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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Essential factors, advanced strategies, challenges, and approaches involved for efficient expression of recombinant proteins in Escherichia coli. Arch Microbiol 2024; 206:152. [PMID: 38472371 DOI: 10.1007/s00203-024-03871-2] [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] [Received: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Producing recombinant proteins is a major accomplishment of biotechnology in the past century. Heterologous hosts, either eukaryotic or prokaryotic, are used for the production of these proteins. The utilization of microbial host systems continues to dominate as the most efficient and affordable method for biotherapeutics and food industry productions. Hence, it is crucial to analyze the limitations and advantages of microbial hosts to enhance the efficient production of recombinant proteins on a large scale. E. coli is widely used as a host for the production of recombinant proteins. Researchers have identified certain obstacles with this host, and given the growing demand for recombinant protein production, there is an immediate requirement to enhance this host. The following review discusses the elements contributing to the manifestation of recombinant protein. Subsequently, it sheds light on innovative approaches aimed at improving the expression of recombinant protein. Lastly, it delves into the obstacles and optimization methods associated with translation, mentioning both cis-optimization and trans-optimization, producing soluble recombinant protein, and engineering the metal ion transportation. In this context, a comprehensive description of the distinct features will be provided, and this knowledge could potentially enhance the expression of recombinant proteins in E. coli.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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2
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Serrão VHB, Lee JE. Detecting in-solution conformational changes in viral fusogens using tryptophan-induced fluorescence quenching. STAR Protoc 2021; 2:100994. [PMID: 34934961 PMCID: PMC8654978 DOI: 10.1016/j.xpro.2021.100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Dynamic monitoring of protein conformational changes is necessary to fully understand many biological processes. For example, viral entry and membrane fusion require rearrangement of its viral glycoprotein. We present a step-by-step protocol for site-specific bimane labeling of the influenza-C fusogen to map proximity and conformational movements using tryptophan-induced fluorescence quenching. This protocol is adaptable for other proteins and for protein-protein interaction detection. For complete details on the use and execution of this protocol, please refer to Serrão et al., 2021.
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Affiliation(s)
- Vitor Hugo B. Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E. Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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3
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Eaglesham JB, Garcia A, Berkmen M. Production of antibodies in SHuffle Escherichia coli strains. Methods Enzymol 2021; 659:105-144. [PMID: 34752282 DOI: 10.1016/bs.mie.2021.06.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibodies are globally important macromolecules, used for research, diagnostics, and as therapeutics. The common mammalian antibody immunoglobulin G (IgG) is a complex glycosylated macromolecule, composed of two heavy chains and two light chains held together by multiple disulfide bonds. For this reason, IgG and related antibody fragments are usually produced through secretion from mammalian cell lines, such as Chinese Hamster Ovary cells. However, there is growing interest in production of antibodies in prokaryotic systems due to the potential for rapid and cheap production in a highly genetically manipulable system. Research on oxidative protein folding in prokaryotes has enabled engineering of Escherichia coli strains capable of producing IgG and other disulfide bonded proteins in the cytoplasm, known as SHuffle. In this protocol, we provide a review of research on prokaryotic antibody production, guidelines on cloning of antibody expression constructs, conditions for an initial expression and purification experiment, and parameters which may be optimized for increased purification yields. Last, we discuss the limitations of prokaryotic antibody production, and highlight potential future avenues for research on antibody expression and folding.
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4
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Collins JH, Keating KW, Jones TR, Balaji S, Marsan CB, Çomo M, Newlon ZJ, Mitchell T, Bartley B, Adler A, Roehner N, Young EM. Engineered yeast genomes accurately assembled from pure and mixed samples. Nat Commun 2021; 12:1485. [PMID: 33674578 PMCID: PMC7935868 DOI: 10.1038/s41467-021-21656-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.
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Affiliation(s)
- Joseph H Collins
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Kevin W Keating
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Trent R Jones
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Shravani Balaji
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Celeste B Marsan
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Marina Çomo
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Zachary J Newlon
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Tom Mitchell
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Bryan Bartley
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Aaron Adler
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Nicholas Roehner
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Eric M Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
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5
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. eLife 2020; 9:53476. [PMID: 32701056 PMCID: PMC7377907 DOI: 10.7554/elife.53476] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/09/2020] [Indexed: 12/03/2022] Open
Abstract
Protein mutational landscapes are shaped by the cellular environment, but key factors and their quantitative effects are often unknown. Here we show that Lon, a quality control protease naturally absent in common E. coli expression strains, drastically reshapes the mutational landscape of the metabolic enzyme dihydrofolate reductase (DHFR). Selection under conditions that resolve highly active mutants reveals that 23.3% of all single point mutations in DHFR are advantageous in the absence of Lon, but advantageous mutations are largely suppressed when Lon is reintroduced. Protein stability measurements demonstrate extensive activity-stability tradeoffs for the advantageous mutants and provide a mechanistic explanation for Lon’s widespread impact. Our findings suggest possibilities for tuning mutational landscapes by modulating the cellular environment, with implications for protein design and combatting antibiotic resistance.
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Affiliation(s)
- Samuel Thompson
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, United States
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, United States
| | - Christine Ingle
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Tanja Kortemme
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, United States.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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7
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Zhou L, Yu H, Wang K, Chen T, Ma Y, Huang Y, Li J, Liu L, Li Y, Kong Z, Zheng Q, Wang Y, Gu Y, Xia N, Li S. Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions. BMC Genomics 2020; 21:407. [PMID: 32546194 PMCID: PMC7296898 DOI: 10.1186/s12864-020-06818-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Escherichia coli ER2566 strain (NC_CP014268.2) was developed as a BL21 (DE3) derivative strain and had been widely used in recombinant protein expression. However, like many other current RefSeq annotations, the annotation of the ER2566 strain was incomplete, with missing gene names and miscellaneous RNAs, as well as uncorrected annotations of some pseudogenes. Here, we performed a systematic reannotation of the ER2566 genome by combining multiple annotation tools with manual revision to provide a comprehensive understanding of the E. coli ER2566 strain, and used high-throughput sequencing to explore how the strain adapted under external pressure. RESULTS The reannotation included noteworthy corrections to all protein-coding genes, led to the exclusion of 190 hypothetical genes or pseudogenes, and resulted in the addition of 237 coding sequences and 230 miscellaneous noncoding RNAs and 2 tRNAs. In addition, we further manually examined all 194 pseudogenes in the Ref-seq annotation and directly identified 123 (63%) as coding genes. We then used whole-genome sequencing and high-throughput RNA sequencing to assess mutational adaptations under consecutive subculture or overexpression burden. Whereas no mutations were detected in response to consecutive subculture, overexpression of the human papillomavirus 16 type capsid led to the identification of a mutation (position 1,094,824 within the 3' non-coding region) positioned 19-bp away from the lacI gene in the transcribed RNA, which was not detected at the genomic level by Sanger sequencing. CONCLUSION The ER2566 strain was used by both the general scientific community and the biotechnology industry. Reannotation of the E. coli ER2566 strain not only improved the RefSeq data but uncovered a key site that might be involved in the transcription and translation of genes encoding the lactose operon repressor. We proposed that our pipeline might offer a universal method for the reannotation of other bacterial genomes with high speed and accuracy. This study might facilitate a better understanding of gene function for the ER2566 strain under external burden and provided more clues to engineer bacteria for biotechnological applications.
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Affiliation(s)
- Lizhi Zhou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
| | - Kaihang Wang
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Tingting Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yue Ma
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yang Huang
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jiajia Li
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Liqin Liu
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yuqian Li
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zhibo Kong
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yingbin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, Fujian, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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8
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Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO. Metabolic and genetic basis for auxotrophies in Gram-negative species. Proc Natl Acad Sci U S A 2020; 117:6264-6273. [PMID: 32132208 PMCID: PMC7084086 DOI: 10.1073/pnas.1910499117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.
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Affiliation(s)
- Yara Seif
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Kumari Sonal Choudhary
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Ying Hefner
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Amitesh Anand
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Laurence Yang
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122;
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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9
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Reuter WH, Masuch T, Ke N, Lenon M, Radzinski M, Van Loi V, Ren G, Riggs P, Antelmann H, Reichmann D, Leichert LI, Berkmen M. Utilizing redox-sensitive GFP fusions to detect in vivo redox changes in a genetically engineered prokaryote. Redox Biol 2019; 26:101280. [PMID: 31450103 PMCID: PMC6831853 DOI: 10.1016/j.redox.2019.101280] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 11/26/2022] Open
Abstract
Understanding the in vivo redox biology of cells is a complex albeit important biological problem. Studying redox processes within living cells without physical disruption or chemical modifications is essential in determining the native redox states of cells. In this study, the previously characterized reduction-oxidation sensitive green fluorescent protein (roGFP2) was used to elucidate the redox changes of the genetically engineered Escherichia coli strain, SHuffle. SHuffle cells were demonstrated to be under constitutive oxidative stress and responding transcriptionally in an OxyR-dependent manner. Using roGFP2 fused to either glutathione (GSH)- or hydrogen peroxide (H2O2)- sensitive proteins (glutaredoxin 1 or Orp1), the cytosolic redox state of both wild type and SHuffle cells based on GSH/GSSG and H2O2 pools was measured. These probes open the path to in vivo studies of redox changes and genetic selections in prokaryotic hosts.
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Affiliation(s)
| | - Thorsten Masuch
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA; Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany
| | - Na Ke
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Marine Lenon
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Meytal Radzinski
- The Hebrew University of Jerusalem, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, Jerusalem, 91904, Israel
| | - Vu Van Loi
- Institute for Biology-Microbiology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Guoping Ren
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Paul Riggs
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Dana Reichmann
- The Hebrew University of Jerusalem, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, Jerusalem, 91904, Israel
| | - Lars I Leichert
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany
| | - Mehmet Berkmen
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.
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10
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Maresca JA, Keffer JL, Hempel PP, Polson SW, Shevchenko O, Bhavsar J, Powell D, Miller KJ, Singh A, Hahn MW. Light Modulates the Physiology of Nonphototrophic Actinobacteria. J Bacteriol 2019; 201:e00740-18. [PMID: 30692175 PMCID: PMC6482932 DOI: 10.1128/jb.00740-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 11/20/2022] Open
Abstract
Light is a source of energy and an environmental cue that is available in excess in most surface environments. In prokaryotic systems, conversion of light to energy by photoautotrophs and photoheterotrophs is well understood, but the conversion of light to information and the cellular response to that information have been characterized in only a few species. Our goal was to explore the response of freshwater Actinobacteria, which are ubiquitous in illuminated aquatic environments, to light. We found that Actinobacteria without functional photosystems grow faster in the light, likely because sugar transport and metabolism are upregulated in the light. Based on the action spectrum of the growth effect and comparisons of the genomes of three Actinobacteria with this growth rate phenotype, we propose that the photosensor in these strains is a putative CryB-type cryptochrome. The ability to sense light and upregulate carbohydrate transport during the day could allow these cells to coordinate their time of maximum organic carbon uptake with the time of maximum organic carbon release by primary producers.IMPORTANCE Sunlight provides information about both place and time. In sunlit aquatic environments, primary producers release organic carbon and nitrogen along with other growth factors during the day. The ability of Actinobacteria to coordinate organic carbon uptake and utilization with production of photosynthate enables them to grow more efficiently in the daytime, and it potentially gives them a competitive advantage over heterotrophs that constitutively produce carbohydrate transporters, which is energetically costly, or produce transporters only after detection of the substrate(s), which delays their response. Understanding how light cues the transport of organic carbon and its conversion to biomass is key to understanding biochemical mechanisms within the carbon cycle, the fluxes through it, and the variety of mechanisms by which light enhances growth.
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Affiliation(s)
- Julia A Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Jessica L Keffer
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Priscilla P Hempel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Olga Shevchenko
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Jaysheel Bhavsar
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Deborah Powell
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Kelsey J Miller
- Department of Biology, University of Delaware, Newark, Delaware, USA
| | - Archana Singh
- Department of Biology, University of Delaware, Newark, Delaware, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
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11
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Lipońska A, Ousalem F, Aalberts DP, Hunt JF, Boël G. The new strategies to overcome challenges in protein production in bacteria. Microb Biotechnol 2019; 12:44-47. [PMID: 30484965 PMCID: PMC6302713 DOI: 10.1111/1751-7915.13338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/13/2022] Open
Abstract
Recombinant proteins are essential for biotechnology. Here we review some of the key points for improving the production of heterologous proteins, and what can be the future of the field.
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Affiliation(s)
- Anna Lipońska
- Institut de Biologie Physico‐ChimiqueSorbonne Paris CitéUMR 8261 CNRS‐University Paris Diderot13 rue Pierre et Marie Curie75005ParisFrance
| | - Farès Ousalem
- Institut de Biologie Physico‐ChimiqueSorbonne Paris CitéUMR 8261 CNRS‐University Paris Diderot13 rue Pierre et Marie Curie75005ParisFrance
| | | | - John F. Hunt
- Department of Biological SciencesColumbia UniversityNew YorkNY10027USA
| | - Grégory Boël
- Institut de Biologie Physico‐ChimiqueSorbonne Paris CitéUMR 8261 CNRS‐University Paris Diderot13 rue Pierre et Marie Curie75005ParisFrance
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12
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Affiliation(s)
- Paul D. Riggs
- New England Biolabs, Inc., Research; Ipswich Massachusetts
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13
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Hydroxynitrile lyases from cyanogenic millipedes: molecular cloning, heterologous expression, and whole-cell biocatalysis for the production of (R)-mandelonitrile. Sci Rep 2018; 8:3051. [PMID: 29445093 PMCID: PMC5813103 DOI: 10.1038/s41598-018-20190-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/12/2018] [Indexed: 11/18/2022] Open
Abstract
Hydroxynitrile lyases (HNLs), which are key enzymes in cyanogenesis, catalyze the cleavage of cyanohydrins into carbonyl compounds and hydrogen cyanide. Since HNLs also catalyze the reverse reaction, they are used industrially for the asymmetric synthesis of cyanohydrins, which are valuable building blocks of pharmaceuticals and fine chemicals. HNLs have been isolated from cyanogenic plants and bacteria. Recently, an HNL from the cyanogenic millipede Chamberlinius hualienensis was shown to have the highest specific activity for (R)-mandelonitrile synthesis, along with high stability and enantioselectivity. However, no HNLs have been isolated from other cyanogenic millipedes. We identified and characterized HNLs from 10 cyanogenic millipedes in the Paradoxosomatidae and Xystodesmidae. Sequence analyses showed that HNLs are conserved among cyanogenic millipedes and likely evolved from one ancestral gene. The HNL from Parafontaria tonominea was expressed in Escherichia coli SHuffle T7 and showed high specific activity for (R)-mandelonitrile synthesis and stability at a range of pHs and temperatures. The stability of millipede HNLs is likely due to disulfide bond(s). The E. coli cells expressing HNL produced (R)-mandelonitrile with 97.6% enantiomeric excess without organic solvents. These results demonstrate that cyanogenic millipedes are a valuable source of HNLs with high specific activity and stability.
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Fomenkov A, Sun Z, Dila DK, Anton BP, Roberts RJ, Raleigh EA. EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination. PLoS One 2017; 12:e0179853. [PMID: 28654677 PMCID: PMC5487053 DOI: 10.1371/journal.pone.0179853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/24/2022] Open
Abstract
Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in vitro and in its genomic environment. MDE cleavage of modified DNAs protects prokaryote populations from lethal infection by bacteriophage with highly modified DNA, and also stabilizes lineages by reducing gene import when sparse modification occurs in the wrong context. The function and distribution of MDE families are thus important. Here we describe the properties of EcoBLMcrX, an enzyme of the E. coli B lineage, in vivo and in vitro. Restriction in vivo and the genome location of its gene, ecoBLmcrX, were determined during construction and sequencing of a B/K-12 hybrid, ER2566. In classical restriction literature, this B system was named r6 or rglAB. Like many genome defense functions, ecoBLmcrX is found within a genomic island, where gene content is variable among natural E. coli isolates. In vitro, EcoBLMcrX was compared with two related enzymes, BceYI and NhoI. All three degrade fully cytosine-modified phage DNA, as expected for EcoBLMcrX from classical T4 genetic data. A new method of characterizing MDE specificity was developed to better understand action on fully-modified targets such as the phage that provide major evolutionary pressure for MDE maintenance. These enzymes also cleave plasmids with m5C in particular motifs, consistent with a role in lineage-stabilization. The recognition sites were characterized using a site-ranking approach that allows visualization of preferred cleavage sites when fully-modified substrates are digested. A technical constraint on the method is that ligation of one-nucleotide 5' extensions favors G:C over A:T approximately five-fold. Taking this bias into account, we conclude that EcoBLMcrX can cleave 3' to the modified base in the motif Rm5C|. This is compatible with, but less specific than, the site reported by others. Highly-modified site contexts, such as those found in base-substituted virulent phages, are strongly preferred.
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Affiliation(s)
- Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Zhiyi Sun
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Deborah K. Dila
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Brian P. Anton
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Richard J. Roberts
- Research Department, New England Biolabs, Ipswich, MA, United States of America
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