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Santos SP, Garcés LFS, Silva FS, Santiago LF, Pinheiro CS, Alcantara-Neves NM, Pacheco LG. Engineering an optimized expression operating unit for improved recombinant protein production in Escherichia coli. Protein Expr Purif 2022; 199:106150. [DOI: 10.1016/j.pep.2022.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022]
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52
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Masłowska-Górnicz A, van den Bosch MRM, Saccenti E, Suarez-Diez M. A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content, protein functional domains and bacterial phenotypes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194826. [PMID: 35605953 DOI: 10.1016/j.bbagrm.2022.194826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Multiple synonymous codons code for the same amino acid, resulting in the degeneracy of the genetic code and in the preferred used of some codons called codon bias usage (CBU). We performed a large-scale analysis of codon usage bias analysing the distribution of the codon adaptation index (CAI) and the codon relative adaptiveness index (RA) in 4868 bacterial genomes. We found that CAI values differ significantly between protein functional domains and part of the protein outside domains and show how CAI, GC content and preferred usage of polymerase III alpha subunits are related. Additionally, we give evidence of the association between CAI and bacterial phenotypes.
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Affiliation(s)
- Anna Masłowska-Górnicz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Melanie R M van den Bosch
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
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53
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Diez M, Medina-Muñoz SG, Castellano LA, da Silva Pescador G, Wu Q, Bazzini AA. iCodon customizes gene expression based on the codon composition. Sci Rep 2022; 12:12126. [PMID: 35840631 PMCID: PMC9287306 DOI: 10.1038/s41598-022-15526-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.
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Affiliation(s)
- Michay Diez
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Santiago Gerardo Medina-Muñoz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.,National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824, Irapuato, Mexico
| | | | | | - Qiushuang Wu
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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54
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Agustriana E, Nuryana I, Laksmi FA, Dewi KS, Wijaya H, Rahmani N, Yudiargo DR, Ismadara A, Helbert, Hadi MI, Purnawan A, Cameliawati Djohan A. Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system. Prep Biochem Biotechnol 2022; 53:384-393. [PMID: 35792906 DOI: 10.1080/10826068.2022.2095573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Bst DNA polymerase is a DNA polymerase derived from Geobacillus stearothermophilus, has a strand-displacement activity, and is used in loop-mediated isothermal amplification (LAMP) for rapid detection of COVID-19. Despite its potential to be employed in the detection of COVID-19, using commercially available enzymes is not economically feasible. The use of noncommercial enzyme for routine use is desirable. However, research on Bst DNA polymerase is still limited in Indonesia. For those reasons, a preliminary study of scale-up production of recombinant Bst polymerase was conducted. Therefore, the optimization of expression conditions was performed. The optimum conditions for Bst polymerase expression were as follows: 1 mM of IPTG, post-induction incubation time of 6 h, and induction at OD600 1.1. Employing optimum conditions could result in 2.8 times increase in protein yield compared to the initial conditions. Subsequently, an operation in 1 L working volume by a lab-scale bioreactor had been performed, followed by purification and dialysis. The optimum result for a 1 L lab-scale bioreactor was achieved by applying 100 rpm and 3 vvm, giving 11.7 mg/L of protein yield. Bst polymerase was successfully purified showing 813.56 U/mg of polymerase activity.
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Affiliation(s)
- Eva Agustriana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Hans Wijaya
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Nanik Rahmani
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Danu Risqi Yudiargo
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Moch Irfan Hadi
- Department of Biology, Sunan Ampel State Islamic University, Surabaya, Indonesia
| | - Awan Purnawan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Apridah Cameliawati Djohan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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55
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Smith GE, Tolkatchev D, Risi C, Little M, Gregorio CC, Galkin VE, Kostyukova AS. Ca 2+ attenuates nucleation activity of leiomodin. Protein Sci 2022; 31:e4358. [PMID: 35762710 PMCID: PMC9207750 DOI: 10.1002/pro.4358] [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] [Received: 03/02/2022] [Revised: 04/25/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
A transient increase in Ca2+ concentration in sarcomeres is essential for their proper function. Ca2+ drives striated muscle contraction via binding to the troponin complex of the thin filament to activate its interaction with the myosin thick filament. In addition to the troponin complex, the myosin essential light chain and myosin-binding protein C were also found to be Ca2+ sensitive. However, the effects of Ca2+ on the function of the tropomodulin family proteins involved in regulating thin filament formation have not yet been studied. Leiomodin, a member of the tropomodulin family, is an actin nucleator and thin filament elongator. Using pyrene-actin polymerization assay and transmission electron microscopy, we show that the actin nucleation activity of leiomodin is attenuated by Ca2+ . Using circular dichroism and nuclear magnetic resonance spectroscopy, we demonstrate that the mostly disordered, negatively charged region of leiomodin located between its first two actin-binding sites binds Ca2+ . We propose that Ca2+ binding to leiomodin results in the attenuation of its nucleation activity. Our data provide further evidence regarding the role of Ca2+ as an ultimate regulator of the ensemble of sarcomeric proteins essential for muscle function. SUMMARY STATEMENT: Ca2+ fluctuations in striated muscle sarcomeres modulate contractile activity via binding to several distinct families of sarcomeric proteins. The effects of Ca2+ on the activity of leiomodin-an actin nucleator and thin filament length regulator-have remained unknown. In this study, we demonstrate that Ca2+ binds directly to leiomodin and attenuates its actin nucleating activity. Our data emphasizes the ultimate role of Ca2+ in the regulation of the sarcomeric protein interactions.
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Affiliation(s)
- Garry E. Smith
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Dmitri Tolkatchev
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Cristina Risi
- Department of Physiological SciencesEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Madison Little
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research ProgramUniversity of ArizonaTucsonArizonaUSA
| | - Vitold E. Galkin
- Department of Physiological SciencesEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
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56
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Khandia R, Sharma A, Alqahtani T, Alqahtani AM, Asiri YI, Alqahtani S, Alharbi AM, Kamal MA. Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns. Front Neurosci 2022; 16:887929. [PMID: 35757545 PMCID: PMC9226491 DOI: 10.3389/fnins.2022.887929] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Neurodegenerative disorders cause irreversible damage to the neurons and adversely affect the quality of life. Protein misfolding and their aggregation in specific parts of the brain, mitochondrial dysfunction, calcium load, proteolytic stress, and oxidative stress are among the causes of neurodegenerative disorders. In addition, altered metabolism has been associated with neurodegeneration as evidenced by reductions in glutamine and alanine in transient global amnesia patients, higher homocysteine-cysteine disulfide, and lower methionine decline in serum urea have been observed in Alzheimer's disease patients. Neurodegeneration thus appears to be a culmination of altered metabolism. The study's objective is to analyze various attributes like composition, physical properties of the protein, and factors like selectional and mutational forces, influencing codon usage preferences in a panel of genes involved directly or indirectly in metabolism and contributing to neurodegeneration. Various parameters, including gene composition, dinucleotide analysis, Relative synonymous codon usage (RSCU), Codon adaptation index (CAI), neutrality and parity plots, and different protein indices, were computed and analyzed to determine the codon usage pattern and factors affecting it. The correlation of intrinsic protein properties such as the grand average of hydropathicity index (GRAVY), isoelectric point, hydrophobicity, and acidic, basic, and neutral amino acid content has been found to influence codon usage. In genes up to 800 amino acids long, the GC3 content was highly variable, while GC12 content was relatively constant. An optimum CpG content is present in genes to maintain a high expression level as required for genes involved in metabolism. Also observed was a low codon usage bias with a higher protein expression level. Compositional parameters and nucleotides at the second position of codons played essential roles in explaining the extent of bias. Overall analysis indicated that the dominance of selection pressure and compositional constraints and mutational forces shape codon usage.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Anushri Sharma
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Saud Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ahmed M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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57
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Design of typical genes for heterologous gene expression. Sci Rep 2022; 12:9625. [PMID: 35688911 PMCID: PMC9187722 DOI: 10.1038/s41598-022-13089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Heterologous protein expression is an important method for analysing cellular functions of proteins, in genetic circuit engineering and in overexpressing proteins for biopharmaceutical applications and structural biology research. The degeneracy of the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, plays an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. We selected green fluorescent protein (GFP) and human α-synuclein (αSyn) as representatives for stable and intrinsically disordered proteins and representing a benchmark and a challenging test case. A new approach was implemented to design typical genes resembling the codon usage of any subset of endogenous genes. Using this approach, synthetic genes for GFP and αSyn were generated, heterologously expressed and evaluated in yeast. We demonstrate that GFP is expressed at high levels, and that the toxic αSyn can be adapted to endogenous, low-level expression. The new software is publicly available as a web-application for performing host-specific protein adaptations to a set of the most commonly used model organisms ( https://odysseus.motorprotein.de ).
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58
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Leibovich Z, Gronau I. Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites. J Comput Biol 2022; 29:974-986. [PMID: 35648072 DOI: 10.1089/cmb.2021.0417] [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: 11/13/2022] Open
Abstract
Synthesizing DNA molecules by design has become an essential tool in molecular biology and is expected to become ubiquitous in the coming decade. Successful design of a synthetic DNA molecule often requires satisfying multiple objectives, some of which may conflict with others. One particularly important objective is the elimination of unwanted protein binding sites, which may interfere with the desired function of the synthesized molecule. While most design tools offer this fundamental capability, they do not follow a systematic approach that guarantees elimination of all unwanted sites whenever a feasible solution exists. Furthermore, the algorithms these tools use (when published) are often quite naive and inefficient. We present a formal description of the binding site elimination problem and suggest several efficient algorithms that eliminate unwanted patterns with minimum interference to the desired function of the synthesized sequence. These algorithms are simple, efficient, and flexible and, therefore, can be easily incorporated in all existing DNA design tools, enhancing their design capabilities.
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Affiliation(s)
- Zehavit Leibovich
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
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59
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Linde D, González-Benjumea A, Aranda C, Carro J, Gutiérrez A, Martínez AT. Engineering Collariella virescens Peroxygenase for Epoxides Production from Vegetable Oil. Antioxidants (Basel) 2022; 11:antiox11050915. [PMID: 35624779 PMCID: PMC9137900 DOI: 10.3390/antiox11050915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable oils are valuable renewable resources for the production of bio-based chemicals and intermediates, including reactive epoxides of industrial interest. Enzymes are an environmentally friendly alternative to chemical catalysis in oxygenation reactions, epoxidation included, with the added advantage of their potential selectivity. The unspecific peroxygenase of Collariella virescens is only available as a recombinant enzyme (rCviUPO), which is produced in Escherichia coli for protein engineering and analytical-scale optimization of plant lipid oxygenation. Engineering the active site of rCviUPO (by substituting one, two, or up to six residues of its access channel by alanines) improved the epoxidation of individual 18-C unsaturated fatty acids and hydrolyzed sunflower oil. The double mutation at the heme channel (F88A/T158A) enhanced epoxidation of polyunsaturated linoleic and α−linolenic acids, with the desired diepoxides representing > 80% of the products (after 99% substrate conversion). More interestingly, process optimization increased (by 100-fold) the hydrolyzate concentration, with up to 85% epoxidation yield, after 1 h of reaction time with the above double variant. Under these conditions, oleic acid monoepoxide and linoleic acid diepoxide are the main products from the sunflower oil hydrolyzate.
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), Consejo Superior de Investigaciones Científicas (CSIC), E-28040 Madrid, Spain; (D.L.); (J.C.)
| | - Alejandro González-Benjumea
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), E-41012 Seville, Spain; (A.G.-B.); (A.G.)
| | - Carmen Aranda
- Johnson Matthey, Cambridge Science Park U260, Cambridge CB4 0FP, UK;
| | - Juan Carro
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), Consejo Superior de Investigaciones Científicas (CSIC), E-28040 Madrid, Spain; (D.L.); (J.C.)
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), E-41012 Seville, Spain; (A.G.-B.); (A.G.)
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas” (CIB), Consejo Superior de Investigaciones Científicas (CSIC), E-28040 Madrid, Spain; (D.L.); (J.C.)
- Correspondence: ; Tel.: +34-918373112
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60
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He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022; 20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023] Open
Abstract
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Corresponding author.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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61
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Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements. Antioxidants (Basel) 2022; 11:antiox11050891. [PMID: 35624755 PMCID: PMC9137552 DOI: 10.3390/antiox11050891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are extracellular fungal enzymes of biotechnological interest as self-sufficient (and more stable) counterparts of cytochrome P450 monooxygenases, the latter being present in most living cells. Expression hosts and structural information are crucial for exploiting UPO diversity (over eight thousand UPO-type genes were identified in sequenced genomes) in target reactions of industrial interest. However, while many thousands of entries in the Protein Data Bank include molecular coordinates of P450 enzymes, only 19 entries correspond to UPO enzymes, and UPO structures from only two species (Agrocybe aegerita and Hypoxylon sp.) have been published to date. In the present study, two UPOs from the basidiomycete Marasmius rotula (rMroUPO) and the ascomycete Collariella virescens (rCviUPO) were crystallized after sequence optimization and Escherichia coli expression as active soluble enzymes. Crystals of rMroUPO and rCviUPO were obtained at sufficiently high resolution (1.45 and 1.95 Å, respectively) and the corresponding structures were solved by molecular replacement. The crystal structures of the two enzymes (and two mutated variants) showed dimeric proteins. Complementary biophysical and molecular biology studies unveiled the diverse structural bases of the dimeric nature of the two enzymes. Intermolecular disulfide bridge and parallel association between two α-helices, among other interactions, were identified at the dimer interfaces. Interestingly, one of the rCviUPO variants incorporated the ability to produce fatty acid diepoxides—reactive compounds with valuable cross-linking capabilities—due to removal of the enzyme C-terminal tail located near the entrance of the heme access channel. In conclusion, different dimeric arrangements could be described in (short) UPO crystal structures.
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62
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Triple gene expressions in yeast, Escherichia coli, and mammalian cells by transferring DNA fragments amplified from a mother yeast expression plasmid. J Biosci Bioeng 2022; 133:587-595. [DOI: 10.1016/j.jbiosc.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 11/22/2022]
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63
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Sana M, Javed A, Babar Jamal S, Junaid M, Faheem M. Development of multivalent vaccine targeting M segment of Crimean Congo Hemorrhagic Fever Virus (CCHFV) using immunoinformatic approaches. Saudi J Biol Sci 2022; 29:2372-2388. [PMID: 35531180 PMCID: PMC9072894 DOI: 10.1016/j.sjbs.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/25/2021] [Accepted: 12/04/2021] [Indexed: 01/23/2023] Open
Abstract
Crimean-Congo Hemorrhagic Fever (CCHF) is a tick-borne viral infection with no licensed vaccine or therapeutics available for its treatment. In the present study we have developed the first multi-epitope subunit vaccine effective against all the seven genotypes of CCHF virus (CCHFV). The vaccine contains five B-cell, two MHC-II (HTL), and three MHC-I (CTL) epitopes screened from two structural glycoproteins (Gc and Gn in M segment) of CCHFV with an N-terminus human β-defensin as an adjuvant, as well as an N-terminus EAAAK sequence. The epitopes were rigorously investigated for their antigenicity, allergenicity, IFN gamma induction, anti-inflammatory responses, stability, and toxicity. The three-dimensional structure of the vaccine was predicted and docked with TLR-3, TLR-8, and TLR-9 receptors to find the strength of the binding complexes via molecular dynamics simulation. After codon adaptation, the subunit vaccine construct was developed in a pDual-GC plasmid and has population coverage of 98.47% of the world's population (HLA-I & II combined). The immune simulation studies were carried out on the C-ImmSim in-silico interface showing a marked increase in the production of cellular and humoral response (B-cell and T-cell) as well as TGFβ, IL-2, IL-10, and IL-12 indicating that the proposed vaccine would be able to sufficiently provoke both humoral and cell-mediated immune responses. Thus, making it a new and promising vaccine candidate against CCHFV.
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Affiliation(s)
- Maaza Sana
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Sector H-12, Islamabad, Pakistan
| | - Syed Babar Jamal
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
| | - Muhammad Junaid
- Precision Medicine Laboratory, Rehman Medical Institute, Hayatabad, Peshawar, KPK, 25000, Pakistan
| | - Muhammad Faheem
- Deparment of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, Rawalpindi, Punjab 46000, Pakistan
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64
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Tarahomjoo S, Bandehpour M, Aghaebrahimian M, Ahangaran S. Soluble Diphtheria Toxin Variant, CRM 197 was Obtained in Escherichia
coli at High Productivity Using SUMO Fusion and an Adjusted
Expression Strategy. Protein Pept Lett 2022; 29:350-359. [DOI: 10.2174/0929866529666220209155738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 11/22/2022]
Abstract
Background:
CRM197, a non-toxic diphtheria toxin variant, is widely used as a
polysaccharide carrier in a variety of conjugate vaccines and also exhibits antitumor activity. CRM197
commercial production is limited due to the low yield of Corynebacterium diphtheriae C7
(197) tox-. Developing an efficient method for recombinant CRM197 production reduces production
costs and is critical for expanding the application coverage of related medical products and basic research.
Escherichia coli is a frequently used host for heterologous protein synthesis. However, the
primary limitation of this system is the inclusion body formation and the low yield of active protein
recovery.
Objective:
As a result, we attempted to produce CRM197 in the soluble form in E. coli using a
small ubiquitin-related modifier (SUMO) tag fusion and an expression strategy optimized for protein
production.
Methods:
CRM197 was expressed intracellularly in E. coli BL21 (DE3) with its N-terminus fused
to a SUMO tag preceded by a histidine tag (HSCRM197). To improve the solubility of HSCRM197
in E. coli, a response surface method (RSM) experimental design was used based on three
factors: expression temperature, inducer concentration, and sorbitol inclusion in the culture medium.
Metal affinity chromatography was used to purify HSCRM197, and the SUMO tag was removed
using the SUMO protease's catalytic domain. After adsorbing the SUMO tag on a Ni-NTA
column, CRM197 was obtained. DNA degradation activity was determined for both HSCRM197
and CRM197.
Results:
When HSCRM197 was expressed in E. coli under common expression conditions (37ºC,
1000 μM inducer), 15.4% of the protein was found in the cellular soluble fraction. However, when
the RSM-derived expression conditions were used (30ºC, 510 μM inducer, and 200 mM sorbitol),
the obtained HSCRM197 was almost completely soluble (96.5% solubility), and the system productivity
was 32.67 μg ml-1 h-1. HSCRM197 and CRM197 both exhibited nuclease activity. However,
the activity of CRM197 was greater than that of HSCRM197.
Conclusion:
These findings established the utility of the method developed in this study to produce
CRM197 for medical applications.
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Affiliation(s)
- Shirin Tarahomjoo
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO),
Karaj 31975/148, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences,
Tehran, Iran
| | - Mohammad Aghaebrahimian
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO),
Karaj 31975/148, Iran
| | - Salimeh Ahangaran
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO),
Karaj 31975/148, Iran
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Noushahi HA, Khan AH, Noushahi UF, Hussain M, Javed T, Zafar M, Batool M, Ahmed U, Liu K, Harrison MT, Saud S, Fahad S, Shu S. Biosynthetic pathways of triterpenoids and strategies to improve their Biosynthetic Efficiency. PLANT GROWTH REGULATION 2022; 97:439-454. [PMID: 35382096 PMCID: PMC8969394 DOI: 10.1007/s10725-022-00818-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/18/2022] [Indexed: 05/13/2023]
Abstract
"Triterpenoids" can be considered natural products derived from the cyclization of squalene, yielding 3-deoxytriterpenes (hydrocarbons) or 3-hydroxytriterpenes. Triterpenoids are metabolites of these two classes of triterpenes, produced by the functionalization of their carbon skeleton. They can be categorized into different groups based on their structural formula/design. Triterpenoids are an important group of compounds that are widely used in the fields of pharmacology, food, and industrial biotechnology. However, inadequate synthetic methods and insufficient knowledge of the biosynthesis of triterpenoids, such as their structure, enzymatic activity, and the methods used to produce pure and active triterpenoids, are key problems that limit the production of these active metabolites. Here, we summarize the derivatives, pharmaceutical properties, and biosynthetic pathways of triterpenoids and review the enzymes involved in their biosynthetic pathway. Furthermore, we concluded the screening methods, identified the genes involved in the pathways, and highlighted the appropriate strategies used to enhance their biosynthetic production to facilitate the commercial process of triterpenoids through the synthetic biology method.
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Affiliation(s)
- Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, 3460000 Talca, Chile
| | - Aamir Hamid Khan
- National Key Lab of Crop Genetics Improvement, College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Usama Farhan Noushahi
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, 54000 Lahore, Pakistan
| | - Mubashar Hussain
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Maimoona Zafar
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Umair Ahmed
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, 7250 Burnie, Tasmania Australia
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, 7250 Burnie, Tasmania Australia
| | - Shah Saud
- College of Life Science, Linyi University, 276000 Linyi, Shandong China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, 570228 Haikou, China
- Department of Agronomy, The University of Haripur, 22620 Haripur, Pakistan
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
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Fang E, Liu X, Li M, Zhang Z, Song L, Zhu B, Wu X, Liu J, Zhao D, Li Y. Advances in COVID-19 mRNA vaccine development. Signal Transduct Target Ther 2022; 7:94. [PMID: 35322018 PMCID: PMC8940982 DOI: 10.1038/s41392-022-00950-y] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has determined 399,600,607 cases and 5,757,562 deaths worldwide. COVID-19 is a serious threat to human health globally. The World Health Organization (WHO) has declared COVID-19 pandemic a major public health emergency. Vaccination is the most effective and economical intervention for controlling the spread of epidemics, and consequently saving lives and protecting the health of the population. Various techniques have been employed in the development of COVID-19 vaccines. Among these, the COVID-19 messenger RNA (mRNA) vaccine has been drawing increasing attention owing to its great application prospects and advantages, which include short development cycle, easy industrialization, simple production process, flexibility to respond to new variants, and the capacity to induce better immune response. This review summarizes current knowledge on the structural characteristics, antigen design strategies, delivery systems, industrialization potential, quality control, latest clinical trials and real-world data of COVID-19 mRNA vaccines as well as mRNA technology. Current challenges and future directions in the development of preventive mRNA vaccines for major infectious diseases are also discussed.
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Affiliation(s)
- Enyue Fang
- National Institute for Food and Drug Control, Beijing, 102629, China
- Wuhan Institute of Biological Products, Co., Ltd., Wuhan, 430207, China
| | - Xiaohui Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Miao Li
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Zelun Zhang
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Lifang Song
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Baiyu Zhu
- Texas A&M University, College Station, TX, 77843, USA
| | - Xiaohong Wu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Jingjing Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Danhua Zhao
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Yuhua Li
- National Institute for Food and Drug Control, Beijing, 102629, China.
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Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? Life (Basel) 2022; 12:life12030431. [PMID: 35330182 PMCID: PMC8954436 DOI: 10.3390/life12030431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in E. coli K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression.
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Ardestani H, Nazarian S, Hajizadeh A, Sadeghi D, Kordbacheh E. In silico and in vivo approaches to recombinant multi-epitope immunogen of GroEL provides efficient cross protection against S. Typhimurium, S. flexneri, and S. dysenteriae. Mol Immunol 2022; 144:96-105. [PMID: 35217247 DOI: 10.1016/j.molimm.2022.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Stress or Heat Shock Proteins (HSPs) have been included in various operations like protein folding, autophagy, and apoptosis. HSP families recognize as protective antigens in a wide range of bacteria because they have been conserved through evolution. Due to their homology as well as antigenicity they are competent for applying in cross-protection against bacterial diseases. METHODS In the present study, bioinformatics approaches utilized to design epitope-based construction of Hsp60 (or GroEL) protein. In this regard, potential B-cell and T-cell epitopes except for allergenic sequences were selected by immunoinformatic tools. The structural and functional aspects of the DNA, RNA, and protein levels were assessed by bioinformatics software. Following in silico investigations, recombinant GroEL multi-epitope of Salmonella typhi was expressed, purified, and validated. Mouse groups were immunized with recombinant protein and humoral immune response was measured by enzyme linked immunosorbent assay (ELISA). Animal challenge against Salmonella Typhimurium, Shigella flexneri, and Shigella dysenteriae was evaluated. RESULTS recombinant protein expression and purification with 14.3 kilodaltons (kDa) was confirmed by SDS-PAGE and western blotting. After animal administration, the immunoglobulins evaluated increase after each immunization. Immunized antisera exhibited 80%, 40%, and 40% protection against the lethal dose infection by S. Typhimurium, S. flexneri, and S. dysenteriae respectively. Passive immunization conferred 50%, 30%, and 30% protection in mice against S. Typhimurium, S. flexneri and S. dysentery respectively. In addition, bacterial organ load had exhibited a significant decrease in colony forming unit (CFU) in the liver and spleen of the immunized mice compared to the control. CONCLUSION Our study demonstrates the efficacy of S. Typhi recombinant GroEL multi-epitope to consider as a universal immunogen candidate versus multiple bacterial pathogens.
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Affiliation(s)
- Hassan Ardestani
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran.
| | - Abbas Hajizadeh
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Davoud Sadeghi
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Emad Kordbacheh
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
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Abstract
Membrane proteins, particularly those that are α-helical, such as transporters and G-protein-coupled receptors (GPCRs), have significant biological relevance. However, their expression and purification pose difficulties because of their poor water solubilities, which impedes progress in this field. The QTY method, a code-based protein-engineering approach, was recently developed to produce soluble transmembrane proteins. Here, we describe a comprehensive Web server built for QTY design and its relevance for in silico analyses. Typically, the simple design model is expected to require only 2 to 4 min of computer time, and the library design model requires 2 to 5 h, depending on the target protein size and the number of transmembrane helices. Detailed protocols for using the server with both the simple design and library design modules are provided. Methods for experiments following the QTY design are also included to facilitate the implementation of this approach. The design pipeline was further evaluated using microbial transmembrane proteins and structural alignment between the designed proteins and their origins by employing AlphaFold2. The results reveal that mutants generated by the developed pipeline were highly identical to their origins in terms of three-dimensional (3D) structures. In summary, the utilization of our Web server and associated protocols will enable QTY-based protein engineering to be implemented in a convenient, fast, accurate, and rational manner. The Protein Solubilizing Server (PSS) is publicly available at http://pss.sjtu.edu.cn. IMPORTANCE Water-soluble expression and purification are of considerable importance for protein identification and characterization. However, there has been a lack of an effective method for water-soluble expression of membrane proteins, which has severely hampered their studies. Here, an enabling comprehensive Web server, PSS, was developed for designing water-soluble mutants of α-helical membrane proteins, based on QTY design, a code-based protein-engineering approach. With microbial transmembrane proteins and GPCRs as examples, we systematically evaluated the server and demonstrated its successful performance. PSS is readily available for worldwide users as a Web-based tool, rendering QTY-based protein engineering convenient, efficient, accurate, and rational.
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70
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Bu L, Chen B, Xing L, Cai X, Liang S, Zhang L, Wang X, Song W. Generation of a pdmH1N1 2018 Influenza A Reporter Virus Carrying a mCherry Fluorescent Protein in the PA Segment. Front Cell Infect Microbiol 2022; 11:827790. [PMID: 35127568 PMCID: PMC8811159 DOI: 10.3389/fcimb.2021.827790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) is a major human pathogen associated with significant morbidity and mortality worldwide. Through serial passage in mice, we generated a recombinant pdmH1N1 2009 IAV, A/Guangdong/GLW/2018 (GLW/18-MA), which encodes an mCherry gene fused to the C-terminal of a polymerase acidic (PA) segment and demonstrated comparable growth kinetics to the wild-type. Nine mutations were identified in the GLW/18-MA genome: PA (I61M, E351G, and G631S), NP (E292G), HA1 (T164I), HA2 (N117S and P160S), NA (W61R), and NEP (K44R). The recombinant IAV reporter expresses mCherry, a red fluorescent protein, at a high level and maintains its genetic integrity after five generations of serial passages in Madin-Darby Canine Kidney cells (MDCK) cells. Moreover, the imaging is noninvasive and permits the monitoring of infection in living mice. Treatment with oseltamivir or baicalin followed by infection with the reporter IAV led to a decrease in fluorescent protein signal in living mice. This result demonstrates that the IAV reporter virus is a powerful tool to study viral pathogenicity and transmission and to develop and evaluate novel anti-viral drugs, inhibitors, and vaccines in the future.
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Affiliation(s)
- Ling Bu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Boqian Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuejun Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuhua Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liying Zhang
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenjun Song
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Center of Infection and Immunology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Ortega C, Oppezzo P, Correa A. Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production. Methods Mol Biol 2022; 2406:35-64. [PMID: 35089549 DOI: 10.1007/978-1-0716-1859-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, 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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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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Alirezaeizanjani Z, Trösemeier JH, Kamp C, Rudorf S. Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization. Methods Mol Biol 2022; 2406:85-92. [PMID: 35089551 DOI: 10.1007/978-1-0716-1859-2_4] [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: 06/14/2023]
Abstract
For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced the software tool OCTOPOS. This sequence optimizer combines a detailed mechanistic mathematical modeling of in vivo protein synthesis with a state-of-the-art machine learning algorithm to find the sequence that best serves a user's needs. Here, we briefly describe the algorithm and its implementation as well as its application in practice using OCTOPOS.
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Affiliation(s)
| | - Jan-Hendrik Trösemeier
- Division of Microbiology, Section Biostatistics, Paul Ehrlich Institute, Langen, Germany
- Institute of Computer Science, Molecular Bioinformatics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christel Kamp
- Division of Microbiology, Section Biostatistics, Paul Ehrlich Institute, Langen, Germany
| | - Sophia Rudorf
- Max Planck Institute of Colloids and Interfaces, Potsdam-Golm, Potsdam, Germany.
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Wright G, Rodriguez A, Li J, Milenkovic T, Emrich SJ, Clark PL. CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern. Protein Sci 2022; 31:221-231. [PMID: 34738275 PMCID: PMC8740841 DOI: 10.1002/pro.4223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023]
Abstract
There is a growing appreciation that synonymous codon usage, although historically regarded as phenotypically silent, can instead alter a wide range of mechanisms related to functional protein production, a term we use here to describe the net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure. In particular, recent discoveries have highlighted the important role that sub-optimal codons can play in modifying co-translational protein folding. These results have drawn increased attention to the patterns of synonymous codon usage within coding sequences, particularly in light of the discovery that these patterns can be conserved across evolution for homologous proteins. Because synonymous codon usage differs between organisms, for heterologous gene expression it can be desirable to make synonymous codon substitutions to match the codon usage pattern from the original organism in the heterologous expression host. Here we present CHARMING (for Codon HARMonizING), a robust and versatile algorithm to design mRNA sequences for heterologous gene expression and other related codon harmonization tasks. CHARMING can be run as a downloadable Python script or via a web portal at http://www.codons.org.
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Affiliation(s)
- Gabriel Wright
- Department of Computer Science & EngineeringUniversity of Notre DameNotre DameIndianaUSA,Present address:
Department of Electrical Engineering and Computer ScienceMilwaukee School of EngineeringMilwaukeeWIUSA
| | - Anabel Rodriguez
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jun Li
- Department of Applied and Computational Mathematics & StatisticsUniversity of Notre DameNotre DameIndianaUSA
| | - Tijana Milenkovic
- Department of Computer Science & EngineeringUniversity of Notre DameNotre DameIndianaUSA
| | - Scott J. Emrich
- Department of Electrical Engineering & Computer ScienceUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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Martini MC, Berini F, Ausec L, Casciello C, Vacca C, Pistorio M, Lagares A, Mandic-Mulec I, Marinelli F, Del Papa MF. Identification and Characterization of a Novel Plasmid-Encoded Laccase-Like Multicopper Oxidase from Ochrobactrum sp. BF15 Isolated from an On-Farm Bio-Purification System. Food Technol Biotechnol 2021; 59:519-529. [PMID: 35136375 PMCID: PMC8753806 DOI: 10.17113/ftb.59.04.21.7253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
RESEARCH BACKGROUND In recent decades, laccases (p-diphenol-dioxygen oxidoreductases; EC 1.10.3.2) have attracted the attention of researchers due to their wide range of biotechnological and industrial applications. Laccases can oxidize a variety of organic and inorganic compounds, making them suitable as biocatalysts in biotechnological processes. Even though the most traditionally used laccases in the industry are of fungal origin, bacterial laccases have shown an enormous potential given their ability to act on several substrates and in multiple conditions. The present study aims to characterize a plasmid-encoded laccase-like multicopper oxidase (LMCO) from Ochrobactrum sp. BF15, a bacterial strain previously isolated from polluted soil. EXPERIMENTAL APPROACH We used in silico profile hidden Markov models to identify novel laccase-like genes in Ochrobactrum sp. BF15. For laccase characterization, we performed heterologous expression in Escherichia coli, purification and activity measurement on typical laccase substrates. RESULTS AND CONCLUSIONS Profile hidden Markov models allowed us to identify a novel LMCO, named Lac80. In silico analysis of Lac80 revealed the presence of three conserved copper oxidase domains characteristic of three-domain laccases. We successfully expressed Lac80 heterologously in E. coli, allowing us to purify the protein for further activity evaluation. Of thirteen typical laccase substrates tested, Lac80 showed lower activity on 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), pyrocatechol, pyrogallol and vanillic acid, and higher activity on 2,6-dimethoxyphenol. NOVELTY AND SCIENTIFIC CONTRIBUTION Our results show Lac80 as a promising laccase for use in industrial applications. The present work shows the relevance of bacterial laccases and highlights the importance of environmental plasmids as valuable sources of new genes encoding enzymes with potential use in biotechnological processes.
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Affiliation(s)
- María Carla Martini
- IBBM - Institute of Biotechnology and Molecular Biology, CONICET - Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Luka Ausec
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Carmine Casciello
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Carolina Vacca
- IBBM - Institute of Biotechnology and Molecular Biology, CONICET - Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Mariano Pistorio
- IBBM - Institute of Biotechnology and Molecular Biology, CONICET - Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- IBBM - Institute of Biotechnology and Molecular Biology, CONICET - Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - María Florencia Del Papa
- IBBM - Institute of Biotechnology and Molecular Biology, CONICET - Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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Scortica A, Capone M, Narzi D, Frezzini M, Scafati V, Giovannoni M, Angelucci F, Guidoni L, Mattei B, Benedetti M. A molecular dynamics-guided mutagenesis identifies two aspartic acid residues involved in the pH-dependent activity of OG-OXIDASE 1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:171-182. [PMID: 34800821 DOI: 10.1016/j.plaphy.2021.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
During the infection, plant cells secrete different OG-oxidase (OGOX) paralogs, defense flavoproteins that oxidize the oligogalacturonides (OGs), homogalacturonan fragments released from the plant cell wall that act as Damage Associated Molecular Patterns. OGOX-mediated oxidation inactivates their elicitor nature, but on the other hand makes OGs less hydrolysable by microbial endo-polygalacturonases (PGs). Among the different plant defense responses, apoplastic alkalinization can further reduce the degrading potential of PGs by boosting the oxidizing activity of OGOXs. Accordingly, the different OGOXs so far characterized showed an optimal activity at pH values greater than 8. Here, an approach of molecular dynamics (MD)-guided mutagenesis succeeded in identifying the amino acids responsible for the pH dependent activity of OGOX1 from Arabidopsis thaliana. MD simulations indicated that in alkaline conditions (pH 8.5), the residues Asp325 and Asp344 are engaged in the formation of two salt bridges with Arg327 and Lys415, respectively, at the rim of enzyme active site. According to MD analysis, the presence of such ionic bonds modulates the size and flexibility of the cavity used to accommodate the OGs, in turn affecting the activity of OGOX1. Based on functional properties of the site-directed mutants OGOX1.D325A and OGOX.D344A, we demonstrated that Asp325 and Asp344 are major determinants of the alkaline-dependent activity of OGOX1.
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Affiliation(s)
- Anna Scortica
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Matteo Capone
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Daniele Narzi
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - Mario Frezzini
- Dept. of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100, L'Aquila, Italy
| | - Valentina Scafati
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Moira Giovannoni
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Leonardo Guidoni
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Benedetta Mattei
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - Manuel Benedetti
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
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Species-Specific Differences in C-5 Sterol Desaturase Function Influence the Outcome of Azole Antifungal Exposure. Antimicrob Agents Chemother 2021; 65:e0104421. [PMID: 34516249 DOI: 10.1128/aac.01044-21] [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: 11/20/2022] Open
Abstract
The azole antifungals inhibit sterol 14α-demethylase (S14DM), leading to depletion of cellular ergosterol and the synthesis of an aberrant sterol diol that disrupts membrane function. In Candida albicans, sterol diol production is catalyzed by the C-5 sterol desaturase enzyme encoded by ERG3. Accordingly, mutations that inactivate ERG3 enable the fungus to grow in the presence of the azoles. The purpose of this study was to compare the propensities of C-5 sterol desaturases from different fungal pathogens to produce the toxic diol upon S14DM inhibition and thus contribute to antifungal efficacy. The coding sequences of ERG3 homologs from C. albicans (CaERG3), Candida glabrata (CgERG3), Candida auris (CaurERG3), Cryptococcus neoformans (CnERG3), Aspergillus fumigatus (AfERG3A-C) and Rhizopus delemar (RdERG3A/B) were expressed in a C. albicans erg3Δ/Δ mutant to facilitate comparative analysis. All but one of the Erg3p-like proteins (AfErg3C) at least partially restored C-5 sterol desaturase activity and to corresponding degrees rescued the stress and hyphal growth defects of the C. albicans erg3Δ/Δ mutant, confirming functional equivalence. Each C-5 desaturase enzyme conferred markedly different responses to fluconazole exposure in terms of the MIC and residual growth observed at supra-MICs. Upon fluconazole-mediated inhibition of S14DM, the strains expressing each homolog also produced various levels of 14α-methylergosta-8,24(28)-dien-3β,6α-diol. The RdErg3A and AfErg3A proteins are notable for low levels of sterol diol production and failing to confer appreciable azole sensitivity upon the C. albicans erg3Δ/Δ mutant. These findings suggest that species-specific properties of C-5 sterol desaturase may be an important determinant of intrinsic azole sensitivity.
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77
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Wilson FM, Harrison RJ. CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12. Fungal Biol Biotechnol 2021; 8:15. [PMID: 34789333 PMCID: PMC8597179 DOI: 10.1186/s40694-021-00121-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Gene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in various filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™). Results We present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0–40% of isolates. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum. Conclusions Using an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum for use as a research tool, for understanding the controls of secondary metabolism and hyphal development and validating prototypes of strains produced using traditional methods for strain improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-021-00121-8.
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Affiliation(s)
- Fiona M Wilson
- NIAB EMR, New Road, East Malling, West Malling, Kent, ME19 6BJ, UK.
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78
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Cutolo E, Tosoni M, Barera S, Herrera-Estrella L, Dall'Osto L, Bassi R. A chimeric hydrolase-PTXD transgene enables chloroplast-based heterologous protein expression and non-sterile cultivation of Chlamydomonas reinhardtii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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79
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Fox DM, Branson KM, Walker RC. mRNA codon optimization with quantum computers. PLoS One 2021; 16:e0259101. [PMID: 34714834 PMCID: PMC8555812 DOI: 10.1371/journal.pone.0259101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.
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Affiliation(s)
- Dillion M. Fox
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Kim M. Branson
- Artificial Intelligence and Machine Learning, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Ross C. Walker
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, La Jolla, California, United States of America
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80
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Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021; 17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022] Open
Abstract
Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.
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Affiliation(s)
- Bikash K. Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniela M. Remus
- Callaghan Innovation Protein Science and Engineering, University of Canterbury, Christchurch, New Zealand
| | - Augustine Chen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Craig van Dolleweerd
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
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81
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Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities. Antioxidants (Basel) 2021; 10:antiox10091446. [PMID: 34573078 PMCID: PMC8472802 DOI: 10.3390/antiox10091446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H2O2, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds.
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82
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Watts A, Sankaranarayanan S, Watts A, Raipuria RK. Optimizing protein expression in heterologous system: Strategies and tools. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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83
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Matute T, Nuñez I, Rivera M, Reyes J, Blázquez-Sánchez P, Arce A, Brown AJ, Gandini C, Molloy J, Ramírez-Sarmiento CA, Federici F. Homebrew reagents for low-cost RT-LAMP. J Biomol Tech 2021; 32:114-120. [PMID: 35027869 PMCID: PMC8730520 DOI: 10.7171/jbt.21-3203-006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) has gained popularity for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The high specificity, sensitivity, simple protocols, and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents, and their distribution under cold chain shipping limit RT-LAMP's applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus reverse transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits, and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range, and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs; thus, we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low-cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
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Affiliation(s)
- Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexander J. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - César A. Ramírez-Sarmiento
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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84
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Su K, Wu Z, Liu Y, Jiang S, Ma D, Wang Y, Fu C. Highly efficient detoxification of dinitrotoluene by transgenic switchgrass overexpressing bacterial nitroreductase. PLANT, CELL & ENVIRONMENT 2021; 44:3173-3183. [PMID: 34008171 DOI: 10.1111/pce.14099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Dinitrotoluene (DNT) has been extensively used in manufacturing munitions, polyurethane foams and other important chemical products. However, it is highly toxic and mutagenic to most organisms. Here, we synthesized a codon-optimized bacterial nitroreductase gene, NfsI, for plant expression. The kinetic analysis indicates that the recombinant NfsI can detoxify both 2,4-DNT and its sulfonate (DNTS), while it has a 97.6-fold higher catalytic efficiency for 2,4-DNT than DNTS. Furthermore, we overexpressed NfsI in switchgrass (Panicum virgatum L.), which is a multiple-purpose crop used for fodder and biofuel production as well as phytoremediation. The 2,4-DNT treatment inhibited root elongation of wild-type switchgrass plants and promoted reactive oxygen species (ROS) accumulation in roots. In contrast, overexpression of NfsI in switchgrass significantly alleviated 2,4-DNT-induced root growth inhibition and ROS overproduction. Thus, the NfsI overexpressing transgenic switchgrass plant removed 94.1% 2,4-DNT after 6 days, whose efficiency was 1.7-fold higher than control plants. Moreover, the comparative transcriptome analysis suggests that 22.9% of differentially expressed genes induced by 2,4-DNT may participate in NfsI-mediated 2,4-DNT detoxification in switchgrass. Our work sheds light on the function of NfsI during DNT phytoremediation for the first time, revealing the application potential of switchgrass plants engineered with NfsI.
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Affiliation(s)
- Kunlong Su
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yuchen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shanshan Jiang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Dongmei Ma
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- School of ecology environment, Ningxia University, Yinchuan, China
| | - Yan Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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85
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Henson WR, Meyers AW, Jayakody LN, DeCapite A, Black BA, Michener WE, Johnson CW, Beckham GT. Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production. Metab Eng 2021; 68:14-25. [PMID: 34438073 DOI: 10.1016/j.ymben.2021.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. In this work, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.
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Affiliation(s)
- William R Henson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Alex W Meyers
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Lahiru N Jayakody
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Annette DeCapite
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Brenna A Black
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Arias D, Arenas-M A, Flores-Ortiz C, Peirano C, Handford M, Stange C. Daucus carota DcPSY2 and DcLCYB1 as Tools for Carotenoid Metabolic Engineering to Improve the Nutritional Value of Fruits. FRONTIERS IN PLANT SCIENCE 2021; 12:677553. [PMID: 34512681 PMCID: PMC8427143 DOI: 10.3389/fpls.2021.677553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/26/2021] [Indexed: 06/13/2023]
Abstract
Carotenoids are pigments with important nutritional value in the human diet. As antioxidant molecules, they act as scavengers of free radicals enhancing immunity and preventing cancer and cardiovascular diseases. Moreover, α-carotene and β-carotene, the main carotenoids of carrots (Daucus carota) are precursors of vitamin A, whose deficiency in the diet can trigger night blindness and macular degeneration. With the aim of increasing the carotenoid content in fruit flesh, three key genes of the carotenoid pathway, phytoene synthase (DcPSY2) and lycopene cyclase (DcLCYB1) from carrots, and carotene desaturase (XdCrtI) from the yeast Xanthophyllomyces dendrorhous, were optimized for expression in apple and cloned under the Solanum chilense (tomatillo) polygalacturonase (PG) fruit specific promoter. A biotechnological platform was generated and functionally tested by subcellular localization, and single, double and triple combinations were both stably transformed in tomatoes (Solanum lycopersicum var. Microtom) and transiently transformed in Fuji apple fruit flesh (Malus domestica). We demonstrated the functionality of the S. chilense PG promoter by directing the expression of the transgenes specifically to fruits. Transgenic tomato fruits expressing DcPSY2, DcLCYB1, and DcPSY2-XdCRTI, produced 1.34, 2.0, and 1.99-fold more total carotenoids than wild-type fruits, respectively. Furthermore, transgenic tomatoes expressing DcLCYB1, DcPSY2-XdCRTI, and DcPSY2-XdCRTI-DcLCYB1 exhibited an increment in β-carotene levels of 2.5, 3.0, and 2.57-fold in comparison with wild-type fruits, respectively. Additionally, Fuji apple flesh agroinfiltrated with DcPSY2 and DcLCYB1 constructs showed a significant increase of 2.75 and 3.11-fold in total carotenoids and 5.11 and 5.84-fold in β-carotene, respectively whereas the expression of DcPSY2-XdCRTI and DcPSY2-XdCRTI-DcLCYB1 generated lower, but significant changes in the carotenoid profile of infiltrated apple flesh. The results in apple demonstrate that DcPSY2 and DcLCYB1 are suitable biotechnological genes to increase the carotenoid content in fruits of species with reduced amounts of these pigments.
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Affiliation(s)
- Daniela Arias
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
| | - Anita Arenas-M
- Laboratorio de Nutrición y Genómica de Plantas, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Carlos Flores-Ortiz
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
| | - Clio Peirano
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
| | - Michael Handford
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
| | - Claudia Stange
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
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87
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Mulyanti D, Soewandhi SN, Riani C. Insertion of prpoD_rpoS fragment enhances expression of recombinant protein by dps auto-inducible promoter in Escherichia coli. Mol Biol Rep 2021; 48:5833-5845. [PMID: 34342815 DOI: 10.1007/s11033-021-06562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nowadays, recombinant therapeutic proteins have been widely produced and consumed. For the safety and effectiveness of the protein production, an auto-inducible expression vector is required to replace inducer interference, which is uneconomic and could be harmful. In this research, an auto-inducible expression plasmid, pCAD2_sod (a pBR322 derivate plasmid), which was under dps (RpoS-dependent gene) promoter control, was modified to provide RpoS at earlier phase. Hence, accumulates more target protein and resulting a new plasmid, pCAD2+_sod. pCAD2_sod had been constructed to automatically induces the expression of recombinant superoxide dismutase (SOD) from Staphylococcus equorum (rMnSODSeq) in the stationary growth phase of Escherichia coli. This work aimed to obtain pCAD2+_sod and determine the expression level of rMnSODSeq on mRNA and protein level. METHOD AND RESULTS A synthetic rpoS coding region under rpoD promoter control (prpoD_rpoS) was inserted to pCAD2_sod and generated pCAD2+_sod. The rMnSODSeq (24.3 kDa) produced from pCAD2+_sod was ~ 1.5 fold higher at 37 °C and more intense at 43 °C compared to that from pCAD2_sod, likewise shifted to earlier phase (after 1 h of incubation), as shown in the SDS-PAGE. The dismutase activity was also retained after zymography assay. The mRNA level from pCAD2+_sod was determined by qPCR and gave quantification cycle (Cq) values of cDNA lowest among others. It made the relative quantification (RQ) of the mRNA expression towards rho reference gene were high. CONCLUSIONS The prpoD_rpoS insertion shifts and increases the rMnSODSeq production from stationary to exponential phase. The pCAD2+_sod plasmid is potential for further recombinant protein productions.
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Affiliation(s)
- Dina Mulyanti
- School of Pharmacy, Bandung Institute of Technology, Ganesha 10, Bandung, 40132, Indonesia.,Department of Pharmacy, Bandung Islamic University, Ranggagading 8, Bandung, 40116, Indonesia
| | | | - Catur Riani
- School of Pharmacy, Bandung Institute of Technology, Ganesha 10, Bandung, 40132, Indonesia.
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88
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Hyun Y, Baek Y, Lee C, Ki N, Ahn J, Ryu S, Ha NC. Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus. Mol Cells 2021; 44:517-528. [PMID: 34112742 PMCID: PMC8334348 DOI: 10.14348/molcells.2021.0011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/27/2022] Open
Abstract
A recent genetic study with Brucella abortus revealed the secretion activator gene A (SagA) as an autolysin component creating pores in the peptidoglycan (PGN) layer for the type IV secretion system (T4SS) and peptidoglycan hydrolase inhibitor A (PhiA) as an inhibitor of SagA. In this study, we determined the crystal structures of both SagA and PhiA. Notably, the SagA structure contained a PGN fragment in a space between the N- and C-terminal domains, showing the substrate-dependent hinge motion of the domains. The purified SagA fully hydrolyzed the meso-diaminopimelic acid (DAP)-type PGN, showing a higher activity than hen egg-white lysozyme. The PhiA protein exhibiting tetrameric assembly failed to inhibit SagA activity in our experiments. Our findings provide implications for the molecular basis of the SagA-PhiA system of B. abortus. The development of inhibitors of SagA would further contribute to controlling brucellosis by attenuating the function of T4SS, the major virulence factor of Brucella.
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Affiliation(s)
- Yongseong Hyun
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Yeongjin Baek
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Chanyoung Lee
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Nayeon Ki
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Sangryeol Ryu
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, CALS, Seoul National University, Seoul 08826, Korea
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89
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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB. Genes (Basel) 2021; 12:genes12081169. [PMID: 34440343 PMCID: PMC8393687 DOI: 10.3390/genes12081169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/03/2022] Open
Abstract
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
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90
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Meng Q, Yuan Y, Li Y, Wu S, Shi K, Liu S. Optimization of Electrotransformation Parameters and Engineered Promoters for Lactobacillus plantarum from Wine. ACS Synth Biol 2021; 10:1728-1738. [PMID: 34048225 DOI: 10.1021/acssynbio.1c00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Robust and versatile promoters for Lactobacillus plantarum found in wine are necessary gene expression tools for genetic research involving wine stress. We optimized the electrotransformation parameters for L. plantarum XJ25 isolated from wine and engineered five promoters based on the promoter P23; these promoters showed significantly different transcriptional activities under nonstress conditions. The activities of these promoters in vivo and the resulting growth burden to the host strain under different wine stresses were also evaluated. A range of colors (from white to dark pink) of the developing colonies with the plasmid pNZ8148 carrying an X-mCherry expression cassette, namely, P23-mCherry, trcP23-mCherry, POL1-mCherry, POL2-mCherry, POL3-mCherry, or POL4-mCherry, were analyzed. The applicability of the optimized electrotransformation parameters and synthetic promoters with different activities were also verified in several L. plantarum strains. Therefore, the optimized electrotransformation and these characterized promoters were determined to be suitable for applications in wine research in the future.
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Affiliation(s)
- Qiang Meng
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yueyao Li
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shaowen Wu
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
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91
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Bhandari BK, Lim CS, Gardner PP. TISIGNER.com: web services for improving recombinant protein production. Nucleic Acids Res 2021; 49:W654-W661. [PMID: 33744969 PMCID: PMC8265118 DOI: 10.1093/nar/gkab175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022] Open
Abstract
Experiments that are planned using accurate prediction algorithms will mitigate failures in recombinant protein production. We have developed TISIGNER (https://tisigner.com) with the aim of addressing technical challenges to recombinant protein production. We offer three web services, TIsigner (Translation Initiation coding region designer), SoDoPE (Soluble Domain for Protein Expression) and Razor, which are specialised in synonymous optimisation of recombinant protein expression, solubility and signal peptide analysis, respectively. Importantly, TIsigner, SoDoPE and Razor are linked, which allows users to switch between the tools when optimising genes of interest.
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Affiliation(s)
- Bikash K Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Paul P Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
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92
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Bordbar A, Amanlou M, Pooshang Bagheri K, Ready PD, Ebrahimi S, Shahbaz Mohammadi H, Ghafari SM, Parvizi P. Cloning, high-level gene expression and bioinformatics analysis of SP15 and LeIF from Leishmania major and Iranian Phlebotomus papatasi saliva as single and novel fusion proteins: a potential vaccine candidate against leishmaniasis. Trans R Soc Trop Med Hyg 2021; 115:699-713. [PMID: 33155034 DOI: 10.1093/trstmh/traa119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/09/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Early exacerbation of cutaneous leishmaniasis is mainly affected by both the salivary and Leishmania parasite components. Little is known of the vaccine combination made by immunogenic proteins of sandfly saliva (SP15) with Leishmania parasites (LeIF) as a single prophylactic vaccine, namely SaLeish. Also, there are no data available to determine the species-specific sequence of SP15 isolated from the Iranian Phlebotomus papatasi. METHODS Integrated bioinformatics and genetic engineering methods were employed to design, optimize and obtain a vector-parasite-based vaccine formulation in a whole-length fusion form of LeIF-SP15 against leishmaniasis. Holistic gene optimization was initially performed to obtain a high yield of pure 'whole-SaLeish' expression using bioinformatics analyses. Genomic and salivary gland RNAs of wild-caught P. papatasi were extracted and their complementary DNA was amplified and cloned into pJET vector. RESULTS The new chimeric protein of whole-SaLeish and randomly selected transcripts of native PpIRSP15 (GenBank accession nos. MT025054 and MN938854, MN938855 and MN938856) were successfully expressed, purified and validated by immunoblotting assay. Furthermore, despite the single amino acid polymorphisms of PpIRSP15 found at positions Y23 and E73 within the population of wild Iranian sandflies, antigenicity and conservancy of PpIRSP15 epitopes remained constant to activate T cells. CONCLUSIONS The SaLeish vaccine strategy takes advantage of a plethora of vector-parasite immunogenic proteins with potential protective efficacy to stimulate both the innate and specific cellular immune responses against Leishmania parasites.
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Affiliation(s)
- Ali Bordbar
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, Iran.,Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Paul Donald Ready
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, Iran
| | - Hamid Shahbaz Mohammadi
- Department of Biochemistry, Genetics and Metabolism Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Seyedeh Maryam Ghafari
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, Iran
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93
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van Gijtenbeek LA, Singer Q, Steffensen LE, Neuens S, Guldager HS, Bidstrup S, Høgholm T, Madsen MG, Glass K, Siedler S. Lacticaseibacillus rhamnosus Impedes Growth of Listeria spp. in Cottage Cheese through Manganese Limitation. Foods 2021; 10:1353. [PMID: 34208094 PMCID: PMC8230772 DOI: 10.3390/foods10061353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/25/2023] Open
Abstract
Acidification and nutrient depletion by dairy starter cultures is often sufficient to prevent outgrowth of pathogens during post-processing of cultured dairy products. In the case of cottage cheese, however, the addition of cream dressing to the curd and subsequent cooling procedures can create environments that may be hospitable for the growth of Listeria monocytogenes. We report on a non-bacterio-cinogenic Lacticaseibacillus rhamnosus strain that severely limits the growth potential of L. monocytogenes in creamed cottage cheese. The main mechanism underlying Listeria spp. inhibition was found to be caused by depletion of manganese (Mn), thus through competitive exclusion of a trace element essential for the growth of many microorganisms. Growth of Streptococcus thermophilus and Lactococcus lactis that constitute the starter culture, on the other hand, were not influenced by reduced Mn levels. Addition of L. rhamnosus with Mn-based bioprotective properties during cottage cheese production therefore offers a solution to inhibit undesired bacteria in a bacteriocin-independent fashion.
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Affiliation(s)
- Lieke A. van Gijtenbeek
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Quinn Singer
- Food Research Institute, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA; (Q.S.); (K.G.)
| | - Louise E. Steffensen
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Shannon Neuens
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Helle S. Guldager
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Susanne Bidstrup
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Tina Høgholm
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Mikkel G. Madsen
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
| | - Kathleen Glass
- Food Research Institute, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA; (Q.S.); (K.G.)
| | - Solvej Siedler
- Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark; (L.A.v.G.); (L.E.S.); (S.N.); (H.S.G.); (S.B.); (T.H.); (M.G.M.)
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94
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Zrimec J, Buric F, Kokina M, Garcia V, Zelezniak A. Learning the Regulatory Code of Gene Expression. Front Mol Biosci 2021; 8:673363. [PMID: 34179082 PMCID: PMC8223075 DOI: 10.3389/fmolb.2021.673363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Data-driven machine learning is the method of choice for predicting molecular phenotypes from nucleotide sequence, modeling gene expression events including protein-DNA binding, chromatin states as well as mRNA and protein levels. Deep neural networks automatically learn informative sequence representations and interpreting them enables us to improve our understanding of the regulatory code governing gene expression. Here, we review the latest developments that apply shallow or deep learning to quantify molecular phenotypes and decode the cis-regulatory grammar from prokaryotic and eukaryotic sequencing data. Our approach is to build from the ground up, first focusing on the initiating protein-DNA interactions, then specific coding and non-coding regions, and finally on advances that combine multiple parts of the gene and mRNA regulatory structures, achieving unprecedented performance. We thus provide a quantitative view of gene expression regulation from nucleotide sequence, concluding with an information-centric overview of the central dogma of molecular biology.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mariia Kokina
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Victor Garcia
- School of Life Sciences and Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Science for Life Laboratory, Stockholm, Sweden
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95
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Isaguliants M, Krotova O, Petkov S, Jansons J, Bayurova E, Mezale D, Fridrihsone I, Kilpelainen A, Podschwadt P, Agapkina Y, Smirnova O, Kostic L, Saleem M, Latyshev O, Eliseeva O, Malkova A, Gorodnicheva T, Wahren B, Gordeychuk I, Starodubova E, Latanova A. Cellular Immune Response Induced by DNA Immunization of Mice with Drug Resistant Integrases of HIV-1 Clade A Offers Partial Protection against Growth and Metastatic Activity of Integrase-Expressing Adenocarcinoma Cells. Microorganisms 2021; 9:1219. [PMID: 34199989 PMCID: PMC8226624 DOI: 10.3390/microorganisms9061219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 02/07/2023] Open
Abstract
Therapeutic DNA-vaccination against drug-resistant HIV-1 may hinder emergence and spread of drug-resistant HIV-1, allowing for longer successful antiretroviral treatment (ART) up-to relief of ART. We designed DNA-vaccines against drug-resistant HIV-1 based on consensus clade A integrase (IN) resistant to raltegravir: IN_in_r1 (L74M/E92Q/V151I/N155H/G163R) or IN_in_r2 (E138K/G140S/Q148K) carrying D64V abrogating IN activity. INs, overexpressed in mammalian cells from synthetic genes, were assessed for stability, route of proteolytic degradation, and ability to induce oxidative stress. Both were found safe in immunotoxicity tests in mice, with no inherent carcinogenicity: their expression did not enhance tumorigenic or metastatic potential of adenocarcinoma 4T1 cells. DNA-immunization of mice with INs induced potent multicytokine T-cell response mainly against aa 209-239, and moderate IgG response cross-recognizing diverse IN variants. DNA-immunization with IN_in_r1 protected 60% of mice from challenge with 4Tlluc2 cells expressing non-mutated IN, while DNA-immunization with IN_in_r2 protected only 20% of mice, although tumor cells expressed IN matching the immunogen. Tumor size inversely correlated with IN-specific IFN-γ/IL-2 T-cell response. IN-expressing tumors displayed compromised metastatic activity restricted to lungs with reduced metastases size. Protective potential of IN immunogens relied on their immunogenicity for CD8+ T-cells, dependent on proteasomal processing and low level of oxidative stress.
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Affiliation(s)
- Maria Isaguliants
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia; (J.J.); (D.M.); (I.F.)
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
| | - Olga Krotova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Stefan Petkov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Juris Jansons
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia; (J.J.); (D.M.); (I.F.)
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Ekaterina Bayurova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
| | - Dzeina Mezale
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia; (J.J.); (D.M.); (I.F.)
| | - Ilze Fridrihsone
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia; (J.J.); (D.M.); (I.F.)
| | - Athina Kilpelainen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Philip Podschwadt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Yulia Agapkina
- Department of Chemistry and Belozersky Institute of Physicochemical Biology, Moscow State University, 119991 Moscow, Russia;
| | - Olga Smirnova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Linda Kostic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Mina Saleem
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Oleg Latyshev
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
| | - Olesja Eliseeva
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
| | - Anastasia Malkova
- Institute of Medical Biological Research and Technologies, 143090 Krasnoznamensk, Russia;
| | | | - Britta Wahren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (S.P.); (A.K.); (P.P.); (L.K.); (M.S.); (B.W.)
| | - Ilya Gordeychuk
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 127994 Moscow, Russia
| | - Elizaveta Starodubova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anastasia Latanova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (O.K.); (E.B.); (O.S.); (O.L.); (O.E.); (I.G.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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96
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Matute T, Nuñez I, Rivera M, Reyes J, Blázquez-Sánchez P, Arce A, Brown AJ, Gandini C, Molloy J, Ramirez-Sarmiento CA, Federici F. Homebrew reagents for low cost RT-LAMP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.08.21256891. [PMID: 34013302 PMCID: PMC8132288 DOI: 10.1101/2021.05.08.21256891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RT-LAMP (reverse transcription - Loop-mediated isothermal amplification) has gained popularity for the detection of SARS-CoV-2. The high specificity, sensitivity, simple protocols and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents and their distribution under cold chain shipping limits RT-LAMP's applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus (M-MLV) Reverse Transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs, and thus we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
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Affiliation(s)
- Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexander J. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - César A. Ramirez-Sarmiento
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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97
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Zhao T, Huang H, Tan P, Li Y, Xuan X, Li F, Zhao Y, Cao Y, Wu Z, Jiang Y, Zhao Y, Yu A, Wang K, Xu J, Zhou L, Yang D. Enhancement of Solubility, Purification, and Inclusion Body Refolding of Active Human Mitochondrial Aldehyde Dehydrogenase 2. ACS OMEGA 2021; 6:12004-12013. [PMID: 34056354 PMCID: PMC8154035 DOI: 10.1021/acsomega.1c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Mitochondrial aldehyde dehydrogenase 2 (ALDH2) is predominantly linked with acetaldehyde detoxification in the second stage of alcohol metabolism. To intensively study ALDH2 function, a higher purity and uniform composition of the protein is required. An efficient Escherichia coli system for ALDH2 expression was developed by using His and a small ubiquitin-related modifier fusion tag. Most of the recombinant ALDH2s were expressed in the form of inclusion bodies. The ALDH2-enriched inclusion bodies were denatured with 6 M guanidine hydrochloride, and then ALDH2 was ultrafitrated. Finally, ALDH2 was successfully purified through affinity and gel filtration chromatography. The purified ALDH2 was finally preserved by the vacuum freeze-drying method, and its purity was determined to be higher than 95%, with a final media yield of 33.89 mg/L. The specific activity of ALDH2 was 6.1 × 104 U/mg. This work was the first to report pET-SUMO-ALDH2 recombinant plasmid expression in Escherichia coli, and the inclusion bodies were isolated and refolded. Finally, the purified ALDH2 had relatively higher purity, yield, and biological activity.
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Affiliation(s)
- Tingting Zhao
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Hui Huang
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Peizhu Tan
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Yanze Li
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Xiuchen Xuan
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Fenglan Li
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
| | - Yuchen Zhao
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Yuwei Cao
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Zhaojing Wu
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Yu Jiang
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Yuanyuan Zhao
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Aimiao Yu
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Kuo Wang
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Jiaran Xu
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Lingyun Zhou
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
- Translational
Medicine Center of Northern China, Harbin 150081, China
| | - Dan Yang
- Department
of Biochemistry and Molecular Biology, Harbin
Medical University, Harbin 150081, China
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98
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Adina SR, Suwanto A, Meryandini A, Puspitasari E. Expression of novel acidic lipase from Micrococcus luteus in Pichia pastoris and its application in transesterification. J Genet Eng Biotechnol 2021; 19:55. [PMID: 33826047 PMCID: PMC8026790 DOI: 10.1186/s43141-021-00155-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/26/2021] [Indexed: 01/26/2023]
Abstract
Background Lipases are promising biocatalysts for industrial applications and attract attention to be explored. A novel acidic lipase has been isolated from the lipolytic bacteria Micrococcus luteus EMP48-D (LipEMP48-D) screened from tempeh. The lipase gene had previously been overexpressed in Escherichia coli BL21, but the expression level obtained was relatively low. Here, to improve the expression level, the lipase gene was cloned to Pichia pastoris. We eliminated the native signal sequence of M. luteus and replaced it with α-mating factor (α-MF) signal sequence. We also optimized and synthesized the lipase gene based on codon preference in P. pastoris. Results LipEMP48-D lipase was expressed as an extracellular protein. Codon optimization has been conducted for 20 codons, with the codon adaption index reaching 0.995. The highest extracellular lipase activity obtained reached 145.4 ± 4.8 U/mg under AOX1 promoter in P. pastoris KM71 strain, which was 9.7-fold higher than the previous activity in E. coli. LipEMP48-D showed the highest specific activity at pH 5.0 and stable within the pH range 3.0–5.0 at 40 °C. LipEMP48-D also has the capability of hydrolyzing various long-chain triglycerides, particularly olive oil (100%) followed by sunflower oil (88.5%). LipEMP48-D exhibited high tolerance for various polar organic solvents with low log P, such as isopropanol (115.7%) and butanol (114.6%). The metal ions (Na+, K+, Ca2+, Mg2+, Mn+) decreased enzyme activity up to 43.1%, while Fe2+ increased relative activity of enzymes up to 200%. The conversion of free fatty acid (FFA) into fatty acid methyl ester (FAME) was low around 2.95%. Conclusions This study was the first to report overexpression of Micrococcus lipase in yeast. The extracellular expression of this acidic lipase could be potential for biocatalyst in industrial fields, especially organic synthesis, food industry, and production of biodiesel.
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Affiliation(s)
- Selfela Restu Adina
- Graduate School of Microbiology, Department of Biology, Faculty of Mathematics and Natural Science, IPB University, Bogor, 16680, Indonesia
| | - Antonius Suwanto
- Department of Biology, Faculty of Mathematics and Natural Science, IPB University, Bogor, 16680, Indonesia.
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Science, IPB University, Bogor, 16680, Indonesia
| | - Esti Puspitasari
- Department of Biotechnology Research and Development, PT Wilmar Benih Indonesia, Bekasi, 17530, Indonesia
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99
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Sadri Najafabadi Z, Nazarian S, Kargar M, Kafilzadeh F. Designing of a chimeric protein contains StxB, intimin and EscC against toxicity and adherence of enterohemorrhagic Escherichia coli O157:H7 and evaluation of serum antibody titers against it. Mol Immunol 2021; 134:218-227. [PMID: 33823320 DOI: 10.1016/j.molimm.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/08/2021] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain is known as one of the major human foodborne pathogens. Lack of effective clinical treatment for human diarrheal diseases confirms the need for vaccine production against enteric bacteria such as E.coli O157:H7. Shiga-like toxin (Stx), EscC, and Intimin are the main important virulent factors of this enteric pathogen. In the present study, a comparative Omics analysis was conducted to identify most invasion EHEC antigenic factors as a potential immunogen. SEI (Stx-EscC-Intimin) trivalent chimeric protein was designed from the exposed and epitope rich part of these virulence factors. Sequence optimization, physicochemical properties, mRNA folding, three-dimensional structure and immunoinformatics data were investigated. The chimeric gene was synthesized with codon bias of E. coli. Recombinant protein was expressed and confirmed by western blot analysis. To evaluate the immunogenicity of the designed protein, the protein was administered to BALB/c mice and the serum IgG was determined by ELISA. Based on the Ramachandran plot, the validation data showed that 90.1 % of residues lie in the favored region. The high antigenicity of the multimeric protein was predicted by the immunoinformatic analysis. Epitope prediction had shown the proper distribution of linear and conformational B-cell epitopes and the competition of T-cell epitopes to bind MHC molecules too. Recombinant ESI Protein with 74.5 kDa was expressed in E. coli. Western blot analysis by anti-Stx antibody, confirmed a single band of chimeric protein. Consequently, the chimeric gene was designed and constructed after assessments. From in silico approach, the protein deduced from this cassette can be an immunogen candidate, and act against toxicity and adherence of EHEC.
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Affiliation(s)
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran.
| | - Mohammad Kargar
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Farshid Kafilzadeh
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
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100
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Zimmerling J, Oelschlägel M, Großmann C, Voitel M, Schlömann M, Tischler D. Biochemical Characterization of Phenylacetaldehyde Dehydrogenases from Styrene-degrading Soil Bacteria. Appl Biochem Biotechnol 2021; 193:650-667. [PMID: 33106986 PMCID: PMC7910268 DOI: 10.1007/s12010-020-03421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/11/2020] [Indexed: 10/24/2022]
Abstract
Four phenylacetaldehyde dehydrogenases (designated as FeaB or StyD) originating from styrene-degrading soil bacteria were biochemically investigated. In this study, we focused on the Michaelis-Menten kinetics towards the presumed native substrate phenylacetaldehyde and the obviously preferred co-substrate NAD+. Furthermore, the substrate specificity on four substituted phenylacetaldehydes and the co-substrate preference were studied. Moreover, these enzymes were characterized with respect to their temperature as well as long-term stability. Since aldehyde dehydrogenases are known to show often dehydrogenase as well as esterase activity, we tested this capacity, too. Almost all results showed clearly different characteristics between the FeaB and StyD enzymes. Furthermore, FeaB from Sphingopyxis fribergensis Kp5.2 turned out to be the most active enzyme with an apparent specific activity of 17.8 ± 2.1 U mg-1. Compared with that, both StyDs showed only activities less than 0.2 U mg-1 except the overwhelming esterase activity of StyD-CWB2 (1.4 ± 0.1 U mg-1). The clustering of both FeaB and StyD enzymes with respect to their characteristics could also be mirrored in the phylogenetic analysis of twelve dehydrogenases originating from different soil bacteria.
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Affiliation(s)
- Juliane Zimmerling
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
| | - Michel Oelschlägel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Carolin Großmann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Matthias Voitel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Michael Schlömann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Dirk Tischler
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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