructed using genomes extracted from a cell mixture of pure-cultured chitinolytic bacteria, followed by activity-based screening for Escherichia coli clones that exhibit chitinase activity on selective medium. Within one positive chitinolytic clone, one chitinase gene (chi22718_III) was detected and assigned to the arctic marine bacterium, Pseudoalteromonas issachenkonii PAMC 22718, by colony-PCR with chi22718_III-specific primers. When expressed in E. coli, recombinant R-Chi22718_III lost 85 % of its enzyme activity when pre-incubated at 40 °C for 1 h, whereas its mesophilic counterpart R-ChiK only lost 10 % of its activity under the same conditions indicating that R-Chi22718_III is thermolabile, a characteristic of cold-active enzymes.
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Affiliation(s)
- Dockyu Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 406-840, Korea,
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95
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Amplification, Sequencing and Cloning of Iranian Native Bacillus subtilis Alpha-amylase Gene in Saccharomyces cerevisiae. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.7371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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96
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Zhou JH, Zhang J, Sun DJ, Ma Q, Ma B, Pejsak Z, Chen HT, Ma LN, Ding YZ, Liu YS. Potential roles of synonymous codon usage and tRNA concentration in hosts on the two initiation regions of foot-and-mouth disease virus RNA. Virus Res 2013; 176:298-302. [DOI: 10.1016/j.virusres.2013.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/10/2013] [Accepted: 06/14/2013] [Indexed: 12/01/2022]
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97
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Wohlgemuth SE, Gorochowski TE, Roubos JA. Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability. Nucleic Acids Res 2013; 41:8021-33. [PMID: 23842674 PMCID: PMC3783181 DOI: 10.1093/nar/gkt602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary significantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete understanding of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as translation, being more robust than those linked to regulation. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression.
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98
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99
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Gao B, Zhangsun D, Wu Y, Lin B, Zhu X, Luo S. Expression, renaturation and biological activity of recombinant conotoxin GeXIVAWT. Appl Microbiol Biotechnol 2012; 97:1223-30. [PMID: 22825834 DOI: 10.1007/s00253-012-4287-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 12/22/2022]
Abstract
Conotoxins are a diverse array of small peptides mostly with multiple disulfide bridges. These peptides become an increasing significant source of neuro-pharmacological probes and drugs as a result of the high selectivity for ion channels and receptors. Conotoxin GeXIVAWT (CTX-GeXIVAWT) is a 28-amino acid peptide containing five cysteines isolated from the venom of Conus generalis. Here, we present a simple and fast strategy of producing disulfide-rich conotoxins via recombinant expression. The codes of novel conotoxin gene GeXIVAWT were optimized and generated two pairs of primers by chemical synthesis for construction of expression vector. Recombinant expression vector pET22b(+)-GeXIVAWT fused with pelB leader and His-tag was successfully expressed as an insoluble body in Escherichia coli BL21(DE3) cells. Recombinant conotoxin GeXIVAWT (rCTX-GeXIVAWT) was obtained by dissolving the insoluble bodies and purifying with a Ni-NTA affinity column, which was further purified using reverse-phase high-performance liquid chromatography and identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. The rCTX-GeXIVAWT renatured in vitro could inhibited the growth of Sf9 cell with biological activity assay. This expression system may prove valuable for future structure-function studies of conotoxins.
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Affiliation(s)
- Bingmiao Gao
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
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100
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tRNA concentration fine tunes protein solubility. FEBS Lett 2012; 586:3336-40. [PMID: 22819830 DOI: 10.1016/j.febslet.2012.07.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/30/2012] [Accepted: 07/09/2012] [Indexed: 11/20/2022]
Abstract
Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coli increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.
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